Starting phenix.real_space_refine on Sun Feb 18 02:00:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvx_27020/02_2024/8cvx_27020_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvx_27020/02_2024/8cvx_27020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvx_27020/02_2024/8cvx_27020.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvx_27020/02_2024/8cvx_27020.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvx_27020/02_2024/8cvx_27020_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cvx_27020/02_2024/8cvx_27020_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.211 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 4 5.49 5 S 104 5.16 5 C 13097 2.51 5 N 3520 2.21 5 O 3723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 56": "OD1" <-> "OD2" Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 145": "OD1" <-> "OD2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 211": "NH1" <-> "NH2" Residue "A TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A GLU 245": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A ASP 275": "OD1" <-> "OD2" Residue "A ASP 317": "OD1" <-> "OD2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 451": "OD1" <-> "OD2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A ARG 472": "NH1" <-> "NH2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 494": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A GLU 518": "OE1" <-> "OE2" Residue "A PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 554": "OD1" <-> "OD2" Residue "A PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E GLU 326": "OE1" <-> "OE2" Residue "E TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 320": "OE1" <-> "OE2" Residue "H ASP 331": "OD1" <-> "OD2" Residue "H TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 336": "OD1" <-> "OD2" Residue "G GLU 320": "OE1" <-> "OE2" Residue "G GLU 326": "OE1" <-> "OE2" Residue "G ASP 336": "OD1" <-> "OD2" Residue "F GLU 319": "OE1" <-> "OE2" Residue "F GLU 320": "OE1" <-> "OE2" Residue "F GLU 326": "OE1" <-> "OE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ASP 135": "OD1" <-> "OD2" Residue "B TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 145": "OD1" <-> "OD2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 317": "OD1" <-> "OD2" Residue "B PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B ARG 386": "NH1" <-> "NH2" Residue "B GLU 398": "OE1" <-> "OE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B ASP 421": "OD1" <-> "OD2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 451": "OD1" <-> "OD2" Residue "B ASP 454": "OD1" <-> "OD2" Residue "B ARG 472": "NH1" <-> "NH2" Residue "B GLU 480": "OE1" <-> "OE2" Residue "B PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 494": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 510": "OE1" <-> "OE2" Residue "B GLU 518": "OE1" <-> "OE2" Residue "B PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 539": "OE1" <-> "OE2" Residue "B TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 554": "OD1" <-> "OD2" Residue "B PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 23": "OD1" <-> "OD2" Residue "D ASP 56": "OD1" <-> "OD2" Residue "D TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 70": "OE1" <-> "OE2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 89": "NH1" <-> "NH2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 145": "OD1" <-> "OD2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D ARG 211": "NH1" <-> "NH2" Residue "D TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 359": "OE1" <-> "OE2" Residue "D PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 378": "OE1" <-> "OE2" Residue "D ARG 386": "NH1" <-> "NH2" Residue "D GLU 398": "OE1" <-> "OE2" Residue "D TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 415": "OD1" <-> "OD2" Residue "D ASP 421": "OD1" <-> "OD2" Residue "D PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 451": "OD1" <-> "OD2" Residue "D ASP 454": "OD1" <-> "OD2" Residue "D ARG 472": "NH1" <-> "NH2" Residue "D GLU 494": "OE1" <-> "OE2" Residue "D GLU 495": "OE1" <-> "OE2" Residue "D PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 508": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "D GLU 518": "OE1" <-> "OE2" Residue "D PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 539": "OE1" <-> "OE2" Residue "D TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 554": "OD1" <-> "OD2" Residue "D PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C ASP 56": "OD1" <-> "OD2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 70": "OE1" <-> "OE2" Residue "C ARG 74": "NH1" <-> "NH2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C TYR 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 317": "OD1" <-> "OD2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 415": "OD1" <-> "OD2" Residue "C ASP 421": "OD1" <-> "OD2" Residue "C PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 451": "OD1" <-> "OD2" Residue "C ASP 454": "OD1" <-> "OD2" Residue "C ARG 472": "NH1" <-> "NH2" Residue "C GLU 480": "OE1" <-> "OE2" Residue "C PHE 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 494": "OE1" <-> "OE2" Residue "C GLU 495": "OE1" <-> "OE2" Residue "C PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 510": "OE1" <-> "OE2" Residue "C TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 518": "OE1" <-> "OE2" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 539": "OE1" <-> "OE2" Residue "C TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 554": "OD1" <-> "OD2" Residue "C PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 600": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20448 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4830 Classifications: {'peptide': 602} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 577} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 269 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 32} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 269 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 32} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "G" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 262 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 265 Classifications: {'peptide': 32} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4838 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 24, 'TRANS': 578} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "D" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4833 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 578} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 4818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4818 Classifications: {'peptide': 603} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 24, 'TRANS': 578} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 43 Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 16 Unusual residues: {'G6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.44, per 1000 atoms: 0.51 Number of scatterers: 20448 At special positions: 0 Unit cell: (124.331, 155.414, 156.328, 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 104 16.00 P 4 15.00 O 3723 8.00 N 3520 7.00 C 13097 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: 7.57 Conformation dependent library (CDL) restraints added in 3.4 seconds 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4762 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 17 sheets defined 45.6% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.13 Creating SS restraints... Processing helix chain 'A' and resid 43 through 57 removed outlier: 4.082A pdb=" N THR A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 51 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LYS A 52 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 53 " --> pdb=" O THR A 49 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 76 removed outlier: 3.716A pdb=" N ARG A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 95 Processing helix chain 'A' and resid 119 through 136 removed outlier: 4.340A pdb=" N ALA A 123 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA A 125 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N LEU A 126 " --> pdb=" O ALA A 123 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU A 127 " --> pdb=" O TRP A 124 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG A 128 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TRP A 129 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY A 131 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 168 Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.582A pdb=" N LEU A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 216 removed outlier: 4.031A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 Processing helix chain 'A' and resid 239 through 248 removed outlier: 4.088A pdb=" N ALA A 247 " --> pdb=" O CYS A 243 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA A 248 " --> pdb=" O MET A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 292 through 311 removed outlier: 3.629A pdb=" N ALA A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 352 removed outlier: 3.593A pdb=" N GLU A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 391 removed outlier: 3.539A pdb=" N ALA A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 422 through 435 Processing helix chain 'A' and resid 455 through 463 removed outlier: 3.522A pdb=" N THR A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 499 removed outlier: 3.751A pdb=" N ARG A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 533 through 540 Processing helix chain 'A' and resid 560 through 575 Processing helix chain 'A' and resid 579 through 592 removed outlier: 3.553A pdb=" N GLU A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG A 591 " --> pdb=" O ASN A 587 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 592 " --> pdb=" O ARG A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 601 No H-bonds generated for 'chain 'A' and resid 598 through 601' Processing helix chain 'A' and resid 603 through 616 Processing helix chain 'E' and resid 319 through 325 Processing helix chain 'E' and resid 338 through 349 Processing helix chain 'H' and resid 320 through 328 removed outlier: 4.842A pdb=" N GLN H 327 " --> pdb=" O GLU H 323 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY H 328 " --> pdb=" O ARG H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 347 Processing helix chain 'G' and resid 320 through 328 removed outlier: 4.775A pdb=" N GLN G 327 " --> pdb=" O GLU G 323 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY G 328 " --> pdb=" O ARG G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 347 Processing helix chain 'F' and resid 321 through 328 removed outlier: 4.849A pdb=" N GLN F 327 " --> pdb=" O GLU F 323 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY F 328 " --> pdb=" O ARG F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 345 Processing helix chain 'B' and resid 43 through 57 removed outlier: 4.080A pdb=" N THR B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP B 56 " --> pdb=" O LYS B 52 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 57 " --> pdb=" O VAL B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 76 removed outlier: 3.700A pdb=" N THR B 75 " --> pdb=" O GLN B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 95 Processing helix chain 'B' and resid 126 through 136 Processing helix chain 'B' and resid 146 through 168 Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.850A pdb=" N VAL B 186 " --> pdb=" O TRP B 182 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLY B 187 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 188 " --> pdb=" O ALA B 184 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS B 189 " --> pdb=" O GLY B 185 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 190 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS B 191 " --> pdb=" O GLY B 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG B 192 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 216 removed outlier: 4.006A pdb=" N TYR B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA B 215 " --> pdb=" O ARG B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 239 through 248 removed outlier: 4.089A pdb=" N ALA B 247 " --> pdb=" O CYS B 243 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA B 248 " --> pdb=" O MET B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 266 Processing helix chain 'B' and resid 292 through 311 removed outlier: 3.631A pdb=" N ALA B 298 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 352 removed outlier: 3.590A pdb=" N GLU B 344 " --> pdb=" O ASP B 340 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 391 removed outlier: 3.533A pdb=" N ALA B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 422 through 435 Processing helix chain 'B' and resid 455 through 463 removed outlier: 3.523A pdb=" N THR B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 499 removed outlier: 3.751A pdb=" N ARG B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 521 removed outlier: 3.608A pdb=" N CYS B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 540 Processing helix chain 'B' and resid 560 through 575 Processing helix chain 'B' and resid 579 through 592 removed outlier: 3.550A pdb=" N GLU B 590 " --> pdb=" O ARG B 586 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG B 591 " --> pdb=" O ASN B 587 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 616 removed outlier: 4.961A pdb=" N ARG B 603 " --> pdb=" O LYS B 599 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR B 604 " --> pdb=" O TYR B 600 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR B 605 " --> pdb=" O LEU B 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 57 removed outlier: 4.085A pdb=" N THR D 49 " --> pdb=" O THR D 45 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL D 53 " --> pdb=" O THR D 49 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASP D 56 " --> pdb=" O LYS D 52 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU D 57 " --> pdb=" O VAL D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 70 through 76 removed outlier: 3.717A pdb=" N ARG D 74 " --> pdb=" O GLU D 70 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR D 75 " --> pdb=" O GLN D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 98 removed outlier: 4.875A pdb=" N LYS D 97 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLY D 98 " --> pdb=" O MET D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 Processing helix chain 'D' and resid 146 through 168 Processing helix chain 'D' and resid 182 through 194 removed outlier: 3.844A pdb=" N VAL D 186 " --> pdb=" O TRP D 182 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N GLY D 187 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N CYS D 189 " --> pdb=" O GLY D 185 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 190 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS D 191 " --> pdb=" O GLY D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 216 removed outlier: 4.022A pdb=" N TYR D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ALA D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 239 through 251 Processing helix chain 'D' and resid 260 through 268 Processing helix chain 'D' and resid 292 through 311 removed outlier: 3.628A pdb=" N ALA D 298 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG D 303 " --> pdb=" O GLN D 299 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D 307 " --> pdb=" O ARG D 303 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 310 " --> pdb=" O GLU D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 352 removed outlier: 3.587A pdb=" N GLU D 344 " --> pdb=" O ASP D 340 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR D 351 " --> pdb=" O ALA D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 391 Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 422 through 435 Processing helix chain 'D' and resid 455 through 463 removed outlier: 3.523A pdb=" N THR D 459 " --> pdb=" O PRO D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 499 removed outlier: 3.988A pdb=" N ARG D 498 " --> pdb=" O GLU D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 521 removed outlier: 3.608A pdb=" N CYS D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 540 Processing helix chain 'D' and resid 560 through 575 removed outlier: 3.503A pdb=" N SER D 569 " --> pdb=" O SER D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 592 removed outlier: 3.550A pdb=" N GLU D 590 " --> pdb=" O ARG D 586 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG D 591 " --> pdb=" O ASN D 587 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU D 592 " --> pdb=" O ARG D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 616 removed outlier: 4.464A pdb=" N ARG D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TYR D 604 " --> pdb=" O TYR D 600 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR D 605 " --> pdb=" O LEU D 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 57 removed outlier: 4.617A pdb=" N LYS C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL C 53 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP C 56 " --> pdb=" O LYS C 52 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU C 57 " --> pdb=" O VAL C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 76 removed outlier: 3.715A pdb=" N ARG C 74 " --> pdb=" O GLU C 70 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR C 75 " --> pdb=" O GLN C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 96 Processing helix chain 'C' and resid 125 through 134 removed outlier: 3.928A pdb=" N LYS C 130 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 168 Processing helix chain 'C' and resid 182 through 193 removed outlier: 3.845A pdb=" N VAL C 186 " --> pdb=" O TRP C 182 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLY C 187 " --> pdb=" O LEU C 183 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 188 " --> pdb=" O ALA C 184 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N CYS C 189 " --> pdb=" O GLY C 185 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 190 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS C 191 " --> pdb=" O GLY C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 216 removed outlier: 4.143A pdb=" N TYR C 212 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 239 through 248 removed outlier: 4.087A pdb=" N ALA C 247 " --> pdb=" O CYS C 243 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 248 " --> pdb=" O MET C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 268 Processing helix chain 'C' and resid 292 through 311 removed outlier: 3.629A pdb=" N ALA C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 303 " --> pdb=" O GLN C 299 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE C 307 " --> pdb=" O ARG C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 352 removed outlier: 3.594A pdb=" N GLU C 344 " --> pdb=" O ASP C 340 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR C 351 " --> pdb=" O ALA C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 408 removed outlier: 3.551A pdb=" N GLY C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL C 396 " --> pdb=" O THR C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 434 Processing helix chain 'C' and resid 455 through 463 removed outlier: 3.521A pdb=" N THR C 459 " --> pdb=" O PRO C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 499 removed outlier: 3.749A pdb=" N ARG C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 521 removed outlier: 3.609A pdb=" N CYS C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 540 Processing helix chain 'C' and resid 560 through 575 Processing helix chain 'C' and resid 579 through 592 removed outlier: 3.552A pdb=" N GLU C 590 " --> pdb=" O ARG C 586 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG C 591 " --> pdb=" O ASN C 587 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU C 592 " --> pdb=" O ARG C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 601 No H-bonds generated for 'chain 'C' and resid 598 through 601' Processing helix chain 'C' and resid 603 through 616 removed outlier: 3.589A pdb=" N SER C 614 " --> pdb=" O HIS C 610 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 254 through 257 removed outlier: 6.183A pdb=" N VAL A 175 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ILE A 201 " --> pdb=" O VAL A 175 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ALA A 177 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N THR A 203 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N PHE A 179 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N PHE A 30 " --> pdb=" O HIS A 178 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N HIS A 180 " --> pdb=" O PHE A 30 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 32 " --> pdb=" O HIS A 180 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N PHE A 63 " --> pdb=" O GLU A 31 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA A 33 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 65 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU A 113 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLY A 66 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL A 115 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 116 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 323 through 330 removed outlier: 6.755A pdb=" N THR A 361 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N PHE A 326 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL A 363 " --> pdb=" O PHE A 326 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE A 328 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE A 365 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N GLY A 330 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE A 367 " --> pdb=" O GLY A 330 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 502 through 504 No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 372 through 375 removed outlier: 7.129A pdb=" N ASN A 447 " --> pdb=" O ASN A 373 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 113 through 117 removed outlier: 6.365A pdb=" N VAL B 176 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N VAL B 32 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N HIS B 178 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N VAL B 254 " --> pdb=" O PHE B 202 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N THR B 204 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N THR B 256 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 77 through 79 Processing sheet with id= G, first strand: chain 'B' and resid 323 through 330 removed outlier: 6.754A pdb=" N THR B 361 " --> pdb=" O LEU B 324 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N PHE B 326 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 363 " --> pdb=" O PHE B 326 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ILE B 328 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE B 365 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLY B 330 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE B 367 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 502 through 504 No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 372 through 375 removed outlier: 7.056A pdb=" N ASN B 447 " --> pdb=" O ASN B 373 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 113 through 118 removed outlier: 6.568A pdb=" N VAL D 176 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL D 32 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N HIS D 178 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL D 254 " --> pdb=" O PHE D 202 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N THR D 204 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR D 256 " --> pdb=" O THR D 204 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 77 through 79 Processing sheet with id= L, first strand: chain 'D' and resid 323 through 330 removed outlier: 6.754A pdb=" N THR D 361 " --> pdb=" O LEU D 324 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N PHE D 326 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL D 363 " --> pdb=" O PHE D 326 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE D 328 " --> pdb=" O VAL D 363 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE D 365 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N GLY D 330 " --> pdb=" O PHE D 365 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N ILE D 367 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 502 through 504 No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 77 through 79 removed outlier: 3.619A pdb=" N LEU C 116 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 66 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N HIS C 174 " --> pdb=" O VAL C 28 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N PHE C 30 " --> pdb=" O HIS C 174 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL C 176 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL C 32 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N HIS C 178 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL C 254 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N THR C 204 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N THR C 256 " --> pdb=" O THR C 204 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 323 through 330 removed outlier: 6.754A pdb=" N THR C 361 " --> pdb=" O LEU C 324 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N PHE C 326 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 363 " --> pdb=" O PHE C 326 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE C 328 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N PHE C 365 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 8.781A pdb=" N GLY C 330 " --> pdb=" O PHE C 365 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE C 367 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 502 through 504 No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 372 through 375 removed outlier: 7.129A pdb=" N ASN C 447 " --> pdb=" O ASN C 373 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2073 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: 5.89 Time building geometry restraints manager: 8.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3298 1.30 - 1.43: 6025 1.43 - 1.56: 11498 1.56 - 1.69: 4 1.69 - 1.83: 156 Bond restraints: 20981 Sorted by residual: bond pdb=" C ASN B 228 " pdb=" N VAL B 229 " ideal model delta sigma weight residual 1.333 1.227 0.106 1.24e-02 6.50e+03 7.31e+01 bond pdb=" C ASN C 228 " pdb=" N VAL C 229 " ideal model delta sigma weight residual 1.333 1.432 -0.098 1.24e-02 6.50e+03 6.25e+01 bond pdb=" O6 G6P B 701 " pdb=" P G6P B 701 " ideal model delta sigma weight residual 1.722 1.580 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" O6 G6P C 701 " pdb=" P G6P C 701 " ideal model delta sigma weight residual 1.722 1.609 0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" O6 G6P A 701 " pdb=" P G6P A 701 " ideal model delta sigma weight residual 1.722 1.610 0.112 2.00e-02 2.50e+03 3.11e+01 ... (remaining 20976 not shown) Histogram of bond angle deviations from ideal: 98.62 - 105.91: 501 105.91 - 113.19: 9979 113.19 - 120.48: 10191 120.48 - 127.76: 7593 127.76 - 135.04: 188 Bond angle restraints: 28452 Sorted by residual: angle pdb=" N TYR D 514 " pdb=" CA TYR D 514 " pdb=" C TYR D 514 " ideal model delta sigma weight residual 113.55 102.33 11.22 1.26e+00 6.30e-01 7.92e+01 angle pdb=" N TYR C 508 " pdb=" CA TYR C 508 " pdb=" C TYR C 508 " ideal model delta sigma weight residual 113.55 103.69 9.86 1.26e+00 6.30e-01 6.13e+01 angle pdb=" N TYR B 508 " pdb=" CA TYR B 508 " pdb=" C TYR B 508 " ideal model delta sigma weight residual 113.18 103.05 10.13 1.33e+00 5.65e-01 5.80e+01 angle pdb=" N ARG D 603 " pdb=" CA ARG D 603 " pdb=" C ARG D 603 " ideal model delta sigma weight residual 111.36 103.20 8.16 1.09e+00 8.42e-01 5.60e+01 angle pdb=" C PRO C 112 " pdb=" CA PRO C 112 " pdb=" CB PRO C 112 " ideal model delta sigma weight residual 111.46 102.32 9.14 1.29e+00 6.01e-01 5.02e+01 ... (remaining 28447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.84: 10349 14.84 - 29.68: 1356 29.68 - 44.52: 490 44.52 - 59.36: 137 59.36 - 74.20: 42 Dihedral angle restraints: 12374 sinusoidal: 4974 harmonic: 7400 Sorted by residual: dihedral pdb=" C LEU B 488 " pdb=" N LEU B 488 " pdb=" CA LEU B 488 " pdb=" CB LEU B 488 " ideal model delta harmonic sigma weight residual -122.60 -136.32 13.72 0 2.50e+00 1.60e-01 3.01e+01 dihedral pdb=" C PRO C 112 " pdb=" N PRO C 112 " pdb=" CA PRO C 112 " pdb=" CB PRO C 112 " ideal model delta harmonic sigma weight residual -120.70 -107.17 -13.53 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" C PHE A 312 " pdb=" N PHE A 312 " pdb=" CA PHE A 312 " pdb=" CB PHE A 312 " ideal model delta harmonic sigma weight residual -122.60 -109.60 -13.00 0 2.50e+00 1.60e-01 2.70e+01 ... (remaining 12371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2045 0.096 - 0.193: 797 0.193 - 0.289: 184 0.289 - 0.385: 27 0.385 - 0.482: 11 Chirality restraints: 3064 Sorted by residual: chirality pdb=" CA LEU B 488 " pdb=" N LEU B 488 " pdb=" C LEU B 488 " pdb=" CB LEU B 488 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA TYR D 604 " pdb=" N TYR D 604 " pdb=" C TYR D 604 " pdb=" CB TYR D 604 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CG LEU B 126 " pdb=" CB LEU B 126 " pdb=" CD1 LEU B 126 " pdb=" CD2 LEU B 126 " both_signs ideal model delta sigma weight residual False -2.59 -2.14 -0.45 2.00e-01 2.50e+01 5.15e+00 ... (remaining 3061 not shown) Planarity restraints: 3653 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 507 " -0.027 2.00e-02 2.50e+03 5.55e-02 3.09e+01 pdb=" C SER B 507 " 0.096 2.00e-02 2.50e+03 pdb=" O SER B 507 " -0.037 2.00e-02 2.50e+03 pdb=" N TYR B 508 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 399 " 0.026 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C LYS A 399 " -0.094 2.00e-02 2.50e+03 pdb=" O LYS A 399 " 0.036 2.00e-02 2.50e+03 pdb=" N PHE A 400 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 602 " -0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C GLY D 602 " 0.079 2.00e-02 2.50e+03 pdb=" O GLY D 602 " -0.030 2.00e-02 2.50e+03 pdb=" N ARG D 603 " -0.027 2.00e-02 2.50e+03 ... (remaining 3650 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 3624 2.80 - 3.32: 19486 3.32 - 3.85: 35484 3.85 - 4.37: 43825 4.37 - 4.90: 71519 Nonbonded interactions: 173938 Sorted by model distance: nonbonded pdb=" OG SER B 259 " pdb=" O PRO B 511 " model vdw 2.272 2.440 nonbonded pdb=" OG SER A 259 " pdb=" O PRO A 511 " model vdw 2.322 2.440 nonbonded pdb=" OG SER D 259 " pdb=" O PRO D 511 " model vdw 2.364 2.440 nonbonded pdb=" OG SER D 407 " pdb=" O SER D 412 " model vdw 2.364 2.440 nonbonded pdb=" OG SER C 259 " pdb=" O PRO C 511 " model vdw 2.403 2.440 ... (remaining 173933 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 24 through 25 and (name N or name CA or name C or name O \ or name CB )) or resid 26 through 94 or (resid 95 and (name N or name CA or name \ C or name O or name CB )) or resid 96 or (resid 97 and (name N or name CA or na \ me C or name O or name CB )) or resid 98 through 108 or (resid 109 and (name N o \ r name CA or name C or name O or name CB )) or resid 110 through 126 or (resid 1 \ 27 through 128 and (name N or name CA or name C or name O or name CB )) or resid \ 129 through 377 or (resid 378 and (name N or name CA or name C or name O or nam \ e CB )) or resid 379 through 422 or (resid 423 and (name N or name CA or name C \ or name O or name CB )) or resid 424 through 437 or (resid 438 and (name N or na \ me CA or name C or name O or name CB )) or resid 439 through 623 or (resid 624 a \ nd (name N or name CA or name C or name O or name CB )) or resid 625 or resid 70 \ 1)) selection = (chain 'B' and ((resid 24 through 25 and (name N or name CA or name C or name O \ or name CB )) or resid 26 through 77 or (resid 78 and (name N or name CA or name \ C or name O or name CB )) or resid 79 through 94 or (resid 95 and (name N or na \ me CA or name C or name O or name CB )) or resid 96 or (resid 97 and (name N or \ name CA or name C or name O or name CB )) or resid 98 through 108 or (resid 109 \ and (name N or name CA or name C or name O or name CB )) or resid 110 through 13 \ 4 or (resid 135 and (name N or name CA or name C or name O or name CB )) or resi \ d 136 through 377 or (resid 378 and (name N or name CA or name C or name O or na \ me CB )) or resid 379 through 420 or (resid 421 and (name N or name CA or name C \ or name O or name CB )) or resid 422 or (resid 423 and (name N or name CA or na \ me C or name O or name CB )) or resid 424 through 437 or (resid 438 and (name N \ or name CA or name C or name O or name CB )) or resid 439 through 623 or (resid \ 624 and (name N or name CA or name C or name O or name CB )) or resid 625 or res \ id 701)) selection = (chain 'C' and (resid 24 through 126 or (resid 127 through 128 and (name N or na \ me CA or name C or name O or name CB )) or resid 129 through 420 or (resid 421 a \ nd (name N or name CA or name C or name O or name CB )) or resid 422 through 437 \ or (resid 438 and (name N or name CA or name C or name O or name CB )) or resid \ 439 through 622 or (resid 623 through 624 and (name N or name CA or name C or n \ ame O or name CB )) or resid 625 or resid 701)) selection = (chain 'D' and ((resid 24 through 25 and (name N or name CA or name C or name O \ or name CB )) or resid 26 through 94 or (resid 95 and (name N or name CA or name \ C or name O or name CB )) or resid 96 or (resid 97 and (name N or name CA or na \ me C or name O or name CB )) or resid 98 through 108 or (resid 109 and (name N o \ r name CA or name C or name O or name CB )) or resid 110 through 126 or (resid 1 \ 27 through 128 and (name N or name CA or name C or name O or name CB )) or resid \ 129 through 377 or (resid 378 and (name N or name CA or name C or name O or nam \ e CB )) or resid 379 through 420 or (resid 421 and (name N or name CA or name C \ or name O or name CB )) or resid 422 or (resid 423 and (name N or name CA or nam \ e C or name O or name CB )) or resid 424 through 625 or resid 701)) } ncs_group { reference = (chain 'E' and (resid 318 through 325 or (resid 326 through 327 and (name N or n \ ame CA or name C or name O or name CB )) or resid 328 through 330 or (resid 331 \ and (name N or name CA or name C or name O or name CB )) or resid 332 through 34 \ 9)) selection = (chain 'F' and (resid 318 through 323 or (resid 324 and (name N or name CA or na \ me C or name O or name CB )) or resid 325 or (resid 326 through 327 and (name N \ or name CA or name C or name O or name CB )) or resid 328 through 330 or (resid \ 331 and (name N or name CA or name C or name O or name CB )) or resid 332 throug \ h 349)) selection = (chain 'G' and (resid 318 through 323 or (resid 324 and (name N or name CA or na \ me C or name O or name CB )) or resid 325 or (resid 326 through 327 and (name N \ or name CA or name C or name O or name CB )) or resid 328 through 349)) selection = (chain 'H' and (resid 318 through 326 or (resid 327 and (name N or name CA or na \ me C or name O or name CB )) or resid 328 through 330 or (resid 331 and (name N \ or name CA or name C or name O or name CB )) or resid 332 through 349)) } 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: 3.590 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: 0.020 Extract box with map and model: 8.550 Check model and map are aligned: 0.320 Set scattering table: 0.170 Process input model: 51.960 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.080 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 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 : 0.009 0.142 20981 Z= 0.592 Angle : 1.578 11.216 28452 Z= 1.111 Chirality : 0.106 0.482 3064 Planarity : 0.007 0.056 3653 Dihedral : 16.382 74.196 7612 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.29 % Rotamer: Outliers : 5.13 % Allowed : 13.15 % Favored : 81.72 % Cbeta Deviations : 0.67 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.15), residues: 2525 helix: -2.01 (0.12), residues: 1324 sheet: -1.32 (0.30), residues: 310 loop : -1.95 (0.18), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.005 TRP F 325 HIS 0.033 0.004 HIS A 610 PHE 0.032 0.004 PHE A 400 TYR 0.029 0.004 TYR B 102 ARG 0.033 0.002 ARG B 582 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 400 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6542 (tp) REVERT: A 205 HIS cc_start: 0.8224 (m-70) cc_final: 0.7927 (m90) REVERT: A 241 ARG cc_start: 0.7069 (mtt180) cc_final: 0.6674 (mtt180) REVERT: A 244 MET cc_start: 0.7399 (ttm) cc_final: 0.7122 (mtp) REVERT: A 268 HIS cc_start: 0.7716 (m-70) cc_final: 0.7352 (m-70) REVERT: A 611 MET cc_start: 0.7261 (ttm) cc_final: 0.6465 (mmt) REVERT: B 94 MET cc_start: 0.6501 (tpt) cc_final: 0.5906 (ttp) REVERT: B 102 TYR cc_start: 0.6149 (m-80) cc_final: 0.5928 (m-80) REVERT: B 272 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8241 (tpt-90) REVERT: B 606 MET cc_start: 0.6710 (ttt) cc_final: 0.6281 (ttm) REVERT: B 610 HIS cc_start: 0.6519 (m-70) cc_final: 0.5895 (m-70) REVERT: D 58 TRP cc_start: 0.6622 (m-90) cc_final: 0.6146 (m-90) REVERT: D 102 TYR cc_start: 0.6561 (m-80) cc_final: 0.5497 (m-80) REVERT: D 328 ILE cc_start: 0.7490 (tt) cc_final: 0.7264 (tt) REVERT: D 522 MET cc_start: 0.8140 (mtt) cc_final: 0.7834 (mtt) REVERT: C 265 GLU cc_start: 0.6843 (mt-10) cc_final: 0.6511 (mt-10) REVERT: C 352 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8144 (mp) REVERT: C 383 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.8257 (mp10) REVERT: C 388 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6501 (pt0) outliers start: 110 outliers final: 17 residues processed: 485 average time/residue: 0.3681 time to fit residues: 266.7878 Evaluate side-chains 259 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 237 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 294 GLN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 294 GLN Chi-restraints excluded: chain D residue 323 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 489 LEU Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 316 LEU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 352 LEU Chi-restraints excluded: chain C residue 383 GLN Chi-restraints excluded: chain C residue 388 GLN Chi-restraints excluded: chain C residue 622 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 228 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 ASN A 222 ASN A 253 HIS A 291 HIS A 315 HIS A 383 GLN ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 GLN G 340 ASN B 48 GLN B 149 ASN B 250 HIS B 253 HIS B 260 GLN B 360 GLN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 620 HIS D 95 ASN D 178 HIS D 205 HIS D 228 ASN D 250 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 ASN D 291 HIS D 436 GLN D 610 HIS C 26 ASN ** C 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN C 250 HIS C 253 HIS ** C 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN C 436 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20981 Z= 0.238 Angle : 0.600 11.580 28452 Z= 0.313 Chirality : 0.042 0.159 3064 Planarity : 0.004 0.039 3653 Dihedral : 6.421 58.273 2939 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.26 % Allowed : 17.68 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 2525 helix: -0.97 (0.13), residues: 1294 sheet: -0.96 (0.32), residues: 270 loop : -1.52 (0.18), residues: 961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 134 HIS 0.013 0.001 HIS B 240 PHE 0.032 0.002 PHE C 156 TYR 0.024 0.001 TYR A 239 ARG 0.007 0.001 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 277 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 HIS cc_start: 0.8204 (m-70) cc_final: 0.7910 (m-70) REVERT: A 611 MET cc_start: 0.6761 (ttm) cc_final: 0.6163 (mmt) REVERT: B 44 TYR cc_start: 0.8675 (t80) cc_final: 0.8385 (t80) REVERT: B 48 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.6699 (tm-30) REVERT: B 94 MET cc_start: 0.6144 (tpt) cc_final: 0.5610 (ttp) REVERT: B 150 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8155 (t0) REVERT: B 272 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8543 (tpt-90) REVERT: D 58 TRP cc_start: 0.6890 (m-90) cc_final: 0.6417 (m-90) REVERT: D 94 MET cc_start: 0.5526 (ttt) cc_final: 0.4857 (mmm) REVERT: D 102 TYR cc_start: 0.6153 (m-80) cc_final: 0.5426 (m-10) REVERT: D 181 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6426 (pt0) REVERT: D 244 MET cc_start: 0.8510 (mtm) cc_final: 0.8031 (mmm) REVERT: D 268 HIS cc_start: 0.7644 (m-70) cc_final: 0.7309 (m170) REVERT: D 294 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8112 (mm110) REVERT: D 522 MET cc_start: 0.8239 (mtt) cc_final: 0.7845 (mtt) REVERT: D 603 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6875 (ttm170) REVERT: D 606 MET cc_start: 0.6105 (mtp) cc_final: 0.5710 (mtm) REVERT: C 52 LYS cc_start: 0.8217 (tttp) cc_final: 0.7602 (tppt) REVERT: C 94 MET cc_start: 0.5399 (tpt) cc_final: 0.4921 (tpt) REVERT: C 113 LEU cc_start: 0.7099 (mp) cc_final: 0.6628 (mt) REVERT: C 301 LYS cc_start: 0.7806 (tttt) cc_final: 0.7580 (ttpp) REVERT: C 351 TYR cc_start: 0.7586 (t80) cc_final: 0.7315 (t80) REVERT: C 402 ARG cc_start: 0.7676 (ptt90) cc_final: 0.7253 (mtm110) REVERT: C 419 MET cc_start: 0.7719 (mmp) cc_final: 0.7500 (mmp) REVERT: C 428 MET cc_start: 0.8636 (mtm) cc_final: 0.8431 (mtp) outliers start: 70 outliers final: 33 residues processed: 333 average time/residue: 0.3584 time to fit residues: 179.9582 Evaluate side-chains 270 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 232 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 CYS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain E residue 339 ASP Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 250 HIS Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 294 GLN Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 469 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 388 GLN Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 606 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 155 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 247 optimal weight: 0.4980 chunk 204 optimal weight: 8.9990 chunk 227 optimal weight: 0.9990 chunk 78 optimal weight: 0.0000 chunk 183 optimal weight: 0.8980 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 315 HIS ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 GLN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN D 253 HIS C 178 HIS C 205 HIS C 222 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20981 Z= 0.217 Angle : 0.526 6.842 28452 Z= 0.275 Chirality : 0.041 0.225 3064 Planarity : 0.004 0.039 3653 Dihedral : 5.537 59.208 2912 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.71 % Allowed : 18.70 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.16), residues: 2525 helix: -0.38 (0.14), residues: 1296 sheet: -0.96 (0.31), residues: 283 loop : -1.22 (0.19), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 182 HIS 0.024 0.001 HIS D 250 PHE 0.017 0.002 PHE F 338 TYR 0.033 0.001 TYR D 221 ARG 0.009 0.000 ARG A 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 242 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 205 HIS cc_start: 0.8152 (m-70) cc_final: 0.7910 (m-70) REVERT: A 609 ARG cc_start: 0.7068 (mtm180) cc_final: 0.6826 (mtt-85) REVERT: A 611 MET cc_start: 0.6633 (ttm) cc_final: 0.6058 (mmt) REVERT: B 272 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8586 (tpt-90) REVERT: B 402 ARG cc_start: 0.7658 (mtm-85) cc_final: 0.7248 (mtm110) REVERT: B 573 SER cc_start: 0.8066 (t) cc_final: 0.7802 (m) REVERT: B 588 ARG cc_start: 0.7254 (mtt-85) cc_final: 0.7048 (mtt-85) REVERT: D 94 MET cc_start: 0.5443 (ttt) cc_final: 0.4876 (mmm) REVERT: D 102 TYR cc_start: 0.6052 (m-80) cc_final: 0.5338 (m-80) REVERT: D 181 GLU cc_start: 0.7068 (mm-30) cc_final: 0.6558 (pt0) REVERT: D 244 MET cc_start: 0.8520 (mtm) cc_final: 0.7994 (mmm) REVERT: D 294 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8203 (mm110) REVERT: D 471 ASP cc_start: 0.7184 (m-30) cc_final: 0.6938 (m-30) REVERT: D 522 MET cc_start: 0.8394 (mtt) cc_final: 0.7910 (mtt) REVERT: D 603 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6821 (ttm170) REVERT: D 606 MET cc_start: 0.6070 (mtp) cc_final: 0.5523 (mtm) REVERT: C 52 LYS cc_start: 0.8297 (tttp) cc_final: 0.7709 (tppt) REVERT: C 113 LEU cc_start: 0.7419 (mp) cc_final: 0.6930 (mt) REVERT: C 294 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7294 (mt0) REVERT: C 351 TYR cc_start: 0.7806 (t80) cc_final: 0.7211 (t80) REVERT: C 494 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7564 (tt0) REVERT: C 599 LYS cc_start: 0.8654 (mppt) cc_final: 0.8366 (mppt) outliers start: 58 outliers final: 30 residues processed: 284 average time/residue: 0.3787 time to fit residues: 160.8876 Evaluate side-chains 253 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 219 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain B residue 48 GLN Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 294 GLN Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 606 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 118 optimal weight: 0.4980 chunk 25 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 153 optimal weight: 9.9990 chunk 230 optimal weight: 0.7980 chunk 243 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 446 HIS A 478 HIS B 383 GLN ** B 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 GLN D 237 GLN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20981 Z= 0.200 Angle : 0.499 9.981 28452 Z= 0.259 Chirality : 0.040 0.194 3064 Planarity : 0.003 0.037 3653 Dihedral : 4.975 54.876 2902 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.99 % Allowed : 19.08 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.16), residues: 2525 helix: 0.01 (0.14), residues: 1281 sheet: -0.91 (0.32), residues: 258 loop : -1.17 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP C 182 HIS 0.017 0.001 HIS B 240 PHE 0.013 0.001 PHE B 156 TYR 0.016 0.001 TYR C 102 ARG 0.007 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 238 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 PHE cc_start: 0.6918 (t80) cc_final: 0.6709 (t80) REVERT: A 205 HIS cc_start: 0.8196 (m-70) cc_final: 0.7989 (m-70) REVERT: A 530 ASN cc_start: 0.7061 (OUTLIER) cc_final: 0.6658 (t0) REVERT: A 611 MET cc_start: 0.6575 (ttm) cc_final: 0.6053 (mmt) REVERT: B 44 TYR cc_start: 0.8567 (t80) cc_final: 0.8216 (t80) REVERT: B 126 LEU cc_start: 0.6652 (OUTLIER) cc_final: 0.6067 (mp) REVERT: B 272 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8665 (tpt-90) REVERT: B 359 GLU cc_start: 0.5921 (tt0) cc_final: 0.5474 (tt0) REVERT: B 421 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7351 (m-30) REVERT: B 573 SER cc_start: 0.8161 (t) cc_final: 0.7908 (m) REVERT: D 52 LYS cc_start: 0.7609 (tttp) cc_final: 0.7314 (tptt) REVERT: D 94 MET cc_start: 0.5632 (ttt) cc_final: 0.5010 (mmm) REVERT: D 102 TYR cc_start: 0.6083 (m-80) cc_final: 0.5437 (m-80) REVERT: D 181 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6551 (pt0) REVERT: D 244 MET cc_start: 0.8518 (mtm) cc_final: 0.7932 (mmm) REVERT: D 294 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8337 (mm110) REVERT: D 522 MET cc_start: 0.8465 (mtt) cc_final: 0.7916 (mtt) REVERT: D 603 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6940 (ttm170) REVERT: D 606 MET cc_start: 0.5930 (mtp) cc_final: 0.5429 (mtm) REVERT: C 34 TRP cc_start: 0.7184 (t-100) cc_final: 0.6984 (t-100) REVERT: C 49 THR cc_start: 0.8434 (p) cc_final: 0.8194 (p) REVERT: C 113 LEU cc_start: 0.7461 (mp) cc_final: 0.6963 (mt) REVERT: C 294 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7292 (mt0) REVERT: C 540 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6493 (mp0) REVERT: C 599 LYS cc_start: 0.8707 (mppt) cc_final: 0.8432 (mppt) outliers start: 64 outliers final: 34 residues processed: 289 average time/residue: 0.3594 time to fit residues: 154.5158 Evaluate side-chains 258 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 216 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain B residue 47 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 272 ARG Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 294 GLN Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 606 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 207 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 124 optimal weight: 0.4980 chunk 218 optimal weight: 1.9990 chunk 61 optimal weight: 0.0000 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 HIS A 222 ASN B 48 GLN B 250 HIS B 360 GLN B 446 HIS D 250 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20981 Z= 0.208 Angle : 0.500 11.997 28452 Z= 0.257 Chirality : 0.040 0.151 3064 Planarity : 0.003 0.050 3653 Dihedral : 4.900 54.986 2902 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.64 % Allowed : 18.98 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2525 helix: 0.29 (0.14), residues: 1277 sheet: -0.83 (0.33), residues: 249 loop : -1.03 (0.18), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.001 TRP C 182 HIS 0.017 0.001 HIS B 240 PHE 0.015 0.001 PHE D 103 TYR 0.034 0.001 TYR D 221 ARG 0.008 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 236 time to evaluate : 1.949 Fit side-chains revert: symmetry clash REVERT: A 34 TRP cc_start: 0.6469 (t-100) cc_final: 0.6226 (t60) REVERT: A 530 ASN cc_start: 0.7130 (OUTLIER) cc_final: 0.6771 (t0) REVERT: A 611 MET cc_start: 0.6591 (ttm) cc_final: 0.6155 (mmt) REVERT: B 106 TRP cc_start: 0.6293 (OUTLIER) cc_final: 0.5122 (t60) REVERT: B 126 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6174 (mp) REVERT: B 244 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7192 (ttp) REVERT: B 359 GLU cc_start: 0.5888 (tt0) cc_final: 0.5660 (tt0) REVERT: B 421 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7359 (m-30) REVERT: B 573 SER cc_start: 0.8302 (t) cc_final: 0.7991 (m) REVERT: D 52 LYS cc_start: 0.7672 (tttp) cc_final: 0.7344 (tptt) REVERT: D 94 MET cc_start: 0.5626 (ttt) cc_final: 0.5051 (mmm) REVERT: D 102 TYR cc_start: 0.6229 (m-80) cc_final: 0.5410 (m-80) REVERT: D 181 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6496 (pt0) REVERT: D 244 MET cc_start: 0.8533 (mtm) cc_final: 0.7946 (mmm) REVERT: D 294 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.6776 (mt0) REVERT: D 522 MET cc_start: 0.8505 (mtt) cc_final: 0.8186 (mtt) REVERT: D 603 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6895 (ttm170) REVERT: D 606 MET cc_start: 0.5872 (mtp) cc_final: 0.5385 (mtm) REVERT: C 49 THR cc_start: 0.8451 (p) cc_final: 0.8192 (p) REVERT: C 113 LEU cc_start: 0.7698 (mp) cc_final: 0.7291 (mt) REVERT: C 294 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7336 (mt0) REVERT: C 540 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6501 (mp0) outliers start: 78 outliers final: 43 residues processed: 292 average time/residue: 0.3389 time to fit residues: 148.4558 Evaluate side-chains 268 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 216 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 418 LYS Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 250 HIS Chi-restraints excluded: chain D residue 294 GLN Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 435 THR Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 388 GLN Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 606 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 10.0000 chunk 219 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 243 optimal weight: 0.8980 chunk 202 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 388 GLN B 268 HIS ** D 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20981 Z= 0.303 Angle : 0.554 11.755 28452 Z= 0.284 Chirality : 0.042 0.155 3064 Planarity : 0.004 0.033 3653 Dihedral : 5.026 56.220 2898 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.54 % Allowed : 19.78 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.16), residues: 2525 helix: 0.29 (0.14), residues: 1282 sheet: -1.01 (0.32), residues: 266 loop : -1.08 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C 182 HIS 0.037 0.002 HIS D 250 PHE 0.016 0.002 PHE B 477 TYR 0.017 0.001 TYR C 102 ARG 0.008 0.000 ARG B 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 242 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 268 HIS cc_start: 0.7555 (m-70) cc_final: 0.7312 (m170) REVERT: A 530 ASN cc_start: 0.7254 (OUTLIER) cc_final: 0.6882 (t0) REVERT: A 611 MET cc_start: 0.6785 (ttm) cc_final: 0.6422 (mmt) REVERT: B 106 TRP cc_start: 0.6135 (OUTLIER) cc_final: 0.4565 (t60) REVERT: B 126 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6205 (mp) REVERT: B 244 MET cc_start: 0.7903 (OUTLIER) cc_final: 0.7373 (ttp) REVERT: B 351 TYR cc_start: 0.7602 (t80) cc_final: 0.7256 (t80) REVERT: B 421 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: B 573 SER cc_start: 0.8556 (t) cc_final: 0.8215 (m) REVERT: D 52 LYS cc_start: 0.7795 (tttp) cc_final: 0.7335 (tptp) REVERT: D 94 MET cc_start: 0.5792 (ttt) cc_final: 0.5196 (mmm) REVERT: D 102 TYR cc_start: 0.6257 (m-80) cc_final: 0.5450 (m-80) REVERT: D 181 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6506 (pt0) REVERT: D 244 MET cc_start: 0.8466 (mtm) cc_final: 0.7872 (mmm) REVERT: D 603 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.7028 (ttm170) REVERT: D 606 MET cc_start: 0.5994 (mtp) cc_final: 0.5514 (mtm) REVERT: C 49 THR cc_start: 0.8524 (p) cc_final: 0.8272 (p) REVERT: C 113 LEU cc_start: 0.7727 (mp) cc_final: 0.7376 (mt) REVERT: C 540 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: C 597 ASP cc_start: 0.8454 (t0) cc_final: 0.8105 (t0) outliers start: 76 outliers final: 52 residues processed: 296 average time/residue: 0.3465 time to fit residues: 155.2559 Evaluate side-chains 285 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 226 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 388 GLN Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 528 SER Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 214 CYS Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 540 GLU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 606 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 178 optimal weight: 0.4980 chunk 137 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 chunk 242 optimal weight: 0.9980 chunk 152 optimal weight: 10.0000 chunk 148 optimal weight: 0.0980 chunk 112 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN B 205 HIS ** D 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 356 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN ** C 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20981 Z= 0.183 Angle : 0.496 11.988 28452 Z= 0.254 Chirality : 0.040 0.149 3064 Planarity : 0.003 0.035 3653 Dihedral : 4.646 39.384 2895 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.89 % Allowed : 21.04 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.16), residues: 2525 helix: 0.53 (0.14), residues: 1286 sheet: -0.99 (0.31), residues: 269 loop : -1.02 (0.18), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP A 182 HIS 0.014 0.001 HIS B 240 PHE 0.017 0.001 PHE D 103 TYR 0.018 0.001 TYR C 102 ARG 0.007 0.000 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 227 time to evaluate : 2.002 Fit side-chains revert: symmetry clash REVERT: A 268 HIS cc_start: 0.7531 (m-70) cc_final: 0.7307 (m170) REVERT: A 337 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7816 (tppt) REVERT: A 530 ASN cc_start: 0.7185 (OUTLIER) cc_final: 0.6833 (t0) REVERT: A 611 MET cc_start: 0.6739 (ttm) cc_final: 0.6402 (mmt) REVERT: B 102 TYR cc_start: 0.5948 (m-80) cc_final: 0.5301 (m-80) REVERT: B 106 TRP cc_start: 0.6249 (OUTLIER) cc_final: 0.4949 (t60) REVERT: B 126 LEU cc_start: 0.6837 (OUTLIER) cc_final: 0.6243 (mp) REVERT: B 211 ARG cc_start: 0.7229 (mmt180) cc_final: 0.6785 (mmm-85) REVERT: B 351 TYR cc_start: 0.7637 (t80) cc_final: 0.7327 (t80) REVERT: B 421 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: B 573 SER cc_start: 0.8464 (t) cc_final: 0.8143 (m) REVERT: D 52 LYS cc_start: 0.7796 (tttp) cc_final: 0.7368 (tptp) REVERT: D 94 MET cc_start: 0.5711 (ttt) cc_final: 0.5171 (mmm) REVERT: D 102 TYR cc_start: 0.6252 (m-80) cc_final: 0.5470 (m-80) REVERT: D 181 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6433 (pt0) REVERT: D 244 MET cc_start: 0.8456 (mtm) cc_final: 0.7845 (mmm) REVERT: D 536 CYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7125 (m) REVERT: D 603 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.7002 (ttm170) REVERT: C 49 THR cc_start: 0.8470 (p) cc_final: 0.8214 (p) REVERT: C 113 LEU cc_start: 0.7769 (mp) cc_final: 0.7430 (mt) REVERT: C 294 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7322 (mt0) REVERT: C 540 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.6468 (mp0) outliers start: 62 outliers final: 41 residues processed: 266 average time/residue: 0.3455 time to fit residues: 139.7464 Evaluate side-chains 263 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 213 time to evaluate : 2.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 540 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 165 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 585 GLN D 356 ASN C 222 ASN C 268 HIS C 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20981 Z= 0.249 Angle : 0.520 11.810 28452 Z= 0.266 Chirality : 0.041 0.147 3064 Planarity : 0.003 0.032 3653 Dihedral : 4.733 43.670 2895 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.12 % Allowed : 21.08 % Favored : 75.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2525 helix: 0.54 (0.14), residues: 1277 sheet: -1.08 (0.31), residues: 271 loop : -1.06 (0.18), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 182 HIS 0.015 0.001 HIS B 240 PHE 0.013 0.001 PHE B 477 TYR 0.020 0.001 TYR C 102 ARG 0.005 0.000 ARG C 402 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 228 time to evaluate : 2.259 Fit side-chains revert: symmetry clash REVERT: A 117 LEU cc_start: 0.4977 (mp) cc_final: 0.4753 (mm) REVERT: A 337 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7694 (tppt) REVERT: A 530 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.6968 (t0) REVERT: A 611 MET cc_start: 0.6758 (ttm) cc_final: 0.6443 (mmt) REVERT: E 322 LYS cc_start: 0.5241 (tptp) cc_final: 0.4794 (tptm) REVERT: B 106 TRP cc_start: 0.6209 (OUTLIER) cc_final: 0.4975 (t60) REVERT: B 126 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6259 (mp) REVERT: B 421 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7385 (m-30) REVERT: B 573 SER cc_start: 0.8685 (t) cc_final: 0.8290 (m) REVERT: D 52 LYS cc_start: 0.7727 (tttp) cc_final: 0.7266 (tptp) REVERT: D 57 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7183 (tm-30) REVERT: D 94 MET cc_start: 0.5635 (ttt) cc_final: 0.5125 (mmm) REVERT: D 102 TYR cc_start: 0.6249 (m-80) cc_final: 0.5469 (m-80) REVERT: D 181 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6513 (pt0) REVERT: D 244 MET cc_start: 0.8431 (mtm) cc_final: 0.7813 (mmm) REVERT: D 260 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.6883 (mt0) REVERT: D 418 LYS cc_start: 0.7810 (ptpp) cc_final: 0.7491 (pptt) REVERT: D 603 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6946 (ttm170) REVERT: C 49 THR cc_start: 0.8526 (p) cc_final: 0.8247 (p) REVERT: C 113 LEU cc_start: 0.7759 (mp) cc_final: 0.7455 (mt) REVERT: C 129 TRP cc_start: 0.5097 (t60) cc_final: 0.4625 (m100) REVERT: C 182 TRP cc_start: 0.7595 (p-90) cc_final: 0.7029 (p-90) REVERT: C 351 TYR cc_start: 0.8028 (t80) cc_final: 0.7826 (t80) REVERT: C 540 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6556 (mp0) REVERT: C 597 ASP cc_start: 0.8434 (t0) cc_final: 0.8162 (t0) outliers start: 67 outliers final: 52 residues processed: 274 average time/residue: 0.3502 time to fit residues: 143.6026 Evaluate side-chains 283 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 223 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain F residue 349 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 214 CYS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 178 HIS Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 606 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.9980 chunk 212 optimal weight: 8.9990 chunk 226 optimal weight: 0.2980 chunk 136 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 177 optimal weight: 0.7980 chunk 69 optimal weight: 10.0000 chunk 204 optimal weight: 30.0000 chunk 214 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 228 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN D 283 ASN D 356 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 20981 Z= 0.390 Angle : 0.607 11.695 28452 Z= 0.310 Chirality : 0.045 0.214 3064 Planarity : 0.004 0.032 3653 Dihedral : 5.127 53.869 2895 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.22 % Allowed : 21.13 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.71 (0.16), residues: 2525 helix: 0.33 (0.14), residues: 1271 sheet: -1.33 (0.31), residues: 268 loop : -1.16 (0.18), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP A 182 HIS 0.015 0.002 HIS B 240 PHE 0.021 0.002 PHE C 327 TYR 0.023 0.002 TYR C 572 ARG 0.006 0.001 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 242 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.4872 (mp) cc_final: 0.4668 (mm) REVERT: A 530 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.7040 (t0) REVERT: A 611 MET cc_start: 0.6811 (ttm) cc_final: 0.6528 (mmt) REVERT: F 332 TYR cc_start: 0.5110 (OUTLIER) cc_final: 0.4870 (m-80) REVERT: B 31 GLU cc_start: 0.6072 (mt-10) cc_final: 0.4749 (mt-10) REVERT: B 94 MET cc_start: 0.2010 (tpt) cc_final: 0.1423 (ttp) REVERT: B 106 TRP cc_start: 0.6139 (OUTLIER) cc_final: 0.4837 (t60) REVERT: B 126 LEU cc_start: 0.6869 (OUTLIER) cc_final: 0.6268 (mp) REVERT: B 421 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7408 (m-30) REVERT: D 57 GLU cc_start: 0.7493 (tm-30) cc_final: 0.6949 (tm-30) REVERT: D 94 MET cc_start: 0.5592 (ttt) cc_final: 0.5086 (mmm) REVERT: D 102 TYR cc_start: 0.6282 (m-80) cc_final: 0.5511 (m-80) REVERT: D 181 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6536 (pt0) REVERT: D 244 MET cc_start: 0.8455 (mtm) cc_final: 0.7830 (mmm) REVERT: D 260 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: D 273 LYS cc_start: 0.8211 (tmtt) cc_final: 0.7833 (tppt) REVERT: D 603 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.7029 (ttm170) REVERT: D 606 MET cc_start: 0.6012 (mtp) cc_final: 0.5603 (mtm) REVERT: C 49 THR cc_start: 0.8599 (p) cc_final: 0.8315 (p) REVERT: C 113 LEU cc_start: 0.7863 (mp) cc_final: 0.7605 (mt) REVERT: C 129 TRP cc_start: 0.4908 (t-100) cc_final: 0.3573 (t-100) REVERT: C 597 ASP cc_start: 0.8536 (t0) cc_final: 0.8261 (t0) outliers start: 69 outliers final: 49 residues processed: 292 average time/residue: 0.3852 time to fit residues: 172.6975 Evaluate side-chains 287 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 231 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 481 PHE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain D residue 48 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 491 VAL Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 606 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.3980 chunk 146 optimal weight: 5.9990 chunk 113 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 231 optimal weight: 1.9990 chunk 199 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 154 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 chunk 158 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN C 222 ASN C 250 HIS ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20981 Z= 0.262 Angle : 0.557 12.196 28452 Z= 0.283 Chirality : 0.042 0.198 3064 Planarity : 0.003 0.033 3653 Dihedral : 5.029 56.321 2895 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.99 % Allowed : 21.36 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2525 helix: 0.48 (0.15), residues: 1272 sheet: -1.32 (0.31), residues: 270 loop : -1.18 (0.18), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP A 182 HIS 0.015 0.001 HIS B 240 PHE 0.014 0.001 PHE B 327 TYR 0.028 0.001 TYR C 572 ARG 0.004 0.000 ARG B 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5050 Ramachandran restraints generated. 2525 Oldfield, 0 Emsley, 2525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 226 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 337 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.7966 (tppt) REVERT: A 530 ASN cc_start: 0.7450 (OUTLIER) cc_final: 0.6993 (t0) REVERT: A 611 MET cc_start: 0.6555 (ttm) cc_final: 0.6282 (mmt) REVERT: F 332 TYR cc_start: 0.5043 (OUTLIER) cc_final: 0.4825 (m-80) REVERT: B 94 MET cc_start: 0.1539 (tpt) cc_final: 0.0978 (ttp) REVERT: B 106 TRP cc_start: 0.6097 (OUTLIER) cc_final: 0.4838 (t60) REVERT: B 126 LEU cc_start: 0.6862 (OUTLIER) cc_final: 0.6267 (mp) REVERT: B 421 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: D 57 GLU cc_start: 0.7456 (tm-30) cc_final: 0.6964 (tm-30) REVERT: D 94 MET cc_start: 0.5584 (ttt) cc_final: 0.5130 (mmm) REVERT: D 102 TYR cc_start: 0.6246 (m-80) cc_final: 0.5491 (m-80) REVERT: D 182 TRP cc_start: 0.7394 (p-90) cc_final: 0.6235 (p-90) REVERT: D 211 ARG cc_start: 0.7605 (mmt180) cc_final: 0.6820 (mmt90) REVERT: D 244 MET cc_start: 0.8428 (mtm) cc_final: 0.7933 (mmm) REVERT: D 273 LYS cc_start: 0.8183 (tmtt) cc_final: 0.7814 (tppt) REVERT: D 603 ARG cc_start: 0.7274 (OUTLIER) cc_final: 0.7036 (ttm170) REVERT: D 606 MET cc_start: 0.6020 (mtp) cc_final: 0.5612 (mtm) REVERT: C 49 THR cc_start: 0.8556 (p) cc_final: 0.8270 (p) REVERT: C 113 LEU cc_start: 0.7845 (mp) cc_final: 0.7592 (mt) REVERT: C 129 TRP cc_start: 0.4889 (t-100) cc_final: 0.4366 (m100) REVERT: C 294 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.7701 (mt0) REVERT: C 597 ASP cc_start: 0.8512 (t0) cc_final: 0.8234 (t0) outliers start: 64 outliers final: 51 residues processed: 272 average time/residue: 0.3466 time to fit residues: 142.8744 Evaluate side-chains 283 residues out of total 2189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 224 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 189 CYS Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 272 ARG Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 453 SER Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 480 GLU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 526 SER Chi-restraints excluded: chain A residue 530 ASN Chi-restraints excluded: chain A residue 568 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain F residue 332 TYR Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 106 TRP Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 138 ASN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 392 THR Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 456 ILE Chi-restraints excluded: chain B residue 491 VAL Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain D residue 48 GLN Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 443 VAL Chi-restraints excluded: chain D residue 450 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 491 VAL Chi-restraints excluded: chain D residue 528 SER Chi-restraints excluded: chain D residue 536 CYS Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 603 ARG Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 214 CYS Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 305 GLN Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 468 SER Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 540 GLU Chi-restraints excluded: chain C residue 569 SER Chi-restraints excluded: chain C residue 606 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.0770 chunk 61 optimal weight: 9.9990 chunk 184 optimal weight: 0.0170 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 200 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 175 optimal weight: 0.6980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 228 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN D 48 GLN C 222 ASN C 250 HIS ** C 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.200257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.180705 restraints weight = 21960.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.160296 restraints weight = 54158.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.152732 restraints weight = 39481.317| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 20981 Z= 0.158 Angle : 0.511 12.673 28452 Z= 0.260 Chirality : 0.039 0.182 3064 Planarity : 0.003 0.037 3653 Dihedral : 4.840 57.982 2895 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.24 % Allowed : 21.74 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.17), residues: 2525 helix: 0.76 (0.15), residues: 1275 sheet: -1.27 (0.30), residues: 294 loop : -1.14 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP A 182 HIS 0.016 0.001 HIS B 240 PHE 0.019 0.001 PHE D 103 TYR 0.026 0.001 TYR C 572 ARG 0.005 0.000 ARG B 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4068.76 seconds wall clock time: 75 minutes 35.74 seconds (4535.74 seconds total)