Starting phenix.real_space_refine on Tue Apr 16 01:59:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcl_28982/04_2024/8fcl_28982_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcl_28982/04_2024/8fcl_28982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcl_28982/04_2024/8fcl_28982.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcl_28982/04_2024/8fcl_28982.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcl_28982/04_2024/8fcl_28982_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fcl_28982/04_2024/8fcl_28982_updated.pdb" } resolution = 3.51 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= -0.001 sd= 0.054 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 189 5.16 5 C 23162 2.51 5 N 6477 2.21 5 O 7052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 25": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 65": "NH1" <-> "NH2" Residue "A ARG 83": "NH1" <-> "NH2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 93": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 239": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 323": "NH1" <-> "NH2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 359": "NH1" <-> "NH2" Residue "A ARG 362": "NH1" <-> "NH2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 377": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A ARG 453": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 567": "NH1" <-> "NH2" Residue "A ARG 586": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "A ARG 638": "NH1" <-> "NH2" Residue "A ARG 653": "NH1" <-> "NH2" Residue "A ARG 662": "NH1" <-> "NH2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A ARG 732": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A ARG 741": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 745": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "B ARG 25": "NH1" <-> "NH2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B ARG 64": "NH1" <-> "NH2" Residue "B ARG 65": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 86": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 93": "NH1" <-> "NH2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 155": "NH1" <-> "NH2" Residue "B ARG 159": "NH1" <-> "NH2" Residue "B ARG 191": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 239": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B ARG 323": "NH1" <-> "NH2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 359": "NH1" <-> "NH2" Residue "B ARG 362": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 377": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ARG 453": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 567": "NH1" <-> "NH2" Residue "B ARG 586": "NH1" <-> "NH2" Residue "B ARG 599": "NH1" <-> "NH2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "B ARG 638": "NH1" <-> "NH2" Residue "B ARG 653": "NH1" <-> "NH2" Residue "B ARG 662": "NH1" <-> "NH2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 700": "NH1" <-> "NH2" Residue "B ARG 732": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B ARG 741": "NH1" <-> "NH2" Residue "B ARG 744": "NH1" <-> "NH2" Residue "B ARG 745": "NH1" <-> "NH2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "C ARG 25": "NH1" <-> "NH2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 86": "NH1" <-> "NH2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 144": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 155": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 239": "NH1" <-> "NH2" Residue "C ARG 256": "NH1" <-> "NH2" Residue "C ARG 287": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C ARG 349": "NH1" <-> "NH2" Residue "C ARG 358": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 377": "NH1" <-> "NH2" Residue "C ARG 424": "NH1" <-> "NH2" Residue "C ARG 453": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C ARG 567": "NH1" <-> "NH2" Residue "C ARG 586": "NH1" <-> "NH2" Residue "C ARG 599": "NH1" <-> "NH2" Residue "C ARG 625": "NH1" <-> "NH2" Residue "C ARG 635": "NH1" <-> "NH2" Residue "C ARG 638": "NH1" <-> "NH2" Residue "C ARG 653": "NH1" <-> "NH2" Residue "C ARG 662": "NH1" <-> "NH2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 700": "NH1" <-> "NH2" Residue "C ARG 732": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C ARG 741": "NH1" <-> "NH2" Residue "C ARG 744": "NH1" <-> "NH2" Residue "C ARG 745": "NH1" <-> "NH2" Residue "C ARG 753": "NH1" <-> "NH2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 65": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 86": "NH1" <-> "NH2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D ARG 93": "NH1" <-> "NH2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ARG 144": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 155": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 191": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 239": "NH1" <-> "NH2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 256": "NH1" <-> "NH2" Residue "D ARG 287": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ARG 338": "NH1" <-> "NH2" Residue "D ARG 349": "NH1" <-> "NH2" Residue "D ARG 358": "NH1" <-> "NH2" Residue "D ARG 359": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D ARG 377": "NH1" <-> "NH2" Residue "D ARG 424": "NH1" <-> "NH2" Residue "D ARG 453": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D ARG 567": "NH1" <-> "NH2" Residue "D ARG 586": "NH1" <-> "NH2" Residue "D ARG 599": "NH1" <-> "NH2" Residue "D ARG 625": "NH1" <-> "NH2" Residue "D ARG 635": "NH1" <-> "NH2" Residue "D ARG 638": "NH1" <-> "NH2" Residue "D ARG 653": "NH1" <-> "NH2" Residue "D ARG 662": "NH1" <-> "NH2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 700": "NH1" <-> "NH2" Residue "D ARG 732": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D ARG 741": "NH1" <-> "NH2" Residue "D ARG 744": "NH1" <-> "NH2" Residue "D ARG 745": "NH1" <-> "NH2" Residue "D ARG 753": "NH1" <-> "NH2" Residue "E ARG 25": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E ARG 65": "NH1" <-> "NH2" Residue "E ARG 83": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E ARG 147": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E ARG 191": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "E ARG 225": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 256": "NH1" <-> "NH2" Residue "E ARG 287": "NH1" <-> "NH2" Residue "E ARG 313": "NH1" <-> "NH2" Residue "E ARG 322": "NH1" <-> "NH2" Residue "E ARG 323": "NH1" <-> "NH2" Residue "E ARG 338": "NH1" <-> "NH2" Residue "E ARG 349": "NH1" <-> "NH2" Residue "E ARG 358": "NH1" <-> "NH2" Residue "E ARG 359": "NH1" <-> "NH2" Residue "E ARG 362": "NH1" <-> "NH2" Residue "E ARG 365": "NH1" <-> "NH2" Residue "E ARG 377": "NH1" <-> "NH2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "E ARG 453": "NH1" <-> "NH2" Residue "E ARG 465": "NH1" <-> "NH2" Residue "E ARG 487": "NH1" <-> "NH2" Residue "E ARG 560": "NH1" <-> "NH2" Residue "E ARG 567": "NH1" <-> "NH2" Residue "E ARG 586": "NH1" <-> "NH2" Residue "E ARG 599": "NH1" <-> "NH2" Residue "E ARG 625": "NH1" <-> "NH2" Residue "E ARG 635": "NH1" <-> "NH2" Residue "E ARG 638": "NH1" <-> "NH2" Residue "E ARG 653": "NH1" <-> "NH2" Residue "E ARG 662": "NH1" <-> "NH2" Residue "E ARG 693": "NH1" <-> "NH2" Residue "E ARG 700": "NH1" <-> "NH2" Residue "E ARG 732": "NH1" <-> "NH2" Residue "E ARG 733": "NH1" <-> "NH2" Residue "E ARG 741": "NH1" <-> "NH2" Residue "E ARG 744": "NH1" <-> "NH2" Residue "E ARG 745": "NH1" <-> "NH2" Residue "E ARG 753": "NH1" <-> "NH2" Residue "F ARG 25": "NH1" <-> "NH2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 64": "NH1" <-> "NH2" Residue "F ARG 65": "NH1" <-> "NH2" Residue "F ARG 83": "NH1" <-> "NH2" Residue "F ARG 86": "NH1" <-> "NH2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ARG 95": "NH1" <-> "NH2" Residue "F ARG 113": "NH1" <-> "NH2" Residue "F ARG 144": "NH1" <-> "NH2" Residue "F ARG 147": "NH1" <-> "NH2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F ARG 191": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F ARG 225": "NH1" <-> "NH2" Residue "F ARG 239": "NH1" <-> "NH2" Residue "F ARG 256": "NH1" <-> "NH2" Residue "F ARG 287": "NH1" <-> "NH2" Residue "F ARG 313": "NH1" <-> "NH2" Residue "F ARG 322": "NH1" <-> "NH2" Residue "F ARG 323": "NH1" <-> "NH2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "F ARG 349": "NH1" <-> "NH2" Residue "F ARG 358": "NH1" <-> "NH2" Residue "F ARG 359": "NH1" <-> "NH2" Residue "F ARG 362": "NH1" <-> "NH2" Residue "F ARG 365": "NH1" <-> "NH2" Residue "F ARG 377": "NH1" <-> "NH2" Residue "F ARG 424": "NH1" <-> "NH2" Residue "F ARG 453": "NH1" <-> "NH2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F ARG 487": "NH1" <-> "NH2" Residue "F ARG 560": "NH1" <-> "NH2" Residue "F ARG 567": "NH1" <-> "NH2" Residue "F ARG 586": "NH1" <-> "NH2" Residue "F ARG 599": "NH1" <-> "NH2" Residue "F ARG 625": "NH1" <-> "NH2" Residue "F ARG 635": "NH1" <-> "NH2" Residue "F ARG 638": "NH1" <-> "NH2" Residue "F ARG 653": "NH1" <-> "NH2" Residue "F ARG 662": "NH1" <-> "NH2" Residue "F ARG 693": "NH1" <-> "NH2" Residue "F ARG 700": "NH1" <-> "NH2" Residue "F ARG 732": "NH1" <-> "NH2" Residue "F ARG 733": "NH1" <-> "NH2" Residue "F ARG 741": "NH1" <-> "NH2" Residue "F ARG 744": "NH1" <-> "NH2" Residue "F ARG 745": "NH1" <-> "NH2" Residue "F ARG 753": "NH1" <-> "NH2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G ARG 137": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G ARG 207": "NH1" <-> "NH2" Residue "G ARG 255": "NH1" <-> "NH2" Residue "G ARG 267": "NH1" <-> "NH2" Residue "G ARG 272": "NH1" <-> "NH2" Residue "G ARG 274": "NH1" <-> "NH2" Residue "G ARG 275": "NH1" <-> "NH2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G ARG 305": "NH1" <-> "NH2" Residue "G ARG 307": "NH1" <-> "NH2" Residue "G ARG 313": "NH1" <-> "NH2" Residue "G ARG 318": "NH1" <-> "NH2" Residue "G ARG 323": "NH1" <-> "NH2" Residue "G ARG 329": "NH1" <-> "NH2" Residue "G ARG 332": "NH1" <-> "NH2" Residue "G TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 340": "NH1" <-> "NH2" Residue "G ARG 342": "NH1" <-> "NH2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "G ARG 358": "NH1" <-> "NH2" Residue "G ARG 367": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 36904 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "B" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "C" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "D" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "E" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "F" Number of atoms: 5640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5640 Classifications: {'peptide': 721} Link IDs: {'PCIS': 3, 'PTRANS': 35, 'TRANS': 682} Chain breaks: 1 Chain: "G" Number of atoms: 2740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2740 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 325} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.23, per 1000 atoms: 0.52 Number of scatterers: 36904 At special positions: 0 Unit cell: (180.978, 194.322, 111.756, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 189 16.00 P 24 15.00 O 7052 8.00 N 6477 7.00 C 23162 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: 14.08 Conformation dependent library (CDL) restraints added in 6.7 seconds 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8730 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 234 helices and 33 sheets defined 43.5% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.81 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 130 through 133 No H-bonds generated for 'chain 'A' and resid 130 through 133' Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 210 through 225 removed outlier: 4.883A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 281 through 295 Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 319 through 336 removed outlier: 3.763A pdb=" N VAL A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 326 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LYS A 336 " --> pdb=" O MET A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 427 through 430 No H-bonds generated for 'chain 'A' and resid 427 through 430' Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 449 through 458 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 483 through 493 Processing helix chain 'A' and resid 495 through 498 No H-bonds generated for 'chain 'A' and resid 495 through 498' Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 524 through 534 Processing helix chain 'A' and resid 544 through 552 Processing helix chain 'A' and resid 556 through 568 Processing helix chain 'A' and resid 581 through 585 Processing helix chain 'A' and resid 599 through 609 Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 631 through 634 Processing helix chain 'A' and resid 650 through 663 removed outlier: 3.505A pdb=" N ARG A 662 " --> pdb=" O LYS A 658 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LYS A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 706 removed outlier: 3.920A pdb=" N GLU A 706 " --> pdb=" O SER A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 741 removed outlier: 3.721A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 761 Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 210 through 225 removed outlier: 4.479A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 281 through 295 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 319 through 336 removed outlier: 3.572A pdb=" N LEU B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS B 336 " --> pdb=" O MET B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 358 Processing helix chain 'B' and resid 374 through 383 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 408 through 426 Processing helix chain 'B' and resid 439 through 443 Processing helix chain 'B' and resid 449 through 458 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 493 Processing helix chain 'B' and resid 495 through 498 No H-bonds generated for 'chain 'B' and resid 495 through 498' Processing helix chain 'B' and resid 500 through 506 Processing helix chain 'B' and resid 524 through 534 removed outlier: 3.528A pdb=" N ALA B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 581 through 585 Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 631 through 634 Processing helix chain 'B' and resid 650 through 663 removed outlier: 5.029A pdb=" N LYS B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 678 Processing helix chain 'B' and resid 684 through 706 removed outlier: 3.746A pdb=" N GLU B 706 " --> pdb=" O SER B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.758A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 761 Processing helix chain 'C' and resid 43 through 48 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 130 through 133 No H-bonds generated for 'chain 'C' and resid 130 through 133' Processing helix chain 'C' and resid 135 through 139 Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 225 removed outlier: 4.557A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 227 through 232 Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 319 through 336 removed outlier: 3.773A pdb=" N VAL C 325 " --> pdb=" O GLU C 321 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS C 336 " --> pdb=" O MET C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 385 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 408 through 430 removed outlier: 3.625A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU C 429 " --> pdb=" O LYS C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 443 Processing helix chain 'C' and resid 449 through 458 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 483 through 493 Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 500 through 506 Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.546A pdb=" N ALA C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 599 through 609 Processing helix chain 'C' and resid 613 through 615 No H-bonds generated for 'chain 'C' and resid 613 through 615' Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 631 through 634 Processing helix chain 'C' and resid 650 through 660 Processing helix chain 'C' and resid 672 through 678 Processing helix chain 'C' and resid 684 through 706 removed outlier: 3.792A pdb=" N GLU C 706 " --> pdb=" O SER C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 3.907A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 761 Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 86 through 92 Processing helix chain 'D' and resid 130 through 133 No H-bonds generated for 'chain 'D' and resid 130 through 133' Processing helix chain 'D' and resid 135 through 139 Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 225 removed outlier: 4.790A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 251 through 262 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 281 through 295 Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 319 through 336 removed outlier: 3.855A pdb=" N VAL D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS D 336 " --> pdb=" O MET D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 384 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 408 through 430 removed outlier: 3.650A pdb=" N LYS D 426 " --> pdb=" O ALA D 422 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 449 through 458 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 493 Processing helix chain 'D' and resid 495 through 498 No H-bonds generated for 'chain 'D' and resid 495 through 498' Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 556 through 568 Processing helix chain 'D' and resid 581 through 585 Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 613 through 615 No H-bonds generated for 'chain 'D' and resid 613 through 615' Processing helix chain 'D' and resid 626 through 628 No H-bonds generated for 'chain 'D' and resid 626 through 628' Processing helix chain 'D' and resid 631 through 634 Processing helix chain 'D' and resid 650 through 663 removed outlier: 5.029A pdb=" N LYS D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 678 Processing helix chain 'D' and resid 684 through 706 removed outlier: 3.845A pdb=" N GLU D 706 " --> pdb=" O SER D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.852A pdb=" N ARG D 741 " --> pdb=" O GLU D 737 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 761 removed outlier: 4.063A pdb=" N LYS D 754 " --> pdb=" O ASN D 750 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 130 through 133 No H-bonds generated for 'chain 'E' and resid 130 through 133' Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 225 removed outlier: 4.923A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 227 through 232 Processing helix chain 'E' and resid 251 through 262 Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.522A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 319 through 336 removed outlier: 3.710A pdb=" N VAL E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS E 336 " --> pdb=" O MET E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 385 Processing helix chain 'E' and resid 396 through 402 Processing helix chain 'E' and resid 408 through 430 removed outlier: 3.568A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU E 429 " --> pdb=" O LYS E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 449 through 458 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 483 through 493 Processing helix chain 'E' and resid 495 through 498 No H-bonds generated for 'chain 'E' and resid 495 through 498' Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 524 through 534 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 Processing helix chain 'E' and resid 581 through 585 Processing helix chain 'E' and resid 599 through 609 Processing helix chain 'E' and resid 613 through 615 No H-bonds generated for 'chain 'E' and resid 613 through 615' Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 634 Processing helix chain 'E' and resid 650 through 663 removed outlier: 4.926A pdb=" N LYS E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 684 through 706 removed outlier: 3.635A pdb=" N GLU E 706 " --> pdb=" O SER E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.828A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 761 removed outlier: 4.117A pdb=" N LYS E 754 " --> pdb=" O ASN E 750 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 130 through 133 No H-bonds generated for 'chain 'F' and resid 130 through 133' Processing helix chain 'F' and resid 135 through 139 Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 210 through 225 removed outlier: 3.843A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 227 through 231 Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 275 Processing helix chain 'F' and resid 281 through 295 Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 319 through 336 removed outlier: 3.939A pdb=" N VAL F 325 " --> pdb=" O GLU F 321 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LYS F 336 " --> pdb=" O MET F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 358 Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 396 through 402 Processing helix chain 'F' and resid 408 through 430 removed outlier: 4.373A pdb=" N LEU F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 449 through 458 Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 498 removed outlier: 3.579A pdb=" N VAL F 493 " --> pdb=" O LEU F 489 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 556 through 568 Processing helix chain 'F' and resid 581 through 585 Processing helix chain 'F' and resid 599 through 610 removed outlier: 3.850A pdb=" N GLY F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 613 through 615 No H-bonds generated for 'chain 'F' and resid 613 through 615' Processing helix chain 'F' and resid 626 through 628 No H-bonds generated for 'chain 'F' and resid 626 through 628' Processing helix chain 'F' and resid 631 through 634 Processing helix chain 'F' and resid 650 through 660 Processing helix chain 'F' and resid 672 through 678 Processing helix chain 'F' and resid 684 through 706 Processing helix chain 'F' and resid 733 through 741 removed outlier: 3.728A pdb=" N ARG F 741 " --> pdb=" O GLU F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 762 Processing helix chain 'G' and resid 52 through 66 Processing helix chain 'G' and resid 137 through 150 removed outlier: 3.756A pdb=" N PHE G 149 " --> pdb=" O ILE G 145 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N SER G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 163 Processing helix chain 'G' and resid 168 through 187 Processing helix chain 'G' and resid 192 through 194 No H-bonds generated for 'chain 'G' and resid 192 through 194' Processing helix chain 'G' and resid 202 through 207 Processing helix chain 'G' and resid 214 through 220 Processing helix chain 'G' and resid 244 through 247 No H-bonds generated for 'chain 'G' and resid 244 through 247' Processing helix chain 'G' and resid 250 through 261 Processing helix chain 'G' and resid 281 through 284 Processing helix chain 'G' and resid 290 through 293 Processing helix chain 'G' and resid 297 through 315 Processing helix chain 'G' and resid 320 through 331 removed outlier: 3.645A pdb=" N LYS G 325 " --> pdb=" O ALA G 321 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU G 326 " --> pdb=" O MET G 322 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG G 329 " --> pdb=" O LYS G 325 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY G 330 " --> pdb=" O GLU G 326 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU G 331 " --> pdb=" O GLU G 327 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 367 Processing helix chain 'G' and resid 412 through 420 removed outlier: 3.627A pdb=" N ASP G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 436 removed outlier: 5.022A pdb=" N ALA G 436 " --> pdb=" O GLU G 432 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 81 through 83 removed outlier: 7.456A pdb=" N ILE A 82 " --> pdb=" O ARG A 25 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ILE A 27 " --> pdb=" O ILE A 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 181 through 183 removed outlier: 6.975A pdb=" N LEU A 117 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL A 165 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.630A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 removed outlier: 8.583A pdb=" N ILE A 241 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 343 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N LEU A 243 " --> pdb=" O VAL A 343 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ALA A 345 " --> pdb=" O LEU A 243 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA A 299 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N MET A 344 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N ILE A 301 " --> pdb=" O MET A 344 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ALA A 346 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 303 " --> pdb=" O ALA A 346 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N PHE A 265 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N PHE A 302 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N PHE A 267 " --> pdb=" O PHE A 302 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ASP A 304 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 641 through 644 removed outlier: 3.562A pdb=" N GLN A 641 " --> pdb=" O GLY A 513 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 81 through 83 removed outlier: 8.030A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP B 74 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 181 through 183 removed outlier: 6.758A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= I, first strand: chain 'B' and resid 365 through 368 removed outlier: 8.436A pdb=" N ILE B 241 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA B 299 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N MET B 344 " --> pdb=" O ALA B 299 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE B 301 " --> pdb=" O MET B 344 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ALA B 346 " --> pdb=" O ILE B 301 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 303 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE B 265 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N PHE B 302 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE B 267 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N ASP B 304 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE B 269 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 641 through 644 removed outlier: 3.722A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N VAL B 514 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 619 " --> pdb=" O VAL B 514 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE B 516 " --> pdb=" O ILE B 619 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY B 621 " --> pdb=" O PHE B 516 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 81 through 83 removed outlier: 7.515A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.763A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 145 through 147 Processing sheet with id= N, first strand: chain 'C' and resid 365 through 368 removed outlier: 8.493A pdb=" N ILE C 241 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N PHE C 265 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N PHE C 302 " --> pdb=" O PHE C 265 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE C 267 " --> pdb=" O PHE C 302 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP C 304 " --> pdb=" O PHE C 267 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE C 269 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.541A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N VAL C 514 " --> pdb=" O VAL C 617 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N GLY C 518 " --> pdb=" O GLY C 621 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N THR C 623 " --> pdb=" O GLY C 518 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 81 through 84 removed outlier: 7.772A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.583A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 145 through 147 Processing sheet with id= S, first strand: chain 'D' and resid 365 through 368 removed outlier: 3.745A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE D 265 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N PHE D 302 " --> pdb=" O PHE D 265 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE D 267 " --> pdb=" O PHE D 302 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASP D 304 " --> pdb=" O PHE D 267 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 641 through 645 removed outlier: 4.043A pdb=" N GLN D 641 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N VAL D 514 " --> pdb=" O VAL D 617 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE D 619 " --> pdb=" O VAL D 514 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N PHE D 516 " --> pdb=" O ILE D 619 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY D 621 " --> pdb=" O PHE D 516 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N GLY D 518 " --> pdb=" O GLY D 621 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR D 623 " --> pdb=" O GLY D 518 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 81 through 84 removed outlier: 7.871A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET E 84 " --> pdb=" O ILE E 27 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ASP E 29 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP E 74 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 181 through 183 removed outlier: 6.959A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.740A pdb=" N ARG E 144 " --> pdb=" O VAL E 176 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 365 through 368 removed outlier: 8.604A pdb=" N ILE E 241 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA E 299 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N MET E 344 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE E 265 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N PHE E 302 " --> pdb=" O PHE E 265 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N PHE E 267 " --> pdb=" O PHE E 302 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ASP E 304 " --> pdb=" O PHE E 267 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ILE E 269 " --> pdb=" O ASP E 304 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 641 through 645 removed outlier: 3.681A pdb=" N GLN E 641 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N VAL E 514 " --> pdb=" O VAL E 617 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N THR E 623 " --> pdb=" O GLY E 518 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'F' and resid 81 through 83 removed outlier: 7.532A pdb=" N ILE F 82 " --> pdb=" O ARG F 25 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ILE F 27 " --> pdb=" O ILE F 82 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 181 through 183 removed outlier: 6.822A pdb=" N LEU F 117 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N VAL F 165 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 145 through 147 Processing sheet with id= AC, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.512A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N ILE F 241 " --> pdb=" O VAL F 341 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL F 343 " --> pdb=" O ILE F 241 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N LEU F 243 " --> pdb=" O VAL F 343 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ALA F 345 " --> pdb=" O LEU F 243 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N PHE F 265 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE F 302 " --> pdb=" O PHE F 265 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE F 267 " --> pdb=" O PHE F 302 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N ASP F 304 " --> pdb=" O PHE F 267 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE F 269 " --> pdb=" O ASP F 304 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 641 through 645 removed outlier: 8.570A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 122 through 124 Processing sheet with id= AF, first strand: chain 'G' and resid 196 through 198 Processing sheet with id= AG, first strand: chain 'G' and resid 275 through 277 1294 hydrogen bonds defined for protein. 3612 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: 16.55 Time building geometry restraints manager: 15.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7838 1.33 - 1.45: 7678 1.45 - 1.57: 21674 1.57 - 1.69: 36 1.69 - 1.82: 301 Bond restraints: 37527 Sorted by residual: bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C4 ADP B 901 " pdb=" C5 ADP B 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C4 ADP F 901 " pdb=" C5 ADP F 901 " ideal model delta sigma weight residual 1.490 1.379 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C4 ADP A 901 " pdb=" C5 ADP A 901 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 ... (remaining 37522 not shown) Histogram of bond angle deviations from ideal: 99.11 - 106.48: 1287 106.48 - 113.85: 21085 113.85 - 121.21: 18947 121.21 - 128.58: 9254 128.58 - 135.95: 173 Bond angle restraints: 50746 Sorted by residual: angle pdb=" N LEU G 331 " pdb=" CA LEU G 331 " pdb=" C LEU G 331 " ideal model delta sigma weight residual 111.03 123.96 -12.93 1.11e+00 8.12e-01 1.36e+02 angle pdb=" N ARG G 332 " pdb=" CA ARG G 332 " pdb=" C ARG G 332 " ideal model delta sigma weight residual 109.62 124.29 -14.67 1.50e+00 4.44e-01 9.57e+01 angle pdb=" CA GLY D 591 " pdb=" C GLY D 591 " pdb=" O GLY D 591 " ideal model delta sigma weight residual 122.23 118.60 3.63 6.90e-01 2.10e+00 2.78e+01 angle pdb=" N ARG G 137 " pdb=" CA ARG G 137 " pdb=" C ARG G 137 " ideal model delta sigma weight residual 111.02 117.26 -6.24 1.22e+00 6.72e-01 2.62e+01 angle pdb=" C HIS F 226 " pdb=" N PRO F 227 " pdb=" CA PRO F 227 " ideal model delta sigma weight residual 119.28 124.41 -5.13 1.10e+00 8.26e-01 2.18e+01 ... (remaining 50741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 22929 35.63 - 71.26: 249 71.26 - 106.88: 39 106.88 - 142.51: 10 142.51 - 178.14: 6 Dihedral angle restraints: 23233 sinusoidal: 9775 harmonic: 13458 Sorted by residual: dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 118.14 -178.14 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP C 901 " pdb=" O3A ADP C 901 " pdb=" PB ADP C 901 " pdb=" PA ADP C 901 " ideal model delta sinusoidal sigma weight residual 300.00 125.35 174.65 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP E 901 " pdb=" O3A ADP E 901 " pdb=" PB ADP E 901 " pdb=" PA ADP E 901 " ideal model delta sinusoidal sigma weight residual -60.00 114.35 -174.36 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 23230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 5035 0.097 - 0.193: 667 0.193 - 0.290: 20 0.290 - 0.386: 0 0.386 - 0.483: 1 Chirality restraints: 5723 Sorted by residual: chirality pdb=" CA ARG G 332 " pdb=" N ARG G 332 " pdb=" C ARG G 332 " pdb=" CB ARG G 332 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" CA THR G 337 " pdb=" N THR G 337 " pdb=" C THR G 337 " pdb=" CB THR G 337 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA LEU G 331 " pdb=" N LEU G 331 " pdb=" C LEU G 331 " pdb=" CB LEU G 331 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 5720 not shown) Planarity restraints: 6650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 143 " 0.094 2.00e-02 2.50e+03 5.64e-02 6.35e+01 pdb=" CG TYR A 143 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 143 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR A 143 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR A 143 " -0.045 2.00e-02 2.50e+03 pdb=" CE2 TYR A 143 " -0.037 2.00e-02 2.50e+03 pdb=" CZ TYR A 143 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 143 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS F 226 " 0.046 2.00e-02 2.50e+03 3.43e-02 1.77e+01 pdb=" CG HIS F 226 " -0.053 2.00e-02 2.50e+03 pdb=" ND1 HIS F 226 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 HIS F 226 " -0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS F 226 " 0.026 2.00e-02 2.50e+03 pdb=" NE2 HIS F 226 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU G 331 " -0.019 2.00e-02 2.50e+03 4.14e-02 1.71e+01 pdb=" C LEU G 331 " 0.071 2.00e-02 2.50e+03 pdb=" O LEU G 331 " -0.028 2.00e-02 2.50e+03 pdb=" N ARG G 332 " -0.025 2.00e-02 2.50e+03 ... (remaining 6647 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 10396 2.82 - 3.34: 35192 3.34 - 3.86: 61264 3.86 - 4.38: 74724 4.38 - 4.90: 120996 Nonbonded interactions: 302572 Sorted by model distance: nonbonded pdb=" NZ LYS F 211 " pdb=" O ALA F 570 " model vdw 2.300 2.520 nonbonded pdb=" OD2 ASP B 368 " pdb=" NZ LYS B 565 " model vdw 2.398 2.520 nonbonded pdb=" OD1 ASP E 35 " pdb=" N ASN E 36 " model vdw 2.407 2.520 nonbonded pdb=" OD2 ASP E 368 " pdb=" NZ LYS E 565 " model vdw 2.416 2.520 nonbonded pdb=" NZ LYS F 512 " pdb=" O GLY F 637 " model vdw 2.423 2.520 ... (remaining 302567 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.460 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: 15.660 Check model and map are aligned: 0.540 Set scattering table: 0.340 Process input model: 99.940 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 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 : 0.011 0.111 37527 Z= 0.701 Angle : 0.871 14.675 50746 Z= 0.534 Chirality : 0.059 0.483 5723 Planarity : 0.004 0.084 6650 Dihedral : 12.275 178.140 14503 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 0.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.79 % Favored : 98.17 % Rotamer: Outliers : 0.10 % Allowed : 0.63 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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: 0.35 (0.11), residues: 4639 helix: -0.23 (0.10), residues: 2063 sheet: 0.67 (0.17), residues: 774 loop : 0.95 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP F 476 HIS 0.002 0.000 HIS F 226 PHE 0.023 0.001 PHE G 353 TYR 0.096 0.002 TYR A 143 ARG 0.007 0.000 ARG G 323 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1402 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1398 time to evaluate : 4.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 SER cc_start: 0.7100 (m) cc_final: 0.6847 (p) REVERT: C 304 ASP cc_start: 0.6811 (t0) cc_final: 0.6593 (t0) REVERT: D 598 ASP cc_start: 0.4691 (p0) cc_final: 0.4353 (p0) REVERT: F 320 VAL cc_start: 0.7562 (t) cc_final: 0.7218 (p) outliers start: 4 outliers final: 0 residues processed: 1402 average time/residue: 0.5958 time to fit residues: 1277.4252 Evaluate side-chains 697 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 697 time to evaluate : 4.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 393 optimal weight: 0.5980 chunk 353 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 238 optimal weight: 0.9980 chunk 188 optimal weight: 7.9990 chunk 365 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 222 optimal weight: 1.9990 chunk 271 optimal weight: 0.9990 chunk 423 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS A 641 GLN A 660 ASN B 215 GLN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN ** B 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 GLN B 660 ASN C 183 HIS ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 GLN C 660 ASN D 327 GLN D 404 HIS D 660 ASN D 735 HIS E 260 ASN E 443 ASN E 602 ASN E 660 ASN F 226 HIS F 660 ASN ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 37527 Z= 0.215 Angle : 0.689 13.575 50746 Z= 0.331 Chirality : 0.046 0.234 5723 Planarity : 0.005 0.038 6650 Dihedral : 10.093 179.717 5191 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.10 % Favored : 98.84 % Rotamer: Outliers : 2.67 % Allowed : 10.88 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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: 1.23 (0.12), residues: 4639 helix: 0.81 (0.11), residues: 2035 sheet: 0.51 (0.17), residues: 834 loop : 1.29 (0.16), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 454 HIS 0.006 0.001 HIS F 340 PHE 0.027 0.002 PHE B 674 TYR 0.030 0.002 TYR B 244 ARG 0.012 0.001 ARG C 662 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 802 time to evaluate : 4.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 449 MET cc_start: 0.7549 (tpp) cc_final: 0.6898 (tpp) REVERT: A 678 MET cc_start: 0.6596 (tpp) cc_final: 0.5078 (ptt) REVERT: B 60 LYS cc_start: 0.6905 (mtmm) cc_final: 0.6678 (mttm) REVERT: D 551 TRP cc_start: 0.7653 (t60) cc_final: 0.7405 (t60) REVERT: D 600 VAL cc_start: 0.7496 (t) cc_final: 0.7162 (t) REVERT: G 374 TRP cc_start: 0.6005 (p-90) cc_final: 0.5644 (p-90) outliers start: 106 outliers final: 49 residues processed: 866 average time/residue: 0.5165 time to fit residues: 724.0966 Evaluate side-chains 661 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 612 time to evaluate : 4.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 179 ASP Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 217 LYS Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 538 ASN Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 471 VAL Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 190 LYS Chi-restraints excluded: chain F residue 489 LEU Chi-restraints excluded: chain F residue 649 ASP Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain G residue 354 TYR Chi-restraints excluded: chain G residue 390 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 235 optimal weight: 0.5980 chunk 131 optimal weight: 9.9990 chunk 352 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 chunk 116 optimal weight: 0.5980 chunk 423 optimal weight: 0.9990 chunk 457 optimal weight: 10.0000 chunk 377 optimal weight: 0.2980 chunk 420 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 340 optimal weight: 0.9980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 404 HIS A 568 GLN A 602 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 460 ASN B 680 ASN ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN C 641 GLN C 680 ASN ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS E 260 ASN E 337 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37527 Z= 0.179 Angle : 0.633 11.383 50746 Z= 0.300 Chirality : 0.045 0.217 5723 Planarity : 0.004 0.048 6650 Dihedral : 9.589 173.464 5191 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.62 % Allowed : 13.35 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.12), residues: 4639 helix: 0.98 (0.11), residues: 2065 sheet: 0.65 (0.17), residues: 820 loop : 1.20 (0.16), residues: 1754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 551 HIS 0.011 0.001 HIS C 499 PHE 0.024 0.002 PHE A 539 TYR 0.030 0.002 TYR G 334 ARG 0.010 0.000 ARG B 635 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 761 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 657 time to evaluate : 4.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 MET cc_start: 0.6456 (tpp) cc_final: 0.5046 (ptt) REVERT: G 374 TRP cc_start: 0.6034 (p-90) cc_final: 0.5704 (p-90) outliers start: 104 outliers final: 62 residues processed: 719 average time/residue: 0.5052 time to fit residues: 597.9188 Evaluate side-chains 625 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 563 time to evaluate : 4.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 538 ASN Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 641 GLN Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 649 ASP Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 751 ASP Chi-restraints excluded: chain G residue 354 TYR Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 412 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 418 optimal weight: 7.9990 chunk 318 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 284 optimal weight: 10.0000 chunk 425 optimal weight: 0.0770 chunk 450 optimal weight: 0.3980 chunk 222 optimal weight: 0.8980 chunk 403 optimal weight: 0.5980 chunk 121 optimal weight: 3.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A 616 ASN ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 460 ASN C 90 ASN ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS D 387 ASN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 660 ASN D 735 HIS E 760 GLN F 24 ASN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS F 680 ASN ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37527 Z= 0.190 Angle : 0.618 11.051 50746 Z= 0.290 Chirality : 0.044 0.174 5723 Planarity : 0.004 0.044 6650 Dihedral : 9.250 179.510 5191 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.97 % Allowed : 14.18 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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: 1.39 (0.12), residues: 4639 helix: 1.03 (0.11), residues: 2092 sheet: 0.79 (0.18), residues: 783 loop : 1.13 (0.16), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 551 HIS 0.009 0.001 HIS F 226 PHE 0.022 0.002 PHE A 539 TYR 0.035 0.002 TYR G 334 ARG 0.009 0.000 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 622 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 MET cc_start: 0.6989 (mmm) cc_final: 0.6662 (mmm) REVERT: A 624 ASN cc_start: 0.3556 (OUTLIER) cc_final: 0.3176 (m-40) REVERT: A 678 MET cc_start: 0.6443 (tpp) cc_final: 0.4986 (ptt) REVERT: C 611 MET cc_start: 0.5645 (ttm) cc_final: 0.5400 (tpp) REVERT: D 88 VAL cc_start: 0.6208 (t) cc_final: 0.5751 (t) REVERT: E 238 PRO cc_start: 0.7819 (Cg_exo) cc_final: 0.7618 (Cg_endo) REVERT: G 374 TRP cc_start: 0.6014 (p-90) cc_final: 0.5749 (p-90) outliers start: 118 outliers final: 75 residues processed: 694 average time/residue: 0.4977 time to fit residues: 568.2068 Evaluate side-chains 625 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 549 time to evaluate : 4.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 175 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 274 ILE Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 538 ASN Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 199 ASN Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 660 ASN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 402 GLU Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 649 ASP Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 751 ASP Chi-restraints excluded: chain G residue 354 TYR Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 412 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 466 random chunks: chunk 375 optimal weight: 4.9990 chunk 255 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 335 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 384 optimal weight: 6.9990 chunk 311 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 230 optimal weight: 10.0000 chunk 404 optimal weight: 0.0270 chunk 113 optimal weight: 9.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN A 226 HIS ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 406 HIS ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 HIS B 460 ASN C 90 ASN C 199 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN ** D 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN D 735 HIS D 763 GLN ** E 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS ** F 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 763 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6747 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 37527 Z= 0.326 Angle : 0.688 10.246 50746 Z= 0.328 Chirality : 0.046 0.310 5723 Planarity : 0.005 0.048 6650 Dihedral : 8.928 170.586 5191 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.17 % Allowed : 15.19 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.82 % 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: 1.15 (0.12), residues: 4639 helix: 0.90 (0.11), residues: 2104 sheet: 0.65 (0.18), residues: 789 loop : 0.91 (0.16), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 551 HIS 0.009 0.001 HIS D 183 PHE 0.039 0.002 PHE A 575 TYR 0.029 0.002 TYR G 334 ARG 0.012 0.001 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9278 Ramachandran restraints generated. 4639 Oldfield, 0 Emsley, 4639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 593 time to evaluate : 4.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 550 MET cc_start: 0.6920 (mmm) cc_final: 0.6562 (mmm) REVERT: A 575 PHE cc_start: 0.5519 (t80) cc_final: 0.5082 (t80) REVERT: A 678 MET cc_start: 0.6498 (tpp) cc_final: 0.4922 (ptt) REVERT: C 611 MET cc_start: 0.5815 (ttm) cc_final: 0.5598 (tpp) REVERT: D 460 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8130 (p0) REVERT: G 336 TYR cc_start: 0.7240 (m-80) cc_final: 0.6977 (m-80) REVERT: G 374 TRP cc_start: 0.6149 (p-90) cc_final: 0.5859 (p-90) outliers start: 126 outliers final: 94 residues processed: 670 average time/residue: 0.5103 time to fit residues: 564.1873 Evaluate side-chains 631 residues out of total 3971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 536 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 171 SER Chi-restraints excluded: chain A residue 179 ASP Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 457 SER Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 471 VAL Chi-restraints excluded: chain A residue 499 HIS Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 102 ILE Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 270 ASN Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 479 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 559 VAL Chi-restraints excluded: chain B residue 572 CYS Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 670 VAL Chi-restraints excluded: chain B residue 742 PHE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 492 LEU Chi-restraints excluded: chain C residue 504 LEU Chi-restraints excluded: chain C residue 538 ASN Chi-restraints excluded: chain C residue 602 ASN Chi-restraints excluded: chain C residue 613 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 731 ILE Chi-restraints excluded: chain C residue 757 MET Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 79 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 143 TYR Chi-restraints excluded: chain D residue 169 ASP Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 340 HIS Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 395 ASP Chi-restraints excluded: chain D residue 456 LEU Chi-restraints excluded: chain D residue 460 ASN Chi-restraints excluded: chain D residue 522 CYS Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 572 CYS Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 91 ASN Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 122 THR Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain E residue 201 VAL Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 278 LEU Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain E residue 366 GLU Chi-restraints excluded: chain E residue 479 ILE Chi-restraints excluded: chain E residue 572 CYS Chi-restraints excluded: chain E residue 574 LEU Chi-restraints excluded: chain E residue 628 ILE Chi-restraints excluded: chain E residue 749 ASP Chi-restraints excluded: chain E residue 751 ASP Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 140 LEU Chi-restraints excluded: chain F residue 162 GLU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain F residue 169 ASP Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 574 LEU Chi-restraints excluded: chain F residue 649 ASP Chi-restraints excluded: chain F residue 657 LEU Chi-restraints excluded: chain F residue 672 LEU Chi-restraints excluded: chain F residue 747 VAL Chi-restraints excluded: chain F residue 751 ASP Chi-restraints excluded: chain G residue 354 TYR Chi-restraints excluded: chain G residue 397 GLU Chi-restraints excluded: chain G residue 412 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.8023 > 50: distance: 8 - 13: 33.750 distance: 13 - 14: 21.408 distance: 13 - 19: 14.921 distance: 14 - 15: 22.837 distance: 14 - 17: 40.194 distance: 15 - 16: 33.677 distance: 15 - 20: 32.038 distance: 17 - 18: 32.133 distance: 18 - 19: 27.290 distance: 20 - 21: 11.573 distance: 21 - 22: 14.612 distance: 21 - 24: 28.730 distance: 22 - 23: 15.937 distance: 22 - 29: 22.498 distance: 24 - 25: 11.177 distance: 25 - 26: 12.857 distance: 26 - 27: 9.303 distance: 26 - 28: 9.672 distance: 29 - 30: 12.394 distance: 30 - 31: 5.675 distance: 30 - 33: 22.601 distance: 31 - 32: 19.325 distance: 31 - 36: 38.945 distance: 33 - 34: 13.538 distance: 33 - 35: 19.277 distance: 36 - 37: 7.294 distance: 37 - 38: 13.977 distance: 37 - 40: 10.174 distance: 38 - 39: 13.005 distance: 38 - 43: 15.618 distance: 40 - 41: 7.134 distance: 40 - 42: 6.877 distance: 43 - 44: 13.112 distance: 44 - 45: 8.148 distance: 44 - 47: 8.594 distance: 45 - 46: 18.314 distance: 45 - 57: 33.747 distance: 47 - 48: 12.885 distance: 48 - 49: 11.874 distance: 48 - 50: 10.368 distance: 49 - 51: 5.674 distance: 50 - 52: 5.426 distance: 50 - 53: 7.898 distance: 53 - 55: 5.478 distance: 54 - 56: 3.727 distance: 57 - 58: 16.965 distance: 58 - 59: 20.518 distance: 58 - 61: 15.305 distance: 59 - 60: 19.174 distance: 59 - 66: 26.919 distance: 61 - 62: 17.625 distance: 62 - 63: 6.011 distance: 63 - 64: 9.460 distance: 63 - 65: 4.751 distance: 66 - 67: 12.018 distance: 67 - 68: 11.369 distance: 67 - 70: 31.407 distance: 68 - 69: 21.439 distance: 68 - 74: 39.524 distance: 70 - 71: 12.257 distance: 71 - 72: 15.063 distance: 71 - 73: 14.758 distance: 75 - 76: 33.413 distance: 75 - 78: 16.931 distance: 76 - 77: 13.738 distance: 76 - 82: 18.554 distance: 78 - 79: 7.457 distance: 78 - 80: 21.510 distance: 79 - 81: 16.707 distance: 82 - 83: 28.524 distance: 83 - 84: 41.818 distance: 84 - 85: 20.865 distance: 84 - 86: 17.461 distance: 86 - 87: 39.245 distance: 87 - 88: 8.064 distance: 88 - 89: 25.074 distance: 88 - 90: 21.804