Starting phenix.real_space_refine on Sat Feb 24 06:56:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz8_21487/02_2024/6vz8_21487_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz8_21487/02_2024/6vz8_21487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz8_21487/02_2024/6vz8_21487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz8_21487/02_2024/6vz8_21487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz8_21487/02_2024/6vz8_21487_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vz8_21487/02_2024/6vz8_21487_updated.pdb" } resolution = 3.45 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= 0.040 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: 6 Type Number sf(0) Gaussians P 32 5.49 5 Mg 8 5.21 5 S 200 5.16 5 C 26664 2.51 5 N 7372 2.21 5 O 7856 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ASP 101": "OD1" <-> "OD2" Residue "D GLU 152": "OE1" <-> "OE2" Residue "D TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ARG 233": "NH1" <-> "NH2" Residue "D ASP 253": "OD1" <-> "OD2" Residue "D PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 538": "OD1" <-> "OD2" Residue "D ARG 552": "NH1" <-> "NH2" Residue "D TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "E ASP 101": "OD1" <-> "OD2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E ARG 233": "NH1" <-> "NH2" Residue "E ASP 253": "OD1" <-> "OD2" Residue "E ARG 319": "NH1" <-> "NH2" Residue "E PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 362": "OE1" <-> "OE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 429": "NH1" <-> "NH2" Residue "E PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 538": "OD1" <-> "OD2" Residue "E ARG 552": "NH1" <-> "NH2" Residue "E GLU 596": "OE1" <-> "OE2" Residue "E TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 85": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F GLU 115": "OE1" <-> "OE2" Residue "F PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 161": "OE1" <-> "OE2" Residue "F GLU 167": "OE1" <-> "OE2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F ASP 196": "OD1" <-> "OD2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F ARG 218": "NH1" <-> "NH2" Residue "F ARG 226": "NH1" <-> "NH2" Residue "F ARG 237": "NH1" <-> "NH2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F GLU 239": "OE1" <-> "OE2" Residue "G ARG 343": "NH1" <-> "NH2" Residue "G GLU 356": "OE1" <-> "OE2" Residue "G ASP 392": "OD1" <-> "OD2" Residue "G PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 402": "OE1" <-> "OE2" Residue "G ARG 415": "NH1" <-> "NH2" Residue "G ARG 416": "NH1" <-> "NH2" Residue "G ASP 417": "OD1" <-> "OD2" Residue "G PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 444": "OD1" <-> "OD2" Residue "G ASP 446": "OD1" <-> "OD2" Residue "G ARG 453": "NH1" <-> "NH2" Residue "G GLU 456": "OE1" <-> "OE2" Residue "G ARG 473": "NH1" <-> "NH2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 90": "NH1" <-> "NH2" Residue "H ASP 101": "OD1" <-> "OD2" Residue "H GLU 152": "OE1" <-> "OE2" Residue "H TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 208": "OE1" <-> "OE2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "H ARG 233": "NH1" <-> "NH2" Residue "H ASP 253": "OD1" <-> "OD2" Residue "H PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 538": "OD1" <-> "OD2" Residue "H ARG 552": "NH1" <-> "NH2" Residue "H TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 90": "NH1" <-> "NH2" Residue "I ASP 101": "OD1" <-> "OD2" Residue "I GLU 152": "OE1" <-> "OE2" Residue "I TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 208": "OE1" <-> "OE2" Residue "I ARG 216": "NH1" <-> "NH2" Residue "I ARG 233": "NH1" <-> "NH2" Residue "I ASP 253": "OD1" <-> "OD2" Residue "I ARG 319": "NH1" <-> "NH2" Residue "I PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 362": "OE1" <-> "OE2" Residue "I PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 429": "NH1" <-> "NH2" Residue "I PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 538": "OD1" <-> "OD2" Residue "I ARG 552": "NH1" <-> "NH2" Residue "I GLU 596": "OE1" <-> "OE2" Residue "I TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 85": "NH1" <-> "NH2" Residue "J ARG 109": "NH1" <-> "NH2" Residue "J GLU 115": "OE1" <-> "OE2" Residue "J GLU 161": "OE1" <-> "OE2" Residue "J GLU 167": "OE1" <-> "OE2" Residue "J GLU 178": "OE1" <-> "OE2" Residue "J ASP 196": "OD1" <-> "OD2" Residue "J GLU 205": "OE1" <-> "OE2" Residue "J ARG 218": "NH1" <-> "NH2" Residue "J ARG 226": "NH1" <-> "NH2" Residue "J ARG 237": "NH1" <-> "NH2" Residue "J ARG 238": "NH1" <-> "NH2" Residue "J GLU 239": "OE1" <-> "OE2" Residue "K ARG 343": "NH1" <-> "NH2" Residue "K GLU 356": "OE1" <-> "OE2" Residue "K ASP 392": "OD1" <-> "OD2" Residue "K PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 402": "OE1" <-> "OE2" Residue "K ARG 415": "NH1" <-> "NH2" Residue "K ARG 416": "NH1" <-> "NH2" Residue "K ASP 417": "OD1" <-> "OD2" Residue "K PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 444": "OD1" <-> "OD2" Residue "K ASP 446": "OD1" <-> "OD2" Residue "K ARG 453": "NH1" <-> "NH2" Residue "K GLU 456": "OE1" <-> "OE2" Residue "K ARG 473": "NH1" <-> "NH2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 90": "NH1" <-> "NH2" Residue "L ASP 101": "OD1" <-> "OD2" Residue "L GLU 152": "OE1" <-> "OE2" Residue "L TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 208": "OE1" <-> "OE2" Residue "L ARG 216": "NH1" <-> "NH2" Residue "L ARG 233": "NH1" <-> "NH2" Residue "L ASP 253": "OD1" <-> "OD2" Residue "L PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 538": "OD1" <-> "OD2" Residue "L ARG 552": "NH1" <-> "NH2" Residue "L TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 90": "NH1" <-> "NH2" Residue "M ASP 101": "OD1" <-> "OD2" Residue "M GLU 152": "OE1" <-> "OE2" Residue "M TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 208": "OE1" <-> "OE2" Residue "M ARG 216": "NH1" <-> "NH2" Residue "M ARG 233": "NH1" <-> "NH2" Residue "M ASP 253": "OD1" <-> "OD2" Residue "M ARG 319": "NH1" <-> "NH2" Residue "M PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 362": "OE1" <-> "OE2" Residue "M PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 429": "NH1" <-> "NH2" Residue "M PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 538": "OD1" <-> "OD2" Residue "M ARG 552": "NH1" <-> "NH2" Residue "M GLU 596": "OE1" <-> "OE2" Residue "M TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 85": "NH1" <-> "NH2" Residue "N ARG 109": "NH1" <-> "NH2" Residue "N GLU 115": "OE1" <-> "OE2" Residue "N PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 161": "OE1" <-> "OE2" Residue "N GLU 167": "OE1" <-> "OE2" Residue "N GLU 178": "OE1" <-> "OE2" Residue "N ASP 196": "OD1" <-> "OD2" Residue "N GLU 205": "OE1" <-> "OE2" Residue "N ARG 218": "NH1" <-> "NH2" Residue "N ARG 226": "NH1" <-> "NH2" Residue "N ARG 237": "NH1" <-> "NH2" Residue "N ARG 238": "NH1" <-> "NH2" Residue "N GLU 239": "OE1" <-> "OE2" Residue "O PHE 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 343": "NH1" <-> "NH2" Residue "O GLU 356": "OE1" <-> "OE2" Residue "O ASP 392": "OD1" <-> "OD2" Residue "O PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 402": "OE1" <-> "OE2" Residue "O ARG 415": "NH1" <-> "NH2" Residue "O ARG 416": "NH1" <-> "NH2" Residue "O ASP 417": "OD1" <-> "OD2" Residue "O PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 444": "OD1" <-> "OD2" Residue "O ASP 446": "OD1" <-> "OD2" Residue "O ARG 453": "NH1" <-> "NH2" Residue "O GLU 456": "OE1" <-> "OE2" Residue "O ARG 473": "NH1" <-> "NH2" Residue "P PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 90": "NH1" <-> "NH2" Residue "P ASP 101": "OD1" <-> "OD2" Residue "P GLU 152": "OE1" <-> "OE2" Residue "P TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 208": "OE1" <-> "OE2" Residue "P ARG 216": "NH1" <-> "NH2" Residue "P ARG 233": "NH1" <-> "NH2" Residue "P ASP 253": "OD1" <-> "OD2" Residue "P PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 538": "OD1" <-> "OD2" Residue "P ARG 552": "NH1" <-> "NH2" Residue "P TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 90": "NH1" <-> "NH2" Residue "Q ASP 101": "OD1" <-> "OD2" Residue "Q GLU 152": "OE1" <-> "OE2" Residue "Q TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 208": "OE1" <-> "OE2" Residue "Q ARG 216": "NH1" <-> "NH2" Residue "Q ARG 233": "NH1" <-> "NH2" Residue "Q ASP 253": "OD1" <-> "OD2" Residue "Q ARG 319": "NH1" <-> "NH2" Residue "Q PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 362": "OE1" <-> "OE2" Residue "Q PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 429": "NH1" <-> "NH2" Residue "Q PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 538": "OD1" <-> "OD2" Residue "Q ARG 552": "NH1" <-> "NH2" Residue "Q GLU 596": "OE1" <-> "OE2" Residue "Q TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 85": "NH1" <-> "NH2" Residue "R ARG 109": "NH1" <-> "NH2" Residue "R GLU 115": "OE1" <-> "OE2" Residue "R GLU 161": "OE1" <-> "OE2" Residue "R GLU 167": "OE1" <-> "OE2" Residue "R GLU 178": "OE1" <-> "OE2" Residue "R ASP 196": "OD1" <-> "OD2" Residue "R GLU 205": "OE1" <-> "OE2" Residue "R ARG 218": "NH1" <-> "NH2" Residue "R ARG 226": "NH1" <-> "NH2" Residue "R ARG 237": "NH1" <-> "NH2" Residue "R ARG 238": "NH1" <-> "NH2" Residue "R GLU 239": "OE1" <-> "OE2" Residue "S ARG 343": "NH1" <-> "NH2" Residue "S GLU 356": "OE1" <-> "OE2" Residue "S ASP 392": "OD1" <-> "OD2" Residue "S PHE 398": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 402": "OE1" <-> "OE2" Residue "S ARG 415": "NH1" <-> "NH2" Residue "S ARG 416": "NH1" <-> "NH2" Residue "S ASP 417": "OD1" <-> "OD2" Residue "S PHE 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 444": "OD1" <-> "OD2" Residue "S ASP 446": "OD1" <-> "OD2" Residue "S ARG 453": "NH1" <-> "NH2" Residue "S GLU 456": "OE1" <-> "OE2" Residue "S ARG 473": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 42132 Number of models: 1 Model: "" Number of chains: 32 Chain: "D" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 3910 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 495} Chain breaks: 6 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "E" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 3953 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 505} Chain breaks: 4 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 121 Chain: "F" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1266 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 3, 'TRANS': 155} Chain: "G" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1228 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "H" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 3910 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 495} Chain breaks: 6 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "I" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 3953 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 505} Chain breaks: 4 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 121 Chain: "J" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1266 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 3, 'TRANS': 155} Chain: "K" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1228 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "L" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 3910 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 495} Chain breaks: 6 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 3953 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 505} Chain breaks: 4 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 121 Chain: "N" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1266 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 3, 'TRANS': 155} Chain: "O" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1228 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "P" Number of atoms: 3910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 531, 3910 Classifications: {'peptide': 531} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 495} Chain breaks: 6 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "Q" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 3953 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 505} Chain breaks: 4 Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 248 Unresolved non-hydrogen dihedrals: 168 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 4, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 121 Chain: "R" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1266 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 3, 'TRANS': 155} Chain: "S" Number of atoms: 1228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1228 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "D" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "H" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "L" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "O" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "P" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 80 Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "S" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 22.44, per 1000 atoms: 0.53 Number of scatterers: 42132 At special positions: 0 Unit cell: (228.78, 228.78, 96.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 200 16.00 P 32 15.00 Mg 8 11.99 O 7856 8.00 N 7372 7.00 C 26664 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: 17.98 Conformation dependent library (CDL) restraints added in 8.3 seconds 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10232 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 216 helices and 56 sheets defined 40.5% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.18 Creating SS restraints... Processing helix chain 'D' and resid 99 through 110 Processing helix chain 'D' and resid 124 through 132 Processing helix chain 'D' and resid 144 through 158 Processing helix chain 'D' and resid 170 through 185 removed outlier: 3.918A pdb=" N VAL D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP D 181 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU D 184 " --> pdb=" O ALA D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 211 through 218 removed outlier: 4.973A pdb=" N SER D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ILE D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 243 Proline residue: D 232 - end of helix Processing helix chain 'D' and resid 256 through 260 Processing helix chain 'D' and resid 274 through 279 removed outlier: 3.514A pdb=" N SER D 278 " --> pdb=" O PRO D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 292 Processing helix chain 'D' and resid 308 through 310 No H-bonds generated for 'chain 'D' and resid 308 through 310' Processing helix chain 'D' and resid 316 through 322 Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 376 through 379 No H-bonds generated for 'chain 'D' and resid 376 through 379' Processing helix chain 'D' and resid 415 through 433 removed outlier: 3.561A pdb=" N ARG D 429 " --> pdb=" O VAL D 425 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU D 432 " --> pdb=" O ASN D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 450 Processing helix chain 'D' and resid 464 through 475 Processing helix chain 'D' and resid 487 through 494 Processing helix chain 'D' and resid 515 through 526 Processing helix chain 'D' and resid 538 through 554 removed outlier: 4.347A pdb=" N ASN D 544 " --> pdb=" O SER D 540 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLN D 546 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N GLU D 547 " --> pdb=" O MET D 543 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU D 548 " --> pdb=" O ASN D 544 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ALA D 549 " --> pdb=" O VAL D 545 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N THR D 550 " --> pdb=" O GLN D 546 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE D 551 " --> pdb=" O GLU D 547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG D 552 " --> pdb=" O LEU D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 577 Processing helix chain 'D' and resid 601 through 608 removed outlier: 3.533A pdb=" N CYS D 608 " --> pdb=" O PHE D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 630 removed outlier: 4.328A pdb=" N ARG D 622 " --> pdb=" O LYS D 618 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU D 623 " --> pdb=" O ALA D 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 110 Processing helix chain 'E' and resid 124 through 132 Processing helix chain 'E' and resid 144 through 158 removed outlier: 3.557A pdb=" N PHE E 149 " --> pdb=" O GLN E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 185 removed outlier: 3.557A pdb=" N LEU E 175 " --> pdb=" O GLY E 171 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER E 177 " --> pdb=" O THR E 173 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY E 178 " --> pdb=" O ASN E 174 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU E 184 " --> pdb=" O ALA E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 211 through 215 Processing helix chain 'E' and resid 228 through 243 Proline residue: E 232 - end of helix Processing helix chain 'E' and resid 256 through 260 Processing helix chain 'E' and resid 274 through 279 Processing helix chain 'E' and resid 286 through 295 Processing helix chain 'E' and resid 308 through 310 No H-bonds generated for 'chain 'E' and resid 308 through 310' Processing helix chain 'E' and resid 314 through 322 Processing helix chain 'E' and resid 355 through 363 Processing helix chain 'E' and resid 376 through 379 No H-bonds generated for 'chain 'E' and resid 376 through 379' Processing helix chain 'E' and resid 415 through 433 removed outlier: 3.561A pdb=" N ARG E 429 " --> pdb=" O VAL E 425 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU E 432 " --> pdb=" O ASN E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 450 Processing helix chain 'E' and resid 464 through 475 Processing helix chain 'E' and resid 487 through 494 Processing helix chain 'E' and resid 515 through 526 Processing helix chain 'E' and resid 538 through 554 removed outlier: 4.063A pdb=" N MET E 543 " --> pdb=" O GLY E 539 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN E 544 " --> pdb=" O SER E 540 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 545 " --> pdb=" O PHE E 541 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLN E 546 " --> pdb=" O ILE E 542 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N GLU E 547 " --> pdb=" O MET E 543 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU E 548 " --> pdb=" O ASN E 544 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA E 549 " --> pdb=" O VAL E 545 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N THR E 550 " --> pdb=" O GLN E 546 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE E 551 " --> pdb=" O GLU E 547 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG E 552 " --> pdb=" O LEU E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 577 removed outlier: 3.539A pdb=" N TRP E 574 " --> pdb=" O MET E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 608 removed outlier: 3.622A pdb=" N CYS E 608 " --> pdb=" O PHE E 604 " (cutoff:3.500A) Processing helix chain 'E' and resid 618 through 630 removed outlier: 4.439A pdb=" N ARG E 622 " --> pdb=" O LYS E 618 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU E 623 " --> pdb=" O ALA E 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 110 removed outlier: 3.703A pdb=" N VAL F 106 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE F 107 " --> pdb=" O ILE F 103 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG F 110 " --> pdb=" O VAL F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 148 removed outlier: 3.678A pdb=" N GLN F 140 " --> pdb=" O GLU F 136 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN F 141 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN F 147 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS F 148 " --> pdb=" O GLU F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 190 removed outlier: 3.544A pdb=" N TRP F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 222 removed outlier: 4.767A pdb=" N LYS F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 343 removed outlier: 3.558A pdb=" N PHE G 340 " --> pdb=" O VAL G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 383 removed outlier: 3.890A pdb=" N LYS G 383 " --> pdb=" O GLN G 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 425 removed outlier: 3.989A pdb=" N ARG G 416 " --> pdb=" O ALA G 412 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP G 417 " --> pdb=" O ALA G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 445 through 457 removed outlier: 3.614A pdb=" N GLU G 456 " --> pdb=" O GLN G 452 " (cutoff:3.500A) Proline residue: G 457 - end of helix Processing helix chain 'H' and resid 99 through 110 Processing helix chain 'H' and resid 124 through 132 Processing helix chain 'H' and resid 144 through 158 Processing helix chain 'H' and resid 170 through 185 removed outlier: 3.917A pdb=" N VAL H 176 " --> pdb=" O ALA H 172 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER H 177 " --> pdb=" O THR H 173 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLY H 178 " --> pdb=" O ASN H 174 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP H 181 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU H 184 " --> pdb=" O ALA H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 211 through 215 Processing helix chain 'H' and resid 228 through 243 Proline residue: H 232 - end of helix Processing helix chain 'H' and resid 256 through 260 Processing helix chain 'H' and resid 274 through 279 removed outlier: 3.515A pdb=" N SER H 278 " --> pdb=" O PRO H 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 292 Processing helix chain 'H' and resid 308 through 310 No H-bonds generated for 'chain 'H' and resid 308 through 310' Processing helix chain 'H' and resid 316 through 322 Processing helix chain 'H' and resid 355 through 363 Processing helix chain 'H' and resid 376 through 379 No H-bonds generated for 'chain 'H' and resid 376 through 379' Processing helix chain 'H' and resid 415 through 433 removed outlier: 3.561A pdb=" N ARG H 429 " --> pdb=" O VAL H 425 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU H 431 " --> pdb=" O GLU H 427 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU H 432 " --> pdb=" O ASN H 428 " (cutoff:3.500A) Processing helix chain 'H' and resid 438 through 450 Processing helix chain 'H' and resid 464 through 475 Processing helix chain 'H' and resid 487 through 494 Processing helix chain 'H' and resid 515 through 526 Processing helix chain 'H' and resid 538 through 554 removed outlier: 4.347A pdb=" N ASN H 544 " --> pdb=" O SER H 540 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLN H 546 " --> pdb=" O ILE H 542 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLU H 547 " --> pdb=" O MET H 543 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU H 548 " --> pdb=" O ASN H 544 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ALA H 549 " --> pdb=" O VAL H 545 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR H 550 " --> pdb=" O GLN H 546 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE H 551 " --> pdb=" O GLU H 547 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG H 552 " --> pdb=" O LEU H 548 " (cutoff:3.500A) Processing helix chain 'H' and resid 569 through 577 Processing helix chain 'H' and resid 601 through 608 removed outlier: 3.533A pdb=" N CYS H 608 " --> pdb=" O PHE H 604 " (cutoff:3.500A) Processing helix chain 'H' and resid 618 through 630 removed outlier: 4.328A pdb=" N ARG H 622 " --> pdb=" O LYS H 618 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU H 623 " --> pdb=" O ALA H 619 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 110 Processing helix chain 'I' and resid 124 through 132 Processing helix chain 'I' and resid 144 through 158 removed outlier: 3.557A pdb=" N PHE I 149 " --> pdb=" O GLN I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 185 removed outlier: 3.557A pdb=" N LEU I 175 " --> pdb=" O GLY I 171 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL I 176 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLY I 178 " --> pdb=" O ASN I 174 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP I 181 " --> pdb=" O SER I 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU I 184 " --> pdb=" O ALA I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 200 No H-bonds generated for 'chain 'I' and resid 198 through 200' Processing helix chain 'I' and resid 211 through 215 Processing helix chain 'I' and resid 228 through 243 Proline residue: I 232 - end of helix Processing helix chain 'I' and resid 256 through 260 Processing helix chain 'I' and resid 274 through 279 Processing helix chain 'I' and resid 286 through 295 Processing helix chain 'I' and resid 308 through 310 No H-bonds generated for 'chain 'I' and resid 308 through 310' Processing helix chain 'I' and resid 314 through 322 Processing helix chain 'I' and resid 355 through 363 Processing helix chain 'I' and resid 376 through 379 No H-bonds generated for 'chain 'I' and resid 376 through 379' Processing helix chain 'I' and resid 415 through 433 removed outlier: 3.562A pdb=" N ARG I 429 " --> pdb=" O VAL I 425 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU I 431 " --> pdb=" O GLU I 427 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU I 432 " --> pdb=" O ASN I 428 " (cutoff:3.500A) Processing helix chain 'I' and resid 438 through 450 Processing helix chain 'I' and resid 464 through 475 Processing helix chain 'I' and resid 487 through 494 Processing helix chain 'I' and resid 515 through 526 Processing helix chain 'I' and resid 538 through 554 removed outlier: 4.063A pdb=" N MET I 543 " --> pdb=" O GLY I 539 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASN I 544 " --> pdb=" O SER I 540 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL I 545 " --> pdb=" O PHE I 541 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLN I 546 " --> pdb=" O ILE I 542 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU I 547 " --> pdb=" O MET I 543 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU I 548 " --> pdb=" O ASN I 544 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA I 549 " --> pdb=" O VAL I 545 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N THR I 550 " --> pdb=" O GLN I 546 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE I 551 " --> pdb=" O GLU I 547 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG I 552 " --> pdb=" O LEU I 548 " (cutoff:3.500A) Processing helix chain 'I' and resid 569 through 577 removed outlier: 3.539A pdb=" N TRP I 574 " --> pdb=" O MET I 570 " (cutoff:3.500A) Processing helix chain 'I' and resid 601 through 608 removed outlier: 3.621A pdb=" N CYS I 608 " --> pdb=" O PHE I 604 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 630 removed outlier: 4.438A pdb=" N ARG I 622 " --> pdb=" O LYS I 618 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU I 623 " --> pdb=" O ALA I 619 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 110 removed outlier: 3.831A pdb=" N VAL J 106 " --> pdb=" O ARG J 102 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE J 107 " --> pdb=" O ILE J 103 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG J 110 " --> pdb=" O VAL J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 148 removed outlier: 3.615A pdb=" N GLN J 140 " --> pdb=" O GLU J 136 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN J 141 " --> pdb=" O ARG J 137 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLN J 147 " --> pdb=" O ILE J 143 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS J 148 " --> pdb=" O GLU J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 190 removed outlier: 3.545A pdb=" N TRP J 185 " --> pdb=" O ALA J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 222 removed outlier: 4.767A pdb=" N LYS J 222 " --> pdb=" O ARG J 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 343 Processing helix chain 'K' and resid 373 through 383 removed outlier: 3.892A pdb=" N LYS K 383 " --> pdb=" O GLN K 379 " (cutoff:3.500A) Processing helix chain 'K' and resid 412 through 425 removed outlier: 4.150A pdb=" N ARG K 416 " --> pdb=" O ALA K 412 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP K 417 " --> pdb=" O ALA K 413 " (cutoff:3.500A) Processing helix chain 'K' and resid 445 through 457 removed outlier: 3.650A pdb=" N GLU K 456 " --> pdb=" O GLN K 452 " (cutoff:3.500A) Proline residue: K 457 - end of helix Processing helix chain 'L' and resid 99 through 110 Processing helix chain 'L' and resid 124 through 132 Processing helix chain 'L' and resid 144 through 158 Processing helix chain 'L' and resid 170 through 185 removed outlier: 3.918A pdb=" N VAL L 176 " --> pdb=" O ALA L 172 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER L 177 " --> pdb=" O THR L 173 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLY L 178 " --> pdb=" O ASN L 174 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP L 181 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU L 184 " --> pdb=" O ALA L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 198 through 200 No H-bonds generated for 'chain 'L' and resid 198 through 200' Processing helix chain 'L' and resid 211 through 218 removed outlier: 4.977A pdb=" N SER L 217 " --> pdb=" O GLU L 213 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE L 218 " --> pdb=" O VAL L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 243 Proline residue: L 232 - end of helix Processing helix chain 'L' and resid 256 through 260 Processing helix chain 'L' and resid 274 through 279 removed outlier: 3.516A pdb=" N SER L 278 " --> pdb=" O PRO L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 292 Processing helix chain 'L' and resid 308 through 310 No H-bonds generated for 'chain 'L' and resid 308 through 310' Processing helix chain 'L' and resid 316 through 322 Processing helix chain 'L' and resid 355 through 363 Processing helix chain 'L' and resid 376 through 379 No H-bonds generated for 'chain 'L' and resid 376 through 379' Processing helix chain 'L' and resid 415 through 433 removed outlier: 3.560A pdb=" N ARG L 429 " --> pdb=" O VAL L 425 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU L 431 " --> pdb=" O GLU L 427 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU L 432 " --> pdb=" O ASN L 428 " (cutoff:3.500A) Processing helix chain 'L' and resid 438 through 450 Processing helix chain 'L' and resid 464 through 475 Processing helix chain 'L' and resid 487 through 494 Processing helix chain 'L' and resid 515 through 526 Processing helix chain 'L' and resid 538 through 554 removed outlier: 4.347A pdb=" N ASN L 544 " --> pdb=" O SER L 540 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLN L 546 " --> pdb=" O ILE L 542 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLU L 547 " --> pdb=" O MET L 543 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU L 548 " --> pdb=" O ASN L 544 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ALA L 549 " --> pdb=" O VAL L 545 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N THR L 550 " --> pdb=" O GLN L 546 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE L 551 " --> pdb=" O GLU L 547 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG L 552 " --> pdb=" O LEU L 548 " (cutoff:3.500A) Processing helix chain 'L' and resid 569 through 577 Processing helix chain 'L' and resid 601 through 608 removed outlier: 3.532A pdb=" N CYS L 608 " --> pdb=" O PHE L 604 " (cutoff:3.500A) Processing helix chain 'L' and resid 618 through 630 removed outlier: 4.328A pdb=" N ARG L 622 " --> pdb=" O LYS L 618 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU L 623 " --> pdb=" O ALA L 619 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 110 Processing helix chain 'M' and resid 124 through 132 Processing helix chain 'M' and resid 144 through 158 removed outlier: 3.558A pdb=" N PHE M 149 " --> pdb=" O GLN M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 185 removed outlier: 3.556A pdb=" N LEU M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL M 176 " --> pdb=" O ALA M 172 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N SER M 177 " --> pdb=" O THR M 173 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLY M 178 " --> pdb=" O ASN M 174 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP M 181 " --> pdb=" O SER M 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU M 184 " --> pdb=" O ALA M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 198 through 200 No H-bonds generated for 'chain 'M' and resid 198 through 200' Processing helix chain 'M' and resid 211 through 215 Processing helix chain 'M' and resid 228 through 243 Proline residue: M 232 - end of helix Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 274 through 279 Processing helix chain 'M' and resid 286 through 295 Processing helix chain 'M' and resid 308 through 310 No H-bonds generated for 'chain 'M' and resid 308 through 310' Processing helix chain 'M' and resid 314 through 322 Processing helix chain 'M' and resid 355 through 363 Processing helix chain 'M' and resid 376 through 379 No H-bonds generated for 'chain 'M' and resid 376 through 379' Processing helix chain 'M' and resid 415 through 433 removed outlier: 3.562A pdb=" N ARG M 429 " --> pdb=" O VAL M 425 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU M 431 " --> pdb=" O GLU M 427 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU M 432 " --> pdb=" O ASN M 428 " (cutoff:3.500A) Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 464 through 475 Processing helix chain 'M' and resid 487 through 494 Processing helix chain 'M' and resid 515 through 526 Processing helix chain 'M' and resid 538 through 554 removed outlier: 4.063A pdb=" N MET M 543 " --> pdb=" O GLY M 539 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASN M 544 " --> pdb=" O SER M 540 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL M 545 " --> pdb=" O PHE M 541 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLN M 546 " --> pdb=" O ILE M 542 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU M 547 " --> pdb=" O MET M 543 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU M 548 " --> pdb=" O ASN M 544 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA M 549 " --> pdb=" O VAL M 545 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N THR M 550 " --> pdb=" O GLN M 546 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE M 551 " --> pdb=" O GLU M 547 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG M 552 " --> pdb=" O LEU M 548 " (cutoff:3.500A) Processing helix chain 'M' and resid 569 through 577 removed outlier: 3.539A pdb=" N TRP M 574 " --> pdb=" O MET M 570 " (cutoff:3.500A) Processing helix chain 'M' and resid 601 through 608 removed outlier: 3.622A pdb=" N CYS M 608 " --> pdb=" O PHE M 604 " (cutoff:3.500A) Processing helix chain 'M' and resid 618 through 630 removed outlier: 4.439A pdb=" N ARG M 622 " --> pdb=" O LYS M 618 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N GLU M 623 " --> pdb=" O ALA M 619 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 110 removed outlier: 3.967A pdb=" N PHE N 107 " --> pdb=" O ILE N 103 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARG N 110 " --> pdb=" O VAL N 106 " (cutoff:3.500A) Processing helix chain 'N' and resid 136 through 148 removed outlier: 3.650A pdb=" N GLN N 140 " --> pdb=" O GLU N 136 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN N 141 " --> pdb=" O ARG N 137 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLN N 147 " --> pdb=" O ILE N 143 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS N 148 " --> pdb=" O GLU N 144 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 190 removed outlier: 3.544A pdb=" N TRP N 185 " --> pdb=" O ALA N 181 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 222 removed outlier: 4.768A pdb=" N LYS N 222 " --> pdb=" O ARG N 218 " (cutoff:3.500A) Processing helix chain 'O' and resid 332 through 343 removed outlier: 3.620A pdb=" N PHE O 340 " --> pdb=" O VAL O 336 " (cutoff:3.500A) Processing helix chain 'O' and resid 373 through 383 removed outlier: 3.892A pdb=" N LYS O 383 " --> pdb=" O GLN O 379 " (cutoff:3.500A) Processing helix chain 'O' and resid 412 through 424 removed outlier: 3.991A pdb=" N ARG O 416 " --> pdb=" O ALA O 412 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP O 417 " --> pdb=" O ALA O 413 " (cutoff:3.500A) Processing helix chain 'O' and resid 445 through 457 removed outlier: 3.893A pdb=" N GLU O 456 " --> pdb=" O GLN O 452 " (cutoff:3.500A) Proline residue: O 457 - end of helix Processing helix chain 'P' and resid 99 through 110 Processing helix chain 'P' and resid 124 through 132 Processing helix chain 'P' and resid 144 through 158 Processing helix chain 'P' and resid 170 through 185 removed outlier: 3.918A pdb=" N VAL P 176 " --> pdb=" O ALA P 172 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N SER P 177 " --> pdb=" O THR P 173 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLY P 178 " --> pdb=" O ASN P 174 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP P 181 " --> pdb=" O SER P 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU P 184 " --> pdb=" O ALA P 180 " (cutoff:3.500A) Processing helix chain 'P' and resid 198 through 200 No H-bonds generated for 'chain 'P' and resid 198 through 200' Processing helix chain 'P' and resid 211 through 218 removed outlier: 4.998A pdb=" N SER P 217 " --> pdb=" O GLU P 213 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ILE P 218 " --> pdb=" O VAL P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 228 through 243 Proline residue: P 232 - end of helix Processing helix chain 'P' and resid 256 through 260 Processing helix chain 'P' and resid 274 through 279 removed outlier: 3.515A pdb=" N SER P 278 " --> pdb=" O PRO P 274 " (cutoff:3.500A) Processing helix chain 'P' and resid 286 through 292 Processing helix chain 'P' and resid 308 through 310 No H-bonds generated for 'chain 'P' and resid 308 through 310' Processing helix chain 'P' and resid 316 through 322 Processing helix chain 'P' and resid 355 through 363 Processing helix chain 'P' and resid 376 through 379 No H-bonds generated for 'chain 'P' and resid 376 through 379' Processing helix chain 'P' and resid 415 through 433 removed outlier: 3.561A pdb=" N ARG P 429 " --> pdb=" O VAL P 425 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU P 431 " --> pdb=" O GLU P 427 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N GLU P 432 " --> pdb=" O ASN P 428 " (cutoff:3.500A) Processing helix chain 'P' and resid 438 through 450 Processing helix chain 'P' and resid 464 through 475 Processing helix chain 'P' and resid 487 through 494 Processing helix chain 'P' and resid 515 through 526 Processing helix chain 'P' and resid 538 through 554 removed outlier: 4.348A pdb=" N ASN P 544 " --> pdb=" O SER P 540 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLN P 546 " --> pdb=" O ILE P 542 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N GLU P 547 " --> pdb=" O MET P 543 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU P 548 " --> pdb=" O ASN P 544 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N ALA P 549 " --> pdb=" O VAL P 545 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N THR P 550 " --> pdb=" O GLN P 546 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE P 551 " --> pdb=" O GLU P 547 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG P 552 " --> pdb=" O LEU P 548 " (cutoff:3.500A) Processing helix chain 'P' and resid 569 through 577 Processing helix chain 'P' and resid 601 through 608 removed outlier: 3.532A pdb=" N CYS P 608 " --> pdb=" O PHE P 604 " (cutoff:3.500A) Processing helix chain 'P' and resid 618 through 630 removed outlier: 4.328A pdb=" N ARG P 622 " --> pdb=" O LYS P 618 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU P 623 " --> pdb=" O ALA P 619 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 110 Processing helix chain 'Q' and resid 124 through 132 Processing helix chain 'Q' and resid 144 through 158 removed outlier: 3.558A pdb=" N PHE Q 149 " --> pdb=" O GLN Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 185 removed outlier: 3.557A pdb=" N LEU Q 175 " --> pdb=" O GLY Q 171 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL Q 176 " --> pdb=" O ALA Q 172 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N SER Q 177 " --> pdb=" O THR Q 173 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLY Q 178 " --> pdb=" O ASN Q 174 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP Q 181 " --> pdb=" O SER Q 177 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU Q 184 " --> pdb=" O ALA Q 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 198 through 200 No H-bonds generated for 'chain 'Q' and resid 198 through 200' Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 228 through 243 Proline residue: Q 232 - end of helix Processing helix chain 'Q' and resid 256 through 260 Processing helix chain 'Q' and resid 274 through 279 Processing helix chain 'Q' and resid 286 through 295 Processing helix chain 'Q' and resid 308 through 310 No H-bonds generated for 'chain 'Q' and resid 308 through 310' Processing helix chain 'Q' and resid 314 through 322 Processing helix chain 'Q' and resid 355 through 363 Processing helix chain 'Q' and resid 376 through 379 No H-bonds generated for 'chain 'Q' and resid 376 through 379' Processing helix chain 'Q' and resid 415 through 433 removed outlier: 3.562A pdb=" N ARG Q 429 " --> pdb=" O VAL Q 425 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLU Q 431 " --> pdb=" O GLU Q 427 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLU Q 432 " --> pdb=" O ASN Q 428 " (cutoff:3.500A) Processing helix chain 'Q' and resid 438 through 450 Processing helix chain 'Q' and resid 464 through 475 Processing helix chain 'Q' and resid 487 through 494 Processing helix chain 'Q' and resid 515 through 526 Processing helix chain 'Q' and resid 538 through 554 removed outlier: 4.063A pdb=" N MET Q 543 " --> pdb=" O GLY Q 539 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN Q 544 " --> pdb=" O SER Q 540 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL Q 545 " --> pdb=" O PHE Q 541 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLN Q 546 " --> pdb=" O ILE Q 542 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU Q 547 " --> pdb=" O MET Q 543 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU Q 548 " --> pdb=" O ASN Q 544 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA Q 549 " --> pdb=" O VAL Q 545 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N THR Q 550 " --> pdb=" O GLN Q 546 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE Q 551 " --> pdb=" O GLU Q 547 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ARG Q 552 " --> pdb=" O LEU Q 548 " (cutoff:3.500A) Processing helix chain 'Q' and resid 569 through 577 removed outlier: 3.540A pdb=" N TRP Q 574 " --> pdb=" O MET Q 570 " (cutoff:3.500A) Processing helix chain 'Q' and resid 601 through 608 removed outlier: 3.621A pdb=" N CYS Q 608 " --> pdb=" O PHE Q 604 " (cutoff:3.500A) Processing helix chain 'Q' and resid 618 through 630 removed outlier: 4.439A pdb=" N ARG Q 622 " --> pdb=" O LYS Q 618 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU Q 623 " --> pdb=" O ALA Q 619 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 110 removed outlier: 3.624A pdb=" N VAL R 106 " --> pdb=" O ARG R 102 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE R 107 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG R 110 " --> pdb=" O VAL R 106 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 148 removed outlier: 3.651A pdb=" N GLN R 140 " --> pdb=" O GLU R 136 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN R 141 " --> pdb=" O ARG R 137 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN R 147 " --> pdb=" O ILE R 143 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS R 148 " --> pdb=" O GLU R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 190 removed outlier: 3.545A pdb=" N TRP R 185 " --> pdb=" O ALA R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 222 removed outlier: 4.768A pdb=" N LYS R 222 " --> pdb=" O ARG R 218 " (cutoff:3.500A) Processing helix chain 'S' and resid 332 through 343 removed outlier: 3.576A pdb=" N VAL S 339 " --> pdb=" O ILE S 335 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N PHE S 340 " --> pdb=" O VAL S 336 " (cutoff:3.500A) Processing helix chain 'S' and resid 373 through 383 removed outlier: 3.892A pdb=" N LYS S 383 " --> pdb=" O GLN S 379 " (cutoff:3.500A) Processing helix chain 'S' and resid 412 through 425 removed outlier: 3.991A pdb=" N ARG S 416 " --> pdb=" O ALA S 412 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP S 417 " --> pdb=" O ALA S 413 " (cutoff:3.500A) Processing helix chain 'S' and resid 445 through 457 removed outlier: 3.757A pdb=" N GLU S 456 " --> pdb=" O GLN S 452 " (cutoff:3.500A) Proline residue: S 457 - end of helix Processing sheet with id= A, first strand: chain 'D' and resid 114 through 116 removed outlier: 6.457A pdb=" N ARG D 137 " --> pdb=" O VAL D 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'D' and resid 162 through 166 removed outlier: 6.838A pdb=" N HIS D 221 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ASP D 253 " --> pdb=" O HIS D 221 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR D 223 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL D 225 " --> pdb=" O PRO D 255 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 328 through 330 removed outlier: 8.292A pdb=" N ALA D 329 " --> pdb=" O PRO D 302 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU D 304 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU D 366 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR D 305 " --> pdb=" O LEU D 366 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU D 368 " --> pdb=" O TYR D 305 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL D 392 " --> pdb=" O ALA D 369 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL D 409 " --> pdb=" O HIS D 393 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ASP D 395 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL D 411 " --> pdb=" O ASP D 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'D' and resid 480 through 483 removed outlier: 6.648A pdb=" N LYS D 559 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ASP D 536 " --> pdb=" O LYS D 559 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU D 561 " --> pdb=" O ASP D 536 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR D 635 " --> pdb=" O VAL D 560 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU D 562 " --> pdb=" O TYR D 635 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU D 637 " --> pdb=" O LEU D 562 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 114 through 116 removed outlier: 6.456A pdb=" N ARG E 137 " --> pdb=" O VAL E 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'E' and resid 162 through 166 removed outlier: 6.831A pdb=" N HIS E 221 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N ASP E 253 " --> pdb=" O HIS E 221 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR E 223 " --> pdb=" O ASP E 253 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL E 225 " --> pdb=" O PRO E 255 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 328 through 330 removed outlier: 8.293A pdb=" N ALA E 329 " --> pdb=" O PRO E 302 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU E 304 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU E 366 " --> pdb=" O VAL E 303 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR E 305 " --> pdb=" O LEU E 366 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU E 368 " --> pdb=" O TYR E 305 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL E 392 " --> pdb=" O ALA E 369 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL E 409 " --> pdb=" O HIS E 393 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ASP E 395 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL E 411 " --> pdb=" O ASP E 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'E' and resid 504 through 506 removed outlier: 6.421A pdb=" N ILE E 481 " --> pdb=" O LEU E 505 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS E 559 " --> pdb=" O ASP E 534 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASP E 536 " --> pdb=" O LYS E 559 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU E 561 " --> pdb=" O ASP E 536 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR E 635 " --> pdb=" O VAL E 560 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N LEU E 562 " --> pdb=" O TYR E 635 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU E 637 " --> pdb=" O LEU E 562 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN E 564 " --> pdb=" O LEU E 637 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL E 639 " --> pdb=" O ASN E 564 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 152 through 157 removed outlier: 6.711A pdb=" N PHE F 92 " --> pdb=" O LEU F 153 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL F 155 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER F 90 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASP F 157 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR F 88 " --> pdb=" O ASP F 157 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER F 116 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N CYS F 133 " --> pdb=" O ILE F 114 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE F 114 " --> pdb=" O CYS F 133 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 163 through 166 Processing sheet with id= K, first strand: chain 'F' and resid 225 through 230 removed outlier: 6.584A pdb=" N LYS F 172 " --> pdb=" O ARG F 226 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE F 228 " --> pdb=" O LEU F 170 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU F 170 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ARG F 230 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LEU F 168 " --> pdb=" O ARG F 230 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP F 196 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU F 205 " --> pdb=" O VAL F 194 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL F 194 " --> pdb=" O GLU F 205 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 387 through 392 removed outlier: 6.849A pdb=" N LEU G 325 " --> pdb=" O HIS G 388 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL G 390 " --> pdb=" O SER G 323 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER G 323 " --> pdb=" O VAL G 390 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP G 392 " --> pdb=" O THR G 321 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR G 321 " --> pdb=" O ASP G 392 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER G 349 " --> pdb=" O VAL G 366 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE G 347 " --> pdb=" O PRO G 368 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 398 through 401 Processing sheet with id= N, first strand: chain 'G' and resid 459 through 463 removed outlier: 3.974A pdb=" N GLY G 459 " --> pdb=" O ALA G 409 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LYS G 407 " --> pdb=" O CYS G 461 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL G 463 " --> pdb=" O LEU G 405 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU G 405 " --> pdb=" O VAL G 463 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLN G 440 " --> pdb=" O ALA G 429 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N ALA G 429 " --> pdb=" O GLN G 440 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 114 through 116 removed outlier: 6.457A pdb=" N ARG H 137 " --> pdb=" O VAL H 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'H' and resid 162 through 166 removed outlier: 6.838A pdb=" N HIS H 221 " --> pdb=" O LEU H 251 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ASP H 253 " --> pdb=" O HIS H 221 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR H 223 " --> pdb=" O ASP H 253 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL H 225 " --> pdb=" O PRO H 255 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 328 through 330 removed outlier: 8.292A pdb=" N ALA H 329 " --> pdb=" O PRO H 302 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU H 304 " --> pdb=" O ALA H 329 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU H 366 " --> pdb=" O VAL H 303 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR H 305 " --> pdb=" O LEU H 366 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU H 368 " --> pdb=" O TYR H 305 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL H 392 " --> pdb=" O ALA H 369 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL H 409 " --> pdb=" O HIS H 393 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ASP H 395 " --> pdb=" O VAL H 409 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL H 411 " --> pdb=" O ASP H 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'H' and resid 480 through 483 removed outlier: 6.648A pdb=" N LYS H 559 " --> pdb=" O ASP H 534 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASP H 536 " --> pdb=" O LYS H 559 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU H 561 " --> pdb=" O ASP H 536 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR H 635 " --> pdb=" O VAL H 560 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU H 562 " --> pdb=" O TYR H 635 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU H 637 " --> pdb=" O LEU H 562 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 114 through 116 removed outlier: 6.457A pdb=" N ARG I 137 " --> pdb=" O VAL I 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'I' and resid 162 through 166 removed outlier: 6.830A pdb=" N HIS I 221 " --> pdb=" O LEU I 251 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N ASP I 253 " --> pdb=" O HIS I 221 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR I 223 " --> pdb=" O ASP I 253 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N VAL I 225 " --> pdb=" O PRO I 255 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 328 through 330 removed outlier: 8.293A pdb=" N ALA I 329 " --> pdb=" O PRO I 302 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LEU I 304 " --> pdb=" O ALA I 329 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU I 366 " --> pdb=" O VAL I 303 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR I 305 " --> pdb=" O LEU I 366 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU I 368 " --> pdb=" O TYR I 305 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL I 392 " --> pdb=" O ALA I 369 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL I 409 " --> pdb=" O HIS I 393 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ASP I 395 " --> pdb=" O VAL I 409 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL I 411 " --> pdb=" O ASP I 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'I' and resid 504 through 506 removed outlier: 6.421A pdb=" N ILE I 481 " --> pdb=" O LEU I 505 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS I 559 " --> pdb=" O ASP I 534 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ASP I 536 " --> pdb=" O LYS I 559 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU I 561 " --> pdb=" O ASP I 536 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR I 635 " --> pdb=" O VAL I 560 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LEU I 562 " --> pdb=" O TYR I 635 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU I 637 " --> pdb=" O LEU I 562 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN I 564 " --> pdb=" O LEU I 637 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL I 639 " --> pdb=" O ASN I 564 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 152 through 157 removed outlier: 6.803A pdb=" N PHE J 92 " --> pdb=" O LEU J 153 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL J 155 " --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER J 90 " --> pdb=" O VAL J 155 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASP J 157 " --> pdb=" O THR J 88 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR J 88 " --> pdb=" O ASP J 157 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER J 116 " --> pdb=" O VAL J 131 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N CYS J 133 " --> pdb=" O ILE J 114 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE J 114 " --> pdb=" O CYS J 133 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 163 through 166 Processing sheet with id= Y, first strand: chain 'J' and resid 225 through 230 removed outlier: 6.584A pdb=" N LYS J 172 " --> pdb=" O ARG J 226 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE J 228 " --> pdb=" O LEU J 170 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU J 170 " --> pdb=" O ILE J 228 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ARG J 230 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU J 168 " --> pdb=" O ARG J 230 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP J 196 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU J 205 " --> pdb=" O VAL J 194 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL J 194 " --> pdb=" O GLU J 205 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 387 through 392 removed outlier: 6.830A pdb=" N LEU K 325 " --> pdb=" O HIS K 388 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N VAL K 390 " --> pdb=" O SER K 323 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER K 323 " --> pdb=" O VAL K 390 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP K 392 " --> pdb=" O THR K 321 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N THR K 321 " --> pdb=" O ASP K 392 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER K 349 " --> pdb=" O VAL K 366 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N ILE K 347 " --> pdb=" O PRO K 368 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 398 through 401 Processing sheet with id= AB, first strand: chain 'K' and resid 459 through 463 removed outlier: 3.976A pdb=" N GLY K 459 " --> pdb=" O ALA K 409 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS K 407 " --> pdb=" O CYS K 461 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N VAL K 463 " --> pdb=" O LEU K 405 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU K 405 " --> pdb=" O VAL K 463 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N GLN K 440 " --> pdb=" O ALA K 429 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ALA K 429 " --> pdb=" O GLN K 440 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'L' and resid 114 through 116 removed outlier: 6.456A pdb=" N ARG L 137 " --> pdb=" O VAL L 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'L' and resid 162 through 166 removed outlier: 6.837A pdb=" N HIS L 221 " --> pdb=" O LEU L 251 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ASP L 253 " --> pdb=" O HIS L 221 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR L 223 " --> pdb=" O ASP L 253 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL L 225 " --> pdb=" O PRO L 255 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'L' and resid 328 through 330 removed outlier: 8.292A pdb=" N ALA L 329 " --> pdb=" O PRO L 302 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU L 304 " --> pdb=" O ALA L 329 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU L 366 " --> pdb=" O VAL L 303 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR L 305 " --> pdb=" O LEU L 366 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N LEU L 368 " --> pdb=" O TYR L 305 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL L 392 " --> pdb=" O ALA L 369 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL L 409 " --> pdb=" O HIS L 393 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N ASP L 395 " --> pdb=" O VAL L 409 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL L 411 " --> pdb=" O ASP L 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'L' and resid 480 through 483 removed outlier: 6.648A pdb=" N LYS L 559 " --> pdb=" O ASP L 534 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASP L 536 " --> pdb=" O LYS L 559 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU L 561 " --> pdb=" O ASP L 536 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR L 635 " --> pdb=" O VAL L 560 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU L 562 " --> pdb=" O TYR L 635 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU L 637 " --> pdb=" O LEU L 562 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'M' and resid 114 through 116 removed outlier: 6.455A pdb=" N ARG M 137 " --> pdb=" O VAL M 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'M' and resid 162 through 166 removed outlier: 6.824A pdb=" N HIS M 221 " --> pdb=" O LEU M 251 " (cutoff:3.500A) removed outlier: 8.633A pdb=" N ASP M 253 " --> pdb=" O HIS M 221 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR M 223 " --> pdb=" O ASP M 253 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL M 225 " --> pdb=" O PRO M 255 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'M' and resid 328 through 330 removed outlier: 8.293A pdb=" N ALA M 329 " --> pdb=" O PRO M 302 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU M 304 " --> pdb=" O ALA M 329 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N LEU M 366 " --> pdb=" O VAL M 303 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TYR M 305 " --> pdb=" O LEU M 366 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU M 368 " --> pdb=" O TYR M 305 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL M 392 " --> pdb=" O ALA M 369 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL M 409 " --> pdb=" O HIS M 393 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N ASP M 395 " --> pdb=" O VAL M 409 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL M 411 " --> pdb=" O ASP M 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'M' and resid 504 through 506 removed outlier: 6.421A pdb=" N ILE M 481 " --> pdb=" O LEU M 505 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS M 559 " --> pdb=" O ASP M 534 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ASP M 536 " --> pdb=" O LYS M 559 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU M 561 " --> pdb=" O ASP M 536 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N TYR M 635 " --> pdb=" O VAL M 560 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N LEU M 562 " --> pdb=" O TYR M 635 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU M 637 " --> pdb=" O LEU M 562 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN M 564 " --> pdb=" O LEU M 637 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL M 639 " --> pdb=" O ASN M 564 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'N' and resid 152 through 157 removed outlier: 6.805A pdb=" N PHE N 92 " --> pdb=" O LEU N 153 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL N 155 " --> pdb=" O SER N 90 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER N 90 " --> pdb=" O VAL N 155 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ASP N 157 " --> pdb=" O THR N 88 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N THR N 88 " --> pdb=" O ASP N 157 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER N 116 " --> pdb=" O VAL N 131 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'N' and resid 163 through 166 Processing sheet with id= AM, first strand: chain 'N' and resid 225 through 230 removed outlier: 6.584A pdb=" N LYS N 172 " --> pdb=" O ARG N 226 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE N 228 " --> pdb=" O LEU N 170 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU N 170 " --> pdb=" O ILE N 228 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG N 230 " --> pdb=" O LEU N 168 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU N 168 " --> pdb=" O ARG N 230 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP N 196 " --> pdb=" O THR N 203 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU N 205 " --> pdb=" O VAL N 194 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N VAL N 194 " --> pdb=" O GLU N 205 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'O' and resid 349 through 354 removed outlier: 3.859A pdb=" N SER O 349 " --> pdb=" O VAL O 366 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU O 389 " --> pdb=" O LEU O 325 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'O' and resid 398 through 401 Processing sheet with id= AP, first strand: chain 'O' and resid 459 through 463 removed outlier: 3.963A pdb=" N GLY O 459 " --> pdb=" O ALA O 409 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS O 407 " --> pdb=" O CYS O 461 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL O 463 " --> pdb=" O LEU O 405 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU O 405 " --> pdb=" O VAL O 463 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN O 440 " --> pdb=" O ALA O 429 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ALA O 429 " --> pdb=" O GLN O 440 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'P' and resid 114 through 116 removed outlier: 6.456A pdb=" N ARG P 137 " --> pdb=" O VAL P 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'P' and resid 162 through 166 removed outlier: 6.838A pdb=" N HIS P 221 " --> pdb=" O LEU P 251 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ASP P 253 " --> pdb=" O HIS P 221 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR P 223 " --> pdb=" O ASP P 253 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL P 225 " --> pdb=" O PRO P 255 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'P' and resid 328 through 330 removed outlier: 8.292A pdb=" N ALA P 329 " --> pdb=" O PRO P 302 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU P 304 " --> pdb=" O ALA P 329 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU P 366 " --> pdb=" O VAL P 303 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N TYR P 305 " --> pdb=" O LEU P 366 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU P 368 " --> pdb=" O TYR P 305 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL P 392 " --> pdb=" O ALA P 369 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL P 409 " --> pdb=" O HIS P 393 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ASP P 395 " --> pdb=" O VAL P 409 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL P 411 " --> pdb=" O ASP P 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'P' and resid 480 through 483 removed outlier: 6.648A pdb=" N LYS P 559 " --> pdb=" O ASP P 534 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ASP P 536 " --> pdb=" O LYS P 559 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU P 561 " --> pdb=" O ASP P 536 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR P 635 " --> pdb=" O VAL P 560 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N LEU P 562 " --> pdb=" O TYR P 635 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU P 637 " --> pdb=" O LEU P 562 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 114 through 116 removed outlier: 6.455A pdb=" N ARG Q 137 " --> pdb=" O VAL Q 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'Q' and resid 162 through 166 removed outlier: 6.825A pdb=" N HIS Q 221 " --> pdb=" O LEU Q 251 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ASP Q 253 " --> pdb=" O HIS Q 221 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR Q 223 " --> pdb=" O ASP Q 253 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL Q 225 " --> pdb=" O PRO Q 255 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Q' and resid 328 through 330 removed outlier: 8.293A pdb=" N ALA Q 329 " --> pdb=" O PRO Q 302 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU Q 304 " --> pdb=" O ALA Q 329 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU Q 366 " --> pdb=" O VAL Q 303 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N TYR Q 305 " --> pdb=" O LEU Q 366 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU Q 368 " --> pdb=" O TYR Q 305 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N VAL Q 392 " --> pdb=" O ALA Q 369 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N VAL Q 409 " --> pdb=" O HIS Q 393 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N ASP Q 395 " --> pdb=" O VAL Q 409 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL Q 411 " --> pdb=" O ASP Q 395 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'Q' and resid 504 through 506 removed outlier: 6.420A pdb=" N ILE Q 481 " --> pdb=" O LEU Q 505 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS Q 559 " --> pdb=" O ASP Q 534 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ASP Q 536 " --> pdb=" O LYS Q 559 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU Q 561 " --> pdb=" O ASP Q 536 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N TYR Q 635 " --> pdb=" O VAL Q 560 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LEU Q 562 " --> pdb=" O TYR Q 635 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU Q 637 " --> pdb=" O LEU Q 562 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ASN Q 564 " --> pdb=" O LEU Q 637 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL Q 639 " --> pdb=" O ASN Q 564 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'R' and resid 152 through 157 removed outlier: 6.826A pdb=" N PHE R 92 " --> pdb=" O LEU R 153 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL R 155 " --> pdb=" O SER R 90 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER R 90 " --> pdb=" O VAL R 155 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ASP R 157 " --> pdb=" O THR R 88 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N THR R 88 " --> pdb=" O ASP R 157 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER R 116 " --> pdb=" O VAL R 131 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N CYS R 133 " --> pdb=" O ILE R 114 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE R 114 " --> pdb=" O CYS R 133 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'R' and resid 163 through 166 Processing sheet with id= BA, first strand: chain 'R' and resid 225 through 230 removed outlier: 6.583A pdb=" N LYS R 172 " --> pdb=" O ARG R 226 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE R 228 " --> pdb=" O LEU R 170 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU R 170 " --> pdb=" O ILE R 228 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ARG R 230 " --> pdb=" O LEU R 168 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU R 168 " --> pdb=" O ARG R 230 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP R 196 " --> pdb=" O THR R 203 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N GLU R 205 " --> pdb=" O VAL R 194 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL R 194 " --> pdb=" O GLU R 205 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'S' and resid 387 through 392 removed outlier: 6.815A pdb=" N LEU S 325 " --> pdb=" O HIS S 388 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL S 390 " --> pdb=" O SER S 323 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N SER S 323 " --> pdb=" O VAL S 390 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ASP S 392 " --> pdb=" O THR S 321 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N THR S 321 " --> pdb=" O ASP S 392 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER S 349 " --> pdb=" O VAL S 366 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE S 347 " --> pdb=" O PRO S 368 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'S' and resid 398 through 401 Processing sheet with id= BD, first strand: chain 'S' and resid 459 through 465 removed outlier: 3.975A pdb=" N GLY S 459 " --> pdb=" O ALA S 409 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LYS S 407 " --> pdb=" O CYS S 461 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N VAL S 463 " --> pdb=" O LEU S 405 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU S 405 " --> pdb=" O VAL S 463 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ARG S 465 " --> pdb=" O LEU S 403 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N LEU S 403 " --> pdb=" O ARG S 465 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLN S 440 " --> pdb=" O ALA S 429 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ALA S 429 " --> pdb=" O GLN S 440 " (cutoff:3.500A) 1533 hydrogen bonds defined for protein. 4170 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: 17.40 Time building geometry restraints manager: 19.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8049 1.32 - 1.45: 9632 1.45 - 1.57: 24835 1.57 - 1.70: 48 1.70 - 1.82: 344 Bond restraints: 42908 Sorted by residual: bond pdb=" C2 TPP E 703 " pdb=" S1 TPP E 703 " ideal model delta sigma weight residual 1.675 1.748 -0.073 1.00e-02 1.00e+04 5.29e+01 bond pdb=" C2 TPP M 703 " pdb=" S1 TPP M 703 " ideal model delta sigma weight residual 1.675 1.747 -0.072 1.00e-02 1.00e+04 5.23e+01 bond pdb=" C2 TPP I 703 " pdb=" S1 TPP I 703 " ideal model delta sigma weight residual 1.675 1.747 -0.072 1.00e-02 1.00e+04 5.15e+01 bond pdb=" C2 TPP Q 703 " pdb=" S1 TPP Q 703 " ideal model delta sigma weight residual 1.675 1.747 -0.072 1.00e-02 1.00e+04 5.14e+01 bond pdb=" C2 TPP D 703 " pdb=" S1 TPP D 703 " ideal model delta sigma weight residual 1.675 1.738 -0.063 1.00e-02 1.00e+04 3.98e+01 ... (remaining 42903 not shown) Histogram of bond angle deviations from ideal: 89.27 - 98.39: 12 98.39 - 107.52: 2425 107.52 - 116.65: 27581 116.65 - 125.78: 27495 125.78 - 134.90: 903 Bond angle restraints: 58416 Sorted by residual: angle pdb=" PA TPP H 703 " pdb=" O3A TPP H 703 " pdb=" PB TPP H 703 " ideal model delta sigma weight residual 139.87 119.10 20.77 1.00e+00 1.00e+00 4.32e+02 angle pdb=" PA TPP L 703 " pdb=" O3A TPP L 703 " pdb=" PB TPP L 703 " ideal model delta sigma weight residual 139.87 119.15 20.72 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA TPP D 703 " pdb=" O3A TPP D 703 " pdb=" PB TPP D 703 " ideal model delta sigma weight residual 139.87 119.16 20.71 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA TPP P 703 " pdb=" O3A TPP P 703 " pdb=" PB TPP P 703 " ideal model delta sigma weight residual 139.87 119.16 20.71 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA TPP I 703 " pdb=" O3A TPP I 703 " pdb=" PB TPP I 703 " ideal model delta sigma weight residual 139.87 123.46 16.41 1.00e+00 1.00e+00 2.69e+02 ... (remaining 58411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 24086 17.64 - 35.27: 1346 35.27 - 52.91: 314 52.91 - 70.54: 103 70.54 - 88.18: 63 Dihedral angle restraints: 25912 sinusoidal: 10072 harmonic: 15840 Sorted by residual: dihedral pdb=" CA HIS K 391 " pdb=" C HIS K 391 " pdb=" N ASP K 392 " pdb=" CA ASP K 392 " ideal model delta harmonic sigma weight residual 180.00 150.35 29.65 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA HIS S 391 " pdb=" C HIS S 391 " pdb=" N ASP S 392 " pdb=" CA ASP S 392 " ideal model delta harmonic sigma weight residual 180.00 150.71 29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA HIS G 391 " pdb=" C HIS G 391 " pdb=" N ASP G 392 " pdb=" CA ASP G 392 " ideal model delta harmonic sigma weight residual 180.00 151.55 28.45 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 25909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 6660 0.188 - 0.375: 137 0.375 - 0.563: 2 0.563 - 0.750: 0 0.750 - 0.938: 1 Chirality restraints: 6800 Sorted by residual: chirality pdb=" CB VAL J 138 " pdb=" CA VAL J 138 " pdb=" CG1 VAL J 138 " pdb=" CG2 VAL J 138 " both_signs ideal model delta sigma weight residual False -2.63 -1.69 -0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" CA ASP K 328 " pdb=" N ASP K 328 " pdb=" C ASP K 328 " pdb=" CB ASP K 328 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA ASP S 328 " pdb=" N ASP S 328 " pdb=" C ASP S 328 " pdb=" CB ASP S 328 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 6797 not shown) Planarity restraints: 7516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FAD M 702 " 0.671 2.00e-02 2.50e+03 3.07e-01 4.48e+03 pdb=" C10 FAD M 702 " 0.143 2.00e-02 2.50e+03 pdb=" C2 FAD M 702 " -0.294 2.00e-02 2.50e+03 pdb=" C4 FAD M 702 " -0.018 2.00e-02 2.50e+03 pdb=" C4X FAD M 702 " 0.162 2.00e-02 2.50e+03 pdb=" C5X FAD M 702 " 0.275 2.00e-02 2.50e+03 pdb=" C6 FAD M 702 " 0.199 2.00e-02 2.50e+03 pdb=" C7 FAD M 702 " -0.051 2.00e-02 2.50e+03 pdb=" C7M FAD M 702 " -0.181 2.00e-02 2.50e+03 pdb=" C8 FAD M 702 " -0.234 2.00e-02 2.50e+03 pdb=" C8M FAD M 702 " -0.611 2.00e-02 2.50e+03 pdb=" C9 FAD M 702 " -0.088 2.00e-02 2.50e+03 pdb=" C9A FAD M 702 " 0.195 2.00e-02 2.50e+03 pdb=" N1 FAD M 702 " -0.062 2.00e-02 2.50e+03 pdb=" N10 FAD M 702 " 0.335 2.00e-02 2.50e+03 pdb=" N3 FAD M 702 " -0.234 2.00e-02 2.50e+03 pdb=" N5 FAD M 702 " 0.336 2.00e-02 2.50e+03 pdb=" O2 FAD M 702 " -0.547 2.00e-02 2.50e+03 pdb=" O4 FAD M 702 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD Q 702 " -0.672 2.00e-02 2.50e+03 3.07e-01 4.48e+03 pdb=" C10 FAD Q 702 " -0.144 2.00e-02 2.50e+03 pdb=" C2 FAD Q 702 " 0.293 2.00e-02 2.50e+03 pdb=" C4 FAD Q 702 " 0.018 2.00e-02 2.50e+03 pdb=" C4X FAD Q 702 " -0.162 2.00e-02 2.50e+03 pdb=" C5X FAD Q 702 " -0.275 2.00e-02 2.50e+03 pdb=" C6 FAD Q 702 " -0.198 2.00e-02 2.50e+03 pdb=" C7 FAD Q 702 " 0.052 2.00e-02 2.50e+03 pdb=" C7M FAD Q 702 " 0.180 2.00e-02 2.50e+03 pdb=" C8 FAD Q 702 " 0.234 2.00e-02 2.50e+03 pdb=" C8M FAD Q 702 " 0.610 2.00e-02 2.50e+03 pdb=" C9 FAD Q 702 " 0.088 2.00e-02 2.50e+03 pdb=" C9A FAD Q 702 " -0.195 2.00e-02 2.50e+03 pdb=" N1 FAD Q 702 " 0.062 2.00e-02 2.50e+03 pdb=" N10 FAD Q 702 " -0.334 2.00e-02 2.50e+03 pdb=" N3 FAD Q 702 " 0.234 2.00e-02 2.50e+03 pdb=" N5 FAD Q 702 " -0.337 2.00e-02 2.50e+03 pdb=" O2 FAD Q 702 " 0.547 2.00e-02 2.50e+03 pdb=" O4 FAD Q 702 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD E 702 " -0.671 2.00e-02 2.50e+03 3.07e-01 4.47e+03 pdb=" C10 FAD E 702 " -0.144 2.00e-02 2.50e+03 pdb=" C2 FAD E 702 " 0.293 2.00e-02 2.50e+03 pdb=" C4 FAD E 702 " 0.018 2.00e-02 2.50e+03 pdb=" C4X FAD E 702 " -0.162 2.00e-02 2.50e+03 pdb=" C5X FAD E 702 " -0.276 2.00e-02 2.50e+03 pdb=" C6 FAD E 702 " -0.199 2.00e-02 2.50e+03 pdb=" C7 FAD E 702 " 0.052 2.00e-02 2.50e+03 pdb=" C7M FAD E 702 " 0.180 2.00e-02 2.50e+03 pdb=" C8 FAD E 702 " 0.234 2.00e-02 2.50e+03 pdb=" C8M FAD E 702 " 0.611 2.00e-02 2.50e+03 pdb=" C9 FAD E 702 " 0.087 2.00e-02 2.50e+03 pdb=" C9A FAD E 702 " -0.195 2.00e-02 2.50e+03 pdb=" N1 FAD E 702 " 0.063 2.00e-02 2.50e+03 pdb=" N10 FAD E 702 " -0.335 2.00e-02 2.50e+03 pdb=" N3 FAD E 702 " 0.234 2.00e-02 2.50e+03 pdb=" N5 FAD E 702 " -0.336 2.00e-02 2.50e+03 pdb=" O2 FAD E 702 " 0.547 2.00e-02 2.50e+03 pdb=" O4 FAD E 702 " -0.002 2.00e-02 2.50e+03 ... (remaining 7513 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 164 2.51 - 3.11: 32635 3.11 - 3.71: 65194 3.71 - 4.30: 91009 4.30 - 4.90: 150816 Nonbonded interactions: 339818 Sorted by model distance: nonbonded pdb="MG MG I 701 " pdb=" O1A TPP I 703 " model vdw 1.913 2.170 nonbonded pdb="MG MG Q 701 " pdb=" O1A TPP Q 703 " model vdw 1.914 2.170 nonbonded pdb="MG MG M 701 " pdb=" O1A TPP M 703 " model vdw 1.915 2.170 nonbonded pdb="MG MG E 701 " pdb=" O1A TPP E 703 " model vdw 1.915 2.170 nonbonded pdb="MG MG L 701 " pdb=" O2A TPP L 703 " model vdw 1.921 2.170 ... (remaining 339813 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 'D' and (resid 87 through 288 or (resid 289 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 through 312 or (resid 315 a \ nd (name N or name CA or name C or name O or name CB )) or resid 316 or (resid 3 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) or r \ esid 371 through 377 or (resid 378 and (name N or name CA or name C or name O or \ name CB )) or resid 379 through 425 or (resid 426 through 432 and (name N or na \ me CA or name C or name O or name CB )) or resid 433 through 571 or (resid 572 t \ hrough 573 and (name N or name CA or name C or name O or name CB )) or resid 574 \ or (resid 575 through 577 and (name N or name CA or name C or name O or name CB \ )) or resid 578 or (resid 579 through 582 and (name N or name CA or name C or n \ ame O or name CB )) or resid 583 through 584 or (resid 585 and (name N or name C \ A or name C or name O or name CB )) or resid 586 through 616 or (resid 617 and ( \ name N or name CA or name C or name O or name CB )) or resid 618 through 643 or \ resid 701 through 703)) selection = (chain 'E' and (resid 87 through 287 or (resid 288 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB )) or resid 293 or resid 301 through 30 \ 4 or (resid 305 and (name N or name CA or name C or name O or name CB )) or resi \ d 306 through 312 or resid 315 through 318 or (resid 319 and (name N or name CA \ or name C or name O or name CB )) or resid 320 through 343 or (resid 344 and (na \ me N or name CA or name C or name O or name CB )) or resid 345 through 361 or (r \ esid 362 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 428 or (resid 429 through 432 and (name N or name CA or name \ C or name O or name CB )) or resid 433 through 438 or resid 440 through 455 or r \ esid 459 through 535 or (resid 536 and (name N or name CA or name C or name O or \ name CB )) or resid 537 through 593 or resid 597 through 643 or resid 701 throu \ gh 703)) selection = (chain 'H' and (resid 87 through 288 or (resid 289 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 through 312 or (resid 315 a \ nd (name N or name CA or name C or name O or name CB )) or resid 316 or (resid 3 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) or r \ esid 371 through 377 or (resid 378 and (name N or name CA or name C or name O or \ name CB )) or resid 379 through 425 or (resid 426 through 432 and (name N or na \ me CA or name C or name O or name CB )) or resid 433 through 571 or (resid 572 t \ hrough 573 and (name N or name CA or name C or name O or name CB )) or resid 574 \ or (resid 575 through 577 and (name N or name CA or name C or name O or name CB \ )) or resid 578 or (resid 579 through 582 and (name N or name CA or name C or n \ ame O or name CB )) or resid 583 through 584 or (resid 585 and (name N or name C \ A or name C or name O or name CB )) or resid 586 through 616 or (resid 617 and ( \ name N or name CA or name C or name O or name CB )) or resid 618 through 643 or \ resid 701 through 703)) selection = (chain 'I' and (resid 87 through 287 or (resid 288 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB )) or resid 293 or resid 301 through 30 \ 4 or (resid 305 and (name N or name CA or name C or name O or name CB )) or resi \ d 306 through 312 or resid 315 through 318 or (resid 319 and (name N or name CA \ or name C or name O or name CB )) or resid 320 through 343 or (resid 344 and (na \ me N or name CA or name C or name O or name CB )) or resid 345 through 361 or (r \ esid 362 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 428 or (resid 429 through 432 and (name N or name CA or name \ C or name O or name CB )) or resid 433 through 438 or resid 440 through 455 or r \ esid 459 through 535 or (resid 536 and (name N or name CA or name C or name O or \ name CB )) or resid 537 through 593 or resid 597 through 643 or resid 701 throu \ gh 703)) selection = (chain 'L' and (resid 87 through 288 or (resid 289 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 through 312 or (resid 315 a \ nd (name N or name CA or name C or name O or name CB )) or resid 316 or (resid 3 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) or r \ esid 371 through 377 or (resid 378 and (name N or name CA or name C or name O or \ name CB )) or resid 379 through 425 or (resid 426 through 432 and (name N or na \ me CA or name C or name O or name CB )) or resid 433 through 571 or (resid 572 t \ hrough 573 and (name N or name CA or name C or name O or name CB )) or resid 574 \ or (resid 575 through 577 and (name N or name CA or name C or name O or name CB \ )) or resid 578 or (resid 579 through 582 and (name N or name CA or name C or n \ ame O or name CB )) or resid 583 through 584 or (resid 585 and (name N or name C \ A or name C or name O or name CB )) or resid 586 through 616 or (resid 617 and ( \ name N or name CA or name C or name O or name CB )) or resid 618 through 643 or \ resid 701 through 703)) selection = (chain 'M' and (resid 87 through 287 or (resid 288 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB )) or resid 293 or resid 301 through 30 \ 4 or (resid 305 and (name N or name CA or name C or name O or name CB )) or resi \ d 306 through 312 or resid 315 through 318 or (resid 319 and (name N or name CA \ or name C or name O or name CB )) or resid 320 through 343 or (resid 344 and (na \ me N or name CA or name C or name O or name CB )) or resid 345 through 361 or (r \ esid 362 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 428 or (resid 429 through 432 and (name N or name CA or name \ C or name O or name CB )) or resid 433 through 438 or resid 440 through 455 or r \ esid 459 through 535 or (resid 536 and (name N or name CA or name C or name O or \ name CB )) or resid 537 through 593 or resid 597 through 643 or resid 701 throu \ gh 703)) selection = (chain 'P' and (resid 87 through 288 or (resid 289 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 through 312 or (resid 315 a \ nd (name N or name CA or name C or name O or name CB )) or resid 316 or (resid 3 \ 17 and (name N or name CA or name C or name O or name CB )) or resid 318 through \ 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) or r \ esid 371 through 377 or (resid 378 and (name N or name CA or name C or name O or \ name CB )) or resid 379 through 425 or (resid 426 through 432 and (name N or na \ me CA or name C or name O or name CB )) or resid 433 through 571 or (resid 572 t \ hrough 573 and (name N or name CA or name C or name O or name CB )) or resid 574 \ or (resid 575 through 577 and (name N or name CA or name C or name O or name CB \ )) or resid 578 or (resid 579 through 582 and (name N or name CA or name C or n \ ame O or name CB )) or resid 583 through 584 or (resid 585 and (name N or name C \ A or name C or name O or name CB )) or resid 586 through 616 or (resid 617 and ( \ name N or name CA or name C or name O or name CB )) or resid 618 through 643 or \ resid 701 through 703)) selection = (chain 'Q' and (resid 87 through 287 or (resid 288 through 290 and (name N or na \ me CA or name C or name O or name CB )) or resid 291 or (resid 292 and (name N o \ r name CA or name C or name O or name CB )) or resid 293 or resid 301 through 30 \ 4 or (resid 305 and (name N or name CA or name C or name O or name CB )) or resi \ d 306 through 312 or resid 315 through 318 or (resid 319 and (name N or name CA \ or name C or name O or name CB )) or resid 320 through 343 or (resid 344 and (na \ me N or name CA or name C or name O or name CB )) or resid 345 through 361 or (r \ esid 362 through 363 and (name N or name CA or name C or name O or name CB )) or \ resid 364 through 428 or (resid 429 through 432 and (name N or name CA or name \ C or name O or name CB )) or resid 433 through 438 or resid 440 through 455 or r \ esid 459 through 535 or (resid 536 and (name N or name CA or name C or name O or \ name CB )) or resid 537 through 593 or resid 597 through 643 or resid 701 throu \ gh 703)) } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'R' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.730 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: 0.040 Extract box with map and model: 30.160 Check model and map are aligned: 0.580 Set scattering table: 0.380 Process input model: 115.660 Find NCS groups from input model: 3.770 Set up NCS constraints: 0.370 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.087 42908 Z= 0.747 Angle : 1.537 20.774 58416 Z= 0.977 Chirality : 0.075 0.938 6800 Planarity : 0.016 0.307 7516 Dihedral : 13.395 88.179 15680 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.32 % Favored : 96.51 % Rotamer: Outliers : 0.61 % Allowed : 2.88 % Favored : 96.51 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.60 % 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: -1.89 (0.10), residues: 5448 helix: -1.91 (0.08), residues: 2276 sheet: 0.01 (0.14), residues: 1196 loop : -0.94 (0.13), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.014 TRP L 574 HIS 0.017 0.003 HIS M 488 PHE 0.052 0.008 PHE F 107 TYR 0.171 0.014 TYR F 112 ARG 0.094 0.006 ARG Q 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1142 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1116 time to evaluate : 4.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 167 THR cc_start: 0.8006 (t) cc_final: 0.7728 (p) REVERT: D 426 LEU cc_start: 0.6087 (mt) cc_final: 0.5714 (tp) REVERT: D 555 ASN cc_start: 0.5401 (m-40) cc_final: 0.4618 (t0) REVERT: D 570 MET cc_start: 0.7129 (tpp) cc_final: 0.6641 (tpp) REVERT: D 573 GLN cc_start: 0.4924 (tt0) cc_final: 0.4722 (tm-30) REVERT: D 586 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.6926 (p) REVERT: E 392 VAL cc_start: 0.7094 (t) cc_final: 0.6863 (p) REVERT: E 483 THR cc_start: 0.7785 (p) cc_final: 0.7560 (p) REVERT: F 123 ARG cc_start: 0.7632 (ttm110) cc_final: 0.7175 (ptt180) REVERT: F 221 LYS cc_start: 0.9220 (tttp) cc_final: 0.8892 (ttpt) REVERT: F 222 LYS cc_start: 0.8891 (mttm) cc_final: 0.8644 (mmmt) REVERT: F 224 GLN cc_start: 0.7809 (tp40) cc_final: 0.7380 (tp40) REVERT: G 371 ASP cc_start: 0.6769 (p0) cc_final: 0.6034 (t0) REVERT: G 372 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7549 (pp20) REVERT: G 386 ASP cc_start: 0.8348 (m-30) cc_final: 0.8140 (m-30) REVERT: H 271 MET cc_start: 0.8070 (mtm) cc_final: 0.7858 (mtt) REVERT: H 555 ASN cc_start: 0.5439 (m-40) cc_final: 0.4618 (t0) REVERT: H 570 MET cc_start: 0.7162 (tpp) cc_final: 0.6698 (tpp) REVERT: H 572 MET cc_start: 0.4508 (ttp) cc_final: 0.4243 (tmm) REVERT: H 586 THR cc_start: 0.7746 (OUTLIER) cc_final: 0.6993 (p) REVERT: I 392 VAL cc_start: 0.7141 (t) cc_final: 0.6889 (p) REVERT: I 483 THR cc_start: 0.7782 (p) cc_final: 0.7565 (p) REVERT: J 123 ARG cc_start: 0.7586 (ttm110) cc_final: 0.6972 (ptt180) REVERT: J 221 LYS cc_start: 0.9267 (tttp) cc_final: 0.8928 (ttpt) REVERT: J 222 LYS cc_start: 0.8915 (mttm) cc_final: 0.8678 (mmmt) REVERT: K 371 ASP cc_start: 0.6542 (p0) cc_final: 0.5694 (t0) REVERT: K 372 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7461 (tm-30) REVERT: K 380 GLN cc_start: 0.8351 (tp-100) cc_final: 0.7958 (tm-30) REVERT: K 389 GLU cc_start: 0.7854 (pt0) cc_final: 0.7427 (pt0) REVERT: K 401 ARG cc_start: 0.8117 (mmp-170) cc_final: 0.7661 (mmp80) REVERT: L 223 TYR cc_start: 0.8285 (m-80) cc_final: 0.8050 (m-80) REVERT: L 267 TRP cc_start: 0.7155 (m100) cc_final: 0.6405 (m100) REVERT: L 570 MET cc_start: 0.7276 (tpp) cc_final: 0.6761 (tpp) REVERT: L 572 MET cc_start: 0.4855 (ttp) cc_final: 0.4288 (tmm) REVERT: L 573 GLN cc_start: 0.4632 (tt0) cc_final: 0.4276 (tm-30) REVERT: L 586 THR cc_start: 0.7643 (OUTLIER) cc_final: 0.6746 (p) REVERT: M 495 PHE cc_start: 0.6180 (m-80) cc_final: 0.5827 (m-80) REVERT: M 534 ASP cc_start: 0.7100 (t70) cc_final: 0.6852 (t0) REVERT: M 535 ILE cc_start: 0.6367 (mt) cc_final: 0.6141 (mt) REVERT: M 543 MET cc_start: 0.7743 (mtt) cc_final: 0.6672 (mtt) REVERT: N 123 ARG cc_start: 0.7295 (ttm110) cc_final: 0.6644 (ppt170) REVERT: N 148 LYS cc_start: 0.9246 (ttmm) cc_final: 0.8988 (mttt) REVERT: N 184 MET cc_start: 0.8590 (tpp) cc_final: 0.8076 (tpp) REVERT: N 221 LYS cc_start: 0.9277 (tttp) cc_final: 0.8888 (ttpt) REVERT: N 222 LYS cc_start: 0.8919 (mttm) cc_final: 0.8703 (mmmt) REVERT: O 329 ILE cc_start: 0.7734 (mm) cc_final: 0.7512 (pt) REVERT: O 371 ASP cc_start: 0.6770 (p0) cc_final: 0.5906 (t0) REVERT: O 372 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7519 (tm-30) REVERT: O 386 ASP cc_start: 0.8193 (m-30) cc_final: 0.7835 (m-30) REVERT: O 389 GLU cc_start: 0.7791 (pt0) cc_final: 0.7447 (pt0) REVERT: O 401 ARG cc_start: 0.8041 (mmp-170) cc_final: 0.7627 (mmp80) REVERT: O 447 LYS cc_start: 0.4939 (mmtt) cc_final: 0.4720 (mtpt) REVERT: P 227 ASP cc_start: 0.7055 (t0) cc_final: 0.6833 (p0) REVERT: P 277 MET cc_start: 0.7891 (mtt) cc_final: 0.7656 (mmm) REVERT: P 338 TYR cc_start: 0.6856 (t80) cc_final: 0.6336 (t80) REVERT: P 570 MET cc_start: 0.7230 (tpp) cc_final: 0.6920 (tpp) REVERT: P 572 MET cc_start: 0.4857 (ttp) cc_final: 0.4430 (tmm) REVERT: P 586 THR cc_start: 0.7467 (OUTLIER) cc_final: 0.6661 (p) REVERT: Q 483 THR cc_start: 0.8107 (p) cc_final: 0.7893 (p) REVERT: Q 534 ASP cc_start: 0.7054 (t70) cc_final: 0.6779 (t0) REVERT: Q 535 ILE cc_start: 0.6429 (mt) cc_final: 0.6209 (mt) REVERT: Q 543 MET cc_start: 0.7924 (mtt) cc_final: 0.6880 (mtt) REVERT: R 123 ARG cc_start: 0.7281 (ttm110) cc_final: 0.6731 (ptm160) REVERT: R 148 LYS cc_start: 0.9206 (ttmm) cc_final: 0.8983 (mttt) REVERT: R 154 LYS cc_start: 0.6611 (mttm) cc_final: 0.6391 (ttmm) REVERT: R 191 ARG cc_start: 0.8195 (ttt180) cc_final: 0.7955 (mtp180) REVERT: S 348 GLN cc_start: 0.8501 (mt0) cc_final: 0.8249 (mt0) REVERT: S 371 ASP cc_start: 0.6793 (p0) cc_final: 0.6130 (t0) REVERT: S 372 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7509 (pp20) REVERT: S 389 GLU cc_start: 0.7887 (pt0) cc_final: 0.7241 (pt0) REVERT: S 401 ARG cc_start: 0.8040 (mmp-170) cc_final: 0.7645 (mmp80) outliers start: 26 outliers final: 4 residues processed: 1131 average time/residue: 0.5658 time to fit residues: 1018.8091 Evaluate side-chains 619 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 611 time to evaluate : 4.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 586 THR Chi-restraints excluded: chain L residue 586 THR Chi-restraints excluded: chain N residue 152 VAL Chi-restraints excluded: chain P residue 586 THR Chi-restraints excluded: chain R residue 152 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 462 optimal weight: 2.9990 chunk 415 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 280 optimal weight: 0.7980 chunk 221 optimal weight: 0.8980 chunk 429 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 319 optimal weight: 0.9980 chunk 497 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 145 GLN E 449 GLN E 489 GLN E 527 ASN G 320 HIS I 145 GLN I 489 GLN I 527 ASN K 320 HIS K 327 ASN L 127 HIS M 527 ASN N 141 GLN O 320 HIS P 127 HIS Q 489 GLN Q 527 ASN S 320 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 42908 Z= 0.204 Angle : 0.631 9.908 58416 Z= 0.329 Chirality : 0.045 0.221 6800 Planarity : 0.005 0.050 7516 Dihedral : 7.642 75.496 6330 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.22 % Allowed : 10.51 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.22 (0.11), residues: 5448 helix: -0.26 (0.10), residues: 2272 sheet: 0.32 (0.14), residues: 1192 loop : -0.03 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 185 HIS 0.006 0.001 HIS E 143 PHE 0.023 0.002 PHE J 223 TYR 0.020 0.002 TYR P 466 ARG 0.007 0.001 ARG R 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 683 time to evaluate : 4.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 267 TRP cc_start: 0.7468 (m100) cc_final: 0.6607 (m100) REVERT: D 570 MET cc_start: 0.7207 (tpp) cc_final: 0.6770 (tpt) REVERT: D 572 MET cc_start: 0.4307 (tmm) cc_final: 0.4031 (tmm) REVERT: D 601 MET cc_start: 0.8986 (mmt) cc_final: 0.8748 (mmt) REVERT: E 227 ASP cc_start: 0.6623 (t0) cc_final: 0.6254 (t0) REVERT: E 347 HIS cc_start: 0.5847 (OUTLIER) cc_final: 0.5230 (t-90) REVERT: E 392 VAL cc_start: 0.7068 (t) cc_final: 0.6856 (p) REVERT: E 449 GLN cc_start: 0.7336 (mm-40) cc_final: 0.6837 (mm-40) REVERT: F 122 ASN cc_start: 0.7746 (t0) cc_final: 0.7084 (m-40) REVERT: F 154 LYS cc_start: 0.7044 (mttm) cc_final: 0.6537 (tttt) REVERT: F 185 TRP cc_start: 0.8305 (t60) cc_final: 0.7950 (t60) REVERT: F 214 ILE cc_start: 0.8914 (tp) cc_final: 0.8602 (pt) REVERT: F 224 GLN cc_start: 0.7832 (tp40) cc_final: 0.7521 (tp40) REVERT: G 380 GLN cc_start: 0.8339 (tp-100) cc_final: 0.7827 (tp40) REVERT: H 203 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7402 (p) REVERT: H 267 TRP cc_start: 0.7443 (m100) cc_final: 0.6691 (m100) REVERT: H 513 MET cc_start: 0.7529 (mtp) cc_final: 0.7320 (mtp) REVERT: H 572 MET cc_start: 0.4246 (ttp) cc_final: 0.3780 (tmm) REVERT: I 227 ASP cc_start: 0.6649 (t0) cc_final: 0.6292 (t0) REVERT: I 347 HIS cc_start: 0.5872 (OUTLIER) cc_final: 0.5151 (t-90) REVERT: I 392 VAL cc_start: 0.7202 (t) cc_final: 0.6965 (p) REVERT: I 588 LEU cc_start: 0.6895 (tp) cc_final: 0.6343 (mp) REVERT: J 122 ASN cc_start: 0.7613 (t0) cc_final: 0.7246 (m110) REVERT: J 123 ARG cc_start: 0.7721 (ttm110) cc_final: 0.7416 (ppt170) REVERT: J 227 GLU cc_start: 0.7215 (tp30) cc_final: 0.6610 (mm-30) REVERT: K 327 ASN cc_start: 0.8769 (t0) cc_final: 0.8078 (t0) REVERT: K 356 GLU cc_start: 0.6450 (pm20) cc_final: 0.6240 (pm20) REVERT: K 371 ASP cc_start: 0.6476 (p0) cc_final: 0.5749 (t0) REVERT: K 372 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7560 (pp20) REVERT: K 380 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7871 (tm-30) REVERT: K 401 ARG cc_start: 0.7935 (mmp-170) cc_final: 0.7729 (mmp80) REVERT: L 105 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7091 (mm-30) REVERT: L 226 MET cc_start: 0.8287 (mmm) cc_final: 0.8063 (mmt) REVERT: L 277 MET cc_start: 0.8015 (mmm) cc_final: 0.7720 (mmm) REVERT: L 338 TYR cc_start: 0.6917 (t80) cc_final: 0.6651 (t80) REVERT: L 570 MET cc_start: 0.7236 (tpp) cc_final: 0.6689 (tpt) REVERT: L 572 MET cc_start: 0.4640 (ttp) cc_final: 0.4194 (tmm) REVERT: L 573 GLN cc_start: 0.4635 (tt0) cc_final: 0.4314 (tm-30) REVERT: L 574 TRP cc_start: 0.5686 (m-10) cc_final: 0.5367 (m-10) REVERT: L 586 THR cc_start: 0.7993 (OUTLIER) cc_final: 0.7759 (p) REVERT: L 601 MET cc_start: 0.8779 (mmt) cc_final: 0.8531 (mmt) REVERT: M 227 ASP cc_start: 0.6853 (t0) cc_final: 0.6571 (t0) REVERT: M 422 MET cc_start: 0.5469 (mtp) cc_final: 0.5162 (tpp) REVERT: M 495 PHE cc_start: 0.6232 (m-80) cc_final: 0.5906 (m-80) REVERT: M 543 MET cc_start: 0.7607 (mtt) cc_final: 0.7378 (mtt) REVERT: N 122 ASN cc_start: 0.7658 (t0) cc_final: 0.6954 (m-40) REVERT: O 371 ASP cc_start: 0.6774 (p0) cc_final: 0.6126 (t0) REVERT: O 372 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7571 (pp20) REVERT: O 389 GLU cc_start: 0.7809 (pt0) cc_final: 0.7405 (pt0) REVERT: P 105 GLU cc_start: 0.7320 (tt0) cc_final: 0.7066 (tt0) REVERT: P 277 MET cc_start: 0.7980 (mtt) cc_final: 0.7765 (mmm) REVERT: P 513 MET cc_start: 0.7526 (mtp) cc_final: 0.7237 (mtp) REVERT: P 570 MET cc_start: 0.7161 (tpp) cc_final: 0.6817 (tpt) REVERT: P 572 MET cc_start: 0.4667 (ttp) cc_final: 0.4220 (tmm) REVERT: P 601 MET cc_start: 0.8862 (mmt) cc_final: 0.8489 (mmt) REVERT: Q 322 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8359 (mm-30) REVERT: Q 543 MET cc_start: 0.7606 (mtt) cc_final: 0.7365 (mtt) REVERT: R 122 ASN cc_start: 0.7790 (t0) cc_final: 0.7113 (m110) REVERT: R 154 LYS cc_start: 0.6771 (mttm) cc_final: 0.6512 (ttmm) REVERT: S 348 GLN cc_start: 0.8527 (mt0) cc_final: 0.8305 (mt0) REVERT: S 371 ASP cc_start: 0.6794 (p0) cc_final: 0.6154 (t0) REVERT: S 372 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7526 (tm-30) REVERT: S 389 GLU cc_start: 0.7926 (pt0) cc_final: 0.7701 (pt0) outliers start: 95 outliers final: 61 residues processed: 751 average time/residue: 0.5160 time to fit residues: 650.7783 Evaluate side-chains 606 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 541 time to evaluate : 5.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 177 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 433 LEU Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 347 HIS Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 177 SER Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 507 SER Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 347 HIS Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 412 CYS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 160 SER Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 586 THR Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 412 CYS Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 433 LEU Chi-restraints excluded: chain Q residue 167 THR Chi-restraints excluded: chain Q residue 314 SER Chi-restraints excluded: chain Q residue 372 VAL Chi-restraints excluded: chain Q residue 412 CYS Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 200 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 276 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 414 optimal weight: 4.9990 chunk 338 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 498 optimal weight: 9.9990 chunk 538 optimal weight: 0.8980 chunk 443 optimal weight: 8.9990 chunk 494 optimal weight: 0.0570 chunk 169 optimal weight: 10.0000 chunk 399 optimal weight: 5.9990 overall best weight: 2.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 127 HIS ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS E 489 GLN H 127 HIS H 626 GLN I 143 HIS M 143 HIS M 593 GLN N 140 GLN P 527 ASN Q 143 HIS Q 489 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 42908 Z= 0.364 Angle : 0.682 8.653 58416 Z= 0.355 Chirality : 0.047 0.176 6800 Planarity : 0.005 0.056 7516 Dihedral : 7.600 81.505 6325 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.70 % Allowed : 11.40 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.51 (0.11), residues: 5448 helix: -0.45 (0.10), residues: 2296 sheet: 0.36 (0.14), residues: 1196 loop : -0.39 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 440 HIS 0.014 0.002 HIS M 143 PHE 0.021 0.002 PHE E 87 TYR 0.017 0.002 TYR Q 154 ARG 0.009 0.001 ARG J 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 573 time to evaluate : 4.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7366 (mm-30) REVERT: D 112 VAL cc_start: 0.7863 (OUTLIER) cc_final: 0.7627 (m) REVERT: D 277 MET cc_start: 0.8267 (mtp) cc_final: 0.7757 (mmm) REVERT: D 335 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5905 (mp) REVERT: D 570 MET cc_start: 0.7369 (tpp) cc_final: 0.6812 (tpt) REVERT: D 572 MET cc_start: 0.4468 (tmm) cc_final: 0.4192 (tmm) REVERT: D 586 THR cc_start: 0.8372 (OUTLIER) cc_final: 0.7939 (m) REVERT: D 601 MET cc_start: 0.8998 (mmt) cc_final: 0.8645 (mmt) REVERT: E 227 ASP cc_start: 0.6926 (t0) cc_final: 0.6671 (t0) REVERT: E 392 VAL cc_start: 0.7094 (t) cc_final: 0.6854 (p) REVERT: E 449 GLN cc_start: 0.7341 (mm-40) cc_final: 0.6928 (mm-40) REVERT: F 133 CYS cc_start: 0.8230 (m) cc_final: 0.7995 (p) REVERT: F 154 LYS cc_start: 0.7275 (mttm) cc_final: 0.6629 (tttt) REVERT: G 348 GLN cc_start: 0.8638 (mp10) cc_final: 0.8261 (mm-40) REVERT: G 380 GLN cc_start: 0.8444 (tp-100) cc_final: 0.8069 (tp40) REVERT: G 400 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8149 (tm-30) REVERT: H 105 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7325 (mm-30) REVERT: H 112 VAL cc_start: 0.7843 (OUTLIER) cc_final: 0.7621 (m) REVERT: H 203 THR cc_start: 0.7866 (OUTLIER) cc_final: 0.7625 (p) REVERT: H 335 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.6023 (mp) REVERT: H 570 MET cc_start: 0.7220 (tpt) cc_final: 0.6809 (tpt) REVERT: H 572 MET cc_start: 0.4532 (ttp) cc_final: 0.4102 (tmm) REVERT: H 621 LEU cc_start: 0.8166 (tp) cc_final: 0.7856 (tp) REVERT: I 227 ASP cc_start: 0.6923 (t0) cc_final: 0.6618 (t0) REVERT: I 392 VAL cc_start: 0.7226 (t) cc_final: 0.6960 (p) REVERT: I 449 GLN cc_start: 0.7378 (mm110) cc_final: 0.7018 (mm-40) REVERT: I 588 LEU cc_start: 0.7312 (tp) cc_final: 0.7041 (tp) REVERT: J 123 ARG cc_start: 0.7954 (ttm110) cc_final: 0.7603 (ptt90) REVERT: J 133 CYS cc_start: 0.8356 (m) cc_final: 0.8088 (p) REVERT: J 217 GLU cc_start: 0.8403 (tt0) cc_final: 0.8043 (pt0) REVERT: K 356 GLU cc_start: 0.6652 (pm20) cc_final: 0.6420 (pm20) REVERT: K 372 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7996 (tm-30) REVERT: K 380 GLN cc_start: 0.8252 (tp-100) cc_final: 0.7836 (tm-30) REVERT: K 400 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8091 (tm-30) REVERT: L 277 MET cc_start: 0.8079 (mmm) cc_final: 0.7838 (mmm) REVERT: L 570 MET cc_start: 0.7380 (tpp) cc_final: 0.7135 (tpt) REVERT: L 572 MET cc_start: 0.4708 (ttp) cc_final: 0.4360 (tmm) REVERT: L 573 GLN cc_start: 0.4880 (tt0) cc_final: 0.4510 (tm-30) REVERT: L 601 MET cc_start: 0.8794 (mmt) cc_final: 0.8484 (mmt) REVERT: M 277 MET cc_start: 0.8277 (mmm) cc_final: 0.8067 (mmm) REVERT: M 495 PHE cc_start: 0.6359 (m-80) cc_final: 0.6020 (m-80) REVERT: M 543 MET cc_start: 0.7819 (mtt) cc_final: 0.7498 (mtt) REVERT: N 217 GLU cc_start: 0.8438 (tt0) cc_final: 0.8042 (pt0) REVERT: O 348 GLN cc_start: 0.8546 (mp10) cc_final: 0.8166 (mm-40) REVERT: O 371 ASP cc_start: 0.7040 (p0) cc_final: 0.6651 (t0) REVERT: O 372 GLU cc_start: 0.8110 (tm-30) cc_final: 0.7889 (tm-30) REVERT: O 389 GLU cc_start: 0.8007 (pt0) cc_final: 0.7673 (pt0) REVERT: O 400 GLU cc_start: 0.8377 (tm-30) cc_final: 0.8083 (tm-30) REVERT: P 105 GLU cc_start: 0.7573 (tt0) cc_final: 0.7000 (mm-30) REVERT: P 227 ASP cc_start: 0.7236 (t70) cc_final: 0.6697 (t70) REVERT: P 277 MET cc_start: 0.7892 (mtt) cc_final: 0.7619 (mmm) REVERT: P 570 MET cc_start: 0.7448 (tpp) cc_final: 0.6959 (tpt) REVERT: P 572 MET cc_start: 0.4625 (ttp) cc_final: 0.4211 (tmm) REVERT: P 601 MET cc_start: 0.8876 (mmt) cc_final: 0.8521 (mmt) REVERT: Q 322 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8187 (mm-30) REVERT: Q 495 PHE cc_start: 0.6335 (m-80) cc_final: 0.6008 (m-80) REVERT: Q 543 MET cc_start: 0.7797 (mtt) cc_final: 0.7501 (mtt) REVERT: R 112 TYR cc_start: 0.7412 (m-10) cc_final: 0.7211 (m-80) REVERT: R 154 LYS cc_start: 0.7221 (mttm) cc_final: 0.6768 (ttmt) REVERT: R 241 MET cc_start: 0.6690 (mmm) cc_final: 0.6473 (mmm) REVERT: S 372 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7907 (tm-30) REVERT: S 400 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8132 (tm-30) outliers start: 158 outliers final: 99 residues processed: 694 average time/residue: 0.4877 time to fit residues: 574.0638 Evaluate side-chains 605 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 500 time to evaluate : 5.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 586 THR Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 229 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 466 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 507 SER Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 412 CYS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain K residue 438 THR Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 433 LEU Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 254 VAL Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 412 CYS Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 558 VAL Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain O residue 438 THR Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 254 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 433 LEU Chi-restraints excluded: chain P residue 507 SER Chi-restraints excluded: chain P residue 597 ILE Chi-restraints excluded: chain Q residue 167 THR Chi-restraints excluded: chain Q residue 229 GLU Chi-restraints excluded: chain Q residue 254 VAL Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 372 VAL Chi-restraints excluded: chain Q residue 412 CYS Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 383 LYS Chi-restraints excluded: chain S residue 417 ASP Chi-restraints excluded: chain S residue 438 THR Chi-restraints excluded: chain S residue 466 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 492 optimal weight: 9.9990 chunk 374 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 237 optimal weight: 10.0000 chunk 334 optimal weight: 0.8980 chunk 500 optimal weight: 5.9990 chunk 529 optimal weight: 0.9980 chunk 261 optimal weight: 0.9990 chunk 474 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 489 GLN I 489 GLN J 141 GLN M 600 ASN Q 449 GLN R 141 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 42908 Z= 0.184 Angle : 0.545 8.015 58416 Z= 0.278 Chirality : 0.043 0.243 6800 Planarity : 0.004 0.054 7516 Dihedral : 7.239 88.776 6324 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.90 % Allowed : 13.65 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.06 (0.11), residues: 5448 helix: 0.06 (0.11), residues: 2256 sheet: 0.55 (0.15), residues: 1168 loop : -0.31 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 185 HIS 0.004 0.001 HIS K 391 PHE 0.015 0.001 PHE N 223 TYR 0.014 0.001 TYR E 154 ARG 0.009 0.000 ARG G 416 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 678 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 554 time to evaluate : 5.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.8049 (mt-10) cc_final: 0.6973 (mm-30) REVERT: D 267 TRP cc_start: 0.7464 (m100) cc_final: 0.6771 (m100) REVERT: D 335 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5775 (mp) REVERT: D 570 MET cc_start: 0.7479 (tpp) cc_final: 0.7168 (tpt) REVERT: E 213 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7274 (mt-10) REVERT: E 227 ASP cc_start: 0.6824 (t0) cc_final: 0.6560 (t0) REVERT: E 272 ARG cc_start: 0.7237 (mtt180) cc_final: 0.6919 (mtm180) REVERT: E 392 VAL cc_start: 0.7127 (t) cc_final: 0.6877 (p) REVERT: F 154 LYS cc_start: 0.7273 (mttm) cc_final: 0.6578 (tttt) REVERT: G 348 GLN cc_start: 0.8681 (mp10) cc_final: 0.8269 (mm-40) REVERT: G 380 GLN cc_start: 0.8330 (tp-100) cc_final: 0.8095 (tp40) REVERT: G 400 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8208 (tm-30) REVERT: G 404 MET cc_start: 0.8230 (ttt) cc_final: 0.7851 (ttt) REVERT: H 105 GLU cc_start: 0.8050 (mt-10) cc_final: 0.6969 (mm-30) REVERT: H 203 THR cc_start: 0.7939 (OUTLIER) cc_final: 0.7692 (p) REVERT: H 267 TRP cc_start: 0.7489 (m100) cc_final: 0.6769 (m100) REVERT: H 335 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5828 (mp) REVERT: H 513 MET cc_start: 0.7557 (mtp) cc_final: 0.7225 (mtp) REVERT: H 572 MET cc_start: 0.4591 (ttp) cc_final: 0.4218 (tmm) REVERT: I 227 ASP cc_start: 0.6833 (t0) cc_final: 0.6577 (t0) REVERT: I 392 VAL cc_start: 0.7187 (t) cc_final: 0.6911 (p) REVERT: I 422 MET cc_start: 0.5309 (mpp) cc_final: 0.5071 (mtm) REVERT: I 442 ASN cc_start: 0.9261 (t0) cc_final: 0.9039 (p0) REVERT: J 123 ARG cc_start: 0.7959 (ttm110) cc_final: 0.7689 (ptt90) REVERT: J 140 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8627 (mm-40) REVERT: K 380 GLN cc_start: 0.8106 (tp-100) cc_final: 0.7783 (tm-30) REVERT: K 400 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8058 (tm-30) REVERT: K 462 GLU cc_start: 0.8147 (pt0) cc_final: 0.7833 (pt0) REVERT: L 267 TRP cc_start: 0.7514 (m100) cc_final: 0.7005 (m100) REVERT: L 277 MET cc_start: 0.8037 (mmm) cc_final: 0.7798 (mmm) REVERT: L 572 MET cc_start: 0.4660 (ttp) cc_final: 0.4382 (tmm) REVERT: L 601 MET cc_start: 0.8778 (mmt) cc_final: 0.8503 (mmt) REVERT: M 322 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8276 (mm-30) REVERT: M 534 ASP cc_start: 0.7173 (OUTLIER) cc_final: 0.6568 (m-30) REVERT: N 140 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8729 (mm-40) REVERT: N 241 MET cc_start: 0.6719 (mmm) cc_final: 0.6245 (mmm) REVERT: O 348 GLN cc_start: 0.8607 (mp10) cc_final: 0.8192 (mm-40) REVERT: O 400 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8073 (tm-30) REVERT: O 462 GLU cc_start: 0.8363 (pt0) cc_final: 0.8134 (pt0) REVERT: P 91 PHE cc_start: 0.6994 (m-80) cc_final: 0.6737 (m-10) REVERT: P 105 GLU cc_start: 0.7608 (tt0) cc_final: 0.7261 (mm-30) REVERT: P 227 ASP cc_start: 0.7006 (t70) cc_final: 0.6395 (t70) REVERT: P 513 MET cc_start: 0.7457 (mtp) cc_final: 0.7151 (mtp) REVERT: P 570 MET cc_start: 0.7408 (tpp) cc_final: 0.7173 (tpt) REVERT: P 572 MET cc_start: 0.4648 (ttp) cc_final: 0.4383 (tmm) REVERT: Q 322 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8137 (mm-30) REVERT: Q 534 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6422 (m-30) REVERT: Q 543 MET cc_start: 0.7744 (mtt) cc_final: 0.7496 (mtt) REVERT: R 154 LYS cc_start: 0.7121 (mttm) cc_final: 0.6632 (ttmt) REVERT: R 165 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8148 (tm-30) REVERT: R 217 GLU cc_start: 0.8442 (tt0) cc_final: 0.7930 (pt0) REVERT: S 389 GLU cc_start: 0.7935 (pt0) cc_final: 0.7706 (pt0) REVERT: S 400 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8050 (tm-30) outliers start: 124 outliers final: 84 residues processed: 635 average time/residue: 0.4842 time to fit residues: 524.9506 Evaluate side-chains 579 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 489 time to evaluate : 4.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 229 GLU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 507 SER Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 412 CYS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain K residue 371 ASP Chi-restraints excluded: chain K residue 383 LYS Chi-restraints excluded: chain K residue 438 THR Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 412 CYS Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 534 ASP Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 370 THR Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain O residue 438 THR Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 491 TRP Chi-restraints excluded: chain Q residue 167 THR Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 372 VAL Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 534 ASP Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 383 LYS Chi-restraints excluded: chain S residue 438 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 441 optimal weight: 2.9990 chunk 300 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 394 optimal weight: 0.9990 chunk 218 optimal weight: 10.0000 chunk 452 optimal weight: 0.0970 chunk 366 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 270 optimal weight: 0.8980 chunk 475 optimal weight: 0.0570 chunk 133 optimal weight: 7.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 487 GLN E 128 GLN E 489 GLN H 393 HIS H 487 GLN J 113 ASN M 489 GLN Q 489 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 42908 Z= 0.149 Angle : 0.513 8.228 58416 Z= 0.260 Chirality : 0.042 0.167 6800 Planarity : 0.004 0.055 7516 Dihedral : 7.011 89.979 6323 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.90 % Allowed : 14.26 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: 0.21 (0.11), residues: 5448 helix: 0.37 (0.11), residues: 2244 sheet: 0.68 (0.15), residues: 1108 loop : -0.24 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 440 HIS 0.003 0.001 HIS G 391 PHE 0.014 0.001 PHE Q 495 TYR 0.011 0.001 TYR M 154 ARG 0.014 0.000 ARG S 416 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 545 time to evaluate : 4.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.8039 (mt-10) cc_final: 0.6964 (mm-30) REVERT: D 267 TRP cc_start: 0.7454 (m100) cc_final: 0.6745 (m100) REVERT: D 335 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5649 (mp) REVERT: E 227 ASP cc_start: 0.6833 (t0) cc_final: 0.6550 (t0) REVERT: E 272 ARG cc_start: 0.7275 (mtt180) cc_final: 0.6942 (mtm-85) REVERT: E 392 VAL cc_start: 0.7159 (t) cc_final: 0.6871 (p) REVERT: F 154 LYS cc_start: 0.7278 (mttm) cc_final: 0.6551 (tttt) REVERT: F 182 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8604 (pm20) REVERT: F 241 MET cc_start: 0.7092 (mmm) cc_final: 0.5649 (mmm) REVERT: G 348 GLN cc_start: 0.8705 (mp10) cc_final: 0.8276 (mm-40) REVERT: G 400 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8135 (tm-30) REVERT: G 404 MET cc_start: 0.8290 (ttt) cc_final: 0.7969 (ttt) REVERT: G 435 HIS cc_start: 0.5796 (m170) cc_final: 0.5358 (m-70) REVERT: G 462 GLU cc_start: 0.8043 (pt0) cc_final: 0.7699 (pt0) REVERT: H 105 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7095 (mm-30) REVERT: H 203 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7634 (p) REVERT: H 267 TRP cc_start: 0.7473 (m100) cc_final: 0.6802 (m100) REVERT: H 335 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5749 (mp) REVERT: H 572 MET cc_start: 0.4586 (ttp) cc_final: 0.4320 (tmm) REVERT: H 578 PHE cc_start: 0.7239 (m-10) cc_final: 0.7039 (m-10) REVERT: I 227 ASP cc_start: 0.6865 (t0) cc_final: 0.6598 (t0) REVERT: I 392 VAL cc_start: 0.7300 (t) cc_final: 0.7038 (p) REVERT: I 442 ASN cc_start: 0.9257 (t0) cc_final: 0.9024 (p0) REVERT: J 123 ARG cc_start: 0.7935 (ttm110) cc_final: 0.7657 (ptt90) REVERT: J 140 GLN cc_start: 0.8862 (mm-40) cc_final: 0.8659 (mm-40) REVERT: J 217 GLU cc_start: 0.8379 (tt0) cc_final: 0.7930 (pt0) REVERT: K 348 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8175 (mt0) REVERT: K 380 GLN cc_start: 0.8019 (tp-100) cc_final: 0.7766 (tm-30) REVERT: K 400 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8048 (tm-30) REVERT: L 105 GLU cc_start: 0.8031 (mt-10) cc_final: 0.6859 (mm-30) REVERT: L 267 TRP cc_start: 0.7480 (m100) cc_final: 0.6981 (m100) REVERT: L 277 MET cc_start: 0.8028 (mmm) cc_final: 0.7754 (mmm) REVERT: L 422 MET cc_start: 0.4891 (ttt) cc_final: 0.4592 (ttt) REVERT: L 570 MET cc_start: 0.7403 (tpt) cc_final: 0.7055 (tpt) REVERT: L 572 MET cc_start: 0.4618 (ttp) cc_final: 0.4186 (tmm) REVERT: L 573 GLN cc_start: 0.4726 (tt0) cc_final: 0.4354 (tm-30) REVERT: M 322 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8135 (mm-30) REVERT: N 241 MET cc_start: 0.7012 (mmm) cc_final: 0.5510 (mmm) REVERT: O 348 GLN cc_start: 0.8627 (mp10) cc_final: 0.8205 (mm-40) REVERT: O 400 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8027 (tm-30) REVERT: P 91 PHE cc_start: 0.6970 (m-80) cc_final: 0.6713 (m-10) REVERT: P 105 GLU cc_start: 0.7715 (tt0) cc_final: 0.7245 (mm-30) REVERT: P 227 ASP cc_start: 0.7017 (t70) cc_final: 0.6692 (p0) REVERT: P 572 MET cc_start: 0.4597 (ttp) cc_final: 0.4338 (tmm) REVERT: Q 322 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8093 (mm-30) REVERT: R 154 LYS cc_start: 0.7162 (mttm) cc_final: 0.6641 (ttmt) REVERT: R 165 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: S 380 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7833 (tm-30) REVERT: S 389 GLU cc_start: 0.7929 (pt0) cc_final: 0.7692 (pt0) REVERT: S 400 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8022 (tm-30) outliers start: 124 outliers final: 82 residues processed: 627 average time/residue: 0.5148 time to fit residues: 544.4900 Evaluate side-chains 580 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 492 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 229 GLU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 507 SER Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 229 GLU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 412 CYS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain K residue 371 ASP Chi-restraints excluded: chain K residue 383 LYS Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain K residue 438 THR Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 550 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 200 HIS Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 438 THR Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 254 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 167 THR Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 412 CYS Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 200 HIS Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 380 GLN Chi-restraints excluded: chain S residue 438 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 178 optimal weight: 9.9990 chunk 477 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 310 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 530 optimal weight: 4.9990 chunk 440 optimal weight: 9.9990 chunk 245 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 278 optimal weight: 0.0670 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 489 GLN ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 489 GLN S 348 GLN ** S 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 42908 Z= 0.328 Angle : 0.611 8.513 58416 Z= 0.314 Chirality : 0.045 0.175 6800 Planarity : 0.005 0.079 7516 Dihedral : 7.328 86.058 6323 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.89 % Allowed : 13.90 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.22 (0.11), residues: 5448 helix: 0.00 (0.11), residues: 2292 sheet: 0.37 (0.15), residues: 1160 loop : -0.43 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP P 440 HIS 0.007 0.001 HIS P 143 PHE 0.013 0.001 PHE O 340 TYR 0.023 0.002 TYR I 154 ARG 0.015 0.001 ARG K 416 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 509 time to evaluate : 4.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7077 (mm-30) REVERT: D 267 TRP cc_start: 0.7598 (m100) cc_final: 0.6777 (m100) REVERT: D 277 MET cc_start: 0.8203 (mtp) cc_final: 0.7734 (mtm) REVERT: D 335 LEU cc_start: 0.6157 (OUTLIER) cc_final: 0.5826 (mp) REVERT: D 546 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.6688 (pp30) REVERT: E 227 ASP cc_start: 0.6942 (t0) cc_final: 0.6522 (t0) REVERT: E 272 ARG cc_start: 0.7587 (mtt180) cc_final: 0.7252 (mtm-85) REVERT: E 392 VAL cc_start: 0.7078 (t) cc_final: 0.6808 (p) REVERT: F 133 CYS cc_start: 0.8170 (m) cc_final: 0.7924 (p) REVERT: F 182 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8559 (pm20) REVERT: G 348 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8227 (mm-40) REVERT: G 400 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8086 (tm-30) REVERT: H 105 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7078 (mm-30) REVERT: H 203 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7812 (p) REVERT: H 267 TRP cc_start: 0.7597 (m100) cc_final: 0.6770 (m100) REVERT: H 277 MET cc_start: 0.8256 (mtp) cc_final: 0.8022 (mmm) REVERT: H 335 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5704 (mp) REVERT: H 546 GLN cc_start: 0.7795 (OUTLIER) cc_final: 0.6672 (pp30) REVERT: H 572 MET cc_start: 0.4850 (ttp) cc_final: 0.4482 (tmm) REVERT: H 578 PHE cc_start: 0.7248 (m-10) cc_final: 0.7027 (m-10) REVERT: I 227 ASP cc_start: 0.7011 (t0) cc_final: 0.6592 (t0) REVERT: I 392 VAL cc_start: 0.7166 (t) cc_final: 0.6863 (p) REVERT: J 123 ARG cc_start: 0.7912 (ttm110) cc_final: 0.7631 (ptt90) REVERT: J 140 GLN cc_start: 0.8837 (mm-40) cc_final: 0.8595 (mm-40) REVERT: J 217 GLU cc_start: 0.8401 (tt0) cc_final: 0.7913 (pt0) REVERT: K 380 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7861 (tm-30) REVERT: K 400 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7957 (tm-30) REVERT: K 416 ARG cc_start: 0.8679 (mmm160) cc_final: 0.8351 (mmm160) REVERT: L 546 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.6607 (pp30) REVERT: L 572 MET cc_start: 0.4702 (ttp) cc_final: 0.4391 (tmm) REVERT: L 573 GLN cc_start: 0.4768 (tt0) cc_final: 0.4336 (tm-30) REVERT: L 601 MET cc_start: 0.8852 (mmt) cc_final: 0.8557 (mmt) REVERT: M 322 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8127 (mm-30) REVERT: O 348 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8246 (mm-40) REVERT: O 379 GLN cc_start: 0.8542 (tp40) cc_final: 0.8275 (tt0) REVERT: O 389 GLU cc_start: 0.8142 (pt0) cc_final: 0.7936 (pt0) REVERT: O 400 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7979 (tm-30) REVERT: P 91 PHE cc_start: 0.7025 (m-80) cc_final: 0.6772 (m-10) REVERT: P 105 GLU cc_start: 0.7665 (tt0) cc_final: 0.7320 (mm-30) REVERT: P 227 ASP cc_start: 0.7778 (t70) cc_final: 0.7284 (p0) REVERT: P 572 MET cc_start: 0.4595 (ttp) cc_final: 0.4348 (tmm) REVERT: P 601 MET cc_start: 0.8870 (mmt) cc_final: 0.8446 (mmt) REVERT: Q 322 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8061 (mm-30) REVERT: R 165 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: R 227 GLU cc_start: 0.7145 (mm-30) cc_final: 0.6939 (mm-30) REVERT: S 379 GLN cc_start: 0.8599 (tp40) cc_final: 0.8398 (tt0) REVERT: S 400 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7931 (tm-30) outliers start: 166 outliers final: 121 residues processed: 633 average time/residue: 0.5106 time to fit residues: 547.7470 Evaluate side-chains 605 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 474 time to evaluate : 4.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 546 GLN Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 88 ILE Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 550 THR Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 372 GLU Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 507 SER Chi-restraints excluded: chain H residue 525 VAL Chi-restraints excluded: chain H residue 546 GLN Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 217 SER Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 412 CYS Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 133 CYS Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 178 GLU Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain K residue 357 THR Chi-restraints excluded: chain K residue 383 LYS Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain K residue 438 THR Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain L residue 546 GLN Chi-restraints excluded: chain L residue 597 ILE Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 550 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain O residue 370 THR Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain O residue 376 LYS Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain O residue 438 THR Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 254 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 491 TRP Chi-restraints excluded: chain P residue 597 ILE Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 167 THR Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 314 SER Chi-restraints excluded: chain Q residue 344 LEU Chi-restraints excluded: chain Q residue 372 VAL Chi-restraints excluded: chain Q residue 412 CYS Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 119 VAL Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 152 VAL Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 372 GLU Chi-restraints excluded: chain S residue 417 ASP Chi-restraints excluded: chain S residue 438 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 511 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 302 optimal weight: 4.9990 chunk 387 optimal weight: 0.5980 chunk 299 optimal weight: 10.0000 chunk 446 optimal weight: 7.9990 chunk 296 optimal weight: 2.9990 chunk 528 optimal weight: 6.9990 chunk 330 optimal weight: 0.9980 chunk 322 optimal weight: 0.8980 chunk 243 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 449 GLN O 379 GLN R 140 GLN R 141 GLN S 348 GLN ** S 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 42908 Z= 0.162 Angle : 0.528 11.009 58416 Z= 0.266 Chirality : 0.042 0.197 6800 Planarity : 0.004 0.058 7516 Dihedral : 7.006 89.974 6323 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.76 % Allowed : 14.98 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.11), residues: 5448 helix: 0.35 (0.11), residues: 2260 sheet: 0.54 (0.15), residues: 1120 loop : -0.34 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 440 HIS 0.006 0.001 HIS N 176 PHE 0.015 0.001 PHE D 240 TYR 0.013 0.001 TYR M 154 ARG 0.011 0.000 ARG K 416 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 512 time to evaluate : 4.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7061 (mm-30) REVERT: D 267 TRP cc_start: 0.7501 (m100) cc_final: 0.6799 (m100) REVERT: D 335 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.5590 (mp) REVERT: E 227 ASP cc_start: 0.6868 (t0) cc_final: 0.6591 (t0) REVERT: E 267 TRP cc_start: 0.8361 (m100) cc_final: 0.7863 (m100) REVERT: E 272 ARG cc_start: 0.7537 (mtt180) cc_final: 0.7257 (mtm-85) REVERT: E 392 VAL cc_start: 0.7088 (t) cc_final: 0.6818 (p) REVERT: E 442 ASN cc_start: 0.9202 (t0) cc_final: 0.8953 (p0) REVERT: G 348 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.8292 (mm-40) REVERT: G 400 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8077 (tm-30) REVERT: G 462 GLU cc_start: 0.8116 (pt0) cc_final: 0.7882 (pt0) REVERT: H 105 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7100 (mm-30) REVERT: H 203 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7812 (p) REVERT: H 267 TRP cc_start: 0.7546 (m100) cc_final: 0.6812 (m100) REVERT: H 335 LEU cc_start: 0.5998 (OUTLIER) cc_final: 0.5530 (mp) REVERT: H 572 MET cc_start: 0.4639 (ttp) cc_final: 0.4256 (tmm) REVERT: I 227 ASP cc_start: 0.6799 (t0) cc_final: 0.6496 (t0) REVERT: I 392 VAL cc_start: 0.7117 (t) cc_final: 0.6833 (p) REVERT: J 123 ARG cc_start: 0.7881 (ttm110) cc_final: 0.7576 (ptt90) REVERT: K 348 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8128 (mt0) REVERT: K 380 GLN cc_start: 0.8054 (tp-100) cc_final: 0.7792 (tm-30) REVERT: K 389 GLU cc_start: 0.8266 (pt0) cc_final: 0.7896 (pt0) REVERT: K 400 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7947 (tm-30) REVERT: K 462 GLU cc_start: 0.8141 (pt0) cc_final: 0.7803 (pt0) REVERT: L 105 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7259 (mm-30) REVERT: L 572 MET cc_start: 0.4638 (ttp) cc_final: 0.4355 (tmm) REVERT: L 573 GLN cc_start: 0.4834 (tt0) cc_final: 0.4380 (tm-30) REVERT: M 322 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8093 (mm-30) REVERT: M 429 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7530 (mpt-90) REVERT: N 217 GLU cc_start: 0.8559 (tt0) cc_final: 0.8039 (pt0) REVERT: O 348 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8238 (mm-40) REVERT: O 400 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7939 (tm-30) REVERT: P 105 GLU cc_start: 0.7720 (tt0) cc_final: 0.7295 (mm-30) REVERT: P 227 ASP cc_start: 0.7611 (t70) cc_final: 0.7278 (p0) REVERT: P 546 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.6468 (pp30) REVERT: P 572 MET cc_start: 0.4671 (ttp) cc_final: 0.4406 (tmm) REVERT: Q 322 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8091 (mm-30) REVERT: Q 534 ASP cc_start: 0.6851 (OUTLIER) cc_final: 0.6213 (m-30) REVERT: R 165 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8155 (tm-30) REVERT: S 389 GLU cc_start: 0.8139 (pt0) cc_final: 0.7900 (pt0) REVERT: S 400 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7916 (tm-30) outliers start: 118 outliers final: 89 residues processed: 603 average time/residue: 0.5164 time to fit residues: 527.7474 Evaluate side-chains 588 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 491 time to evaluate : 4.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 329 ILE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 372 GLU Chi-restraints excluded: chain G residue 417 ASP Chi-restraints excluded: chain G residue 424 ILE Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 507 SER Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain K residue 383 LYS Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain K residue 424 ILE Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 550 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain O residue 370 THR Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain O residue 372 GLU Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 254 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 491 TRP Chi-restraints excluded: chain P residue 546 GLN Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 167 THR Chi-restraints excluded: chain Q residue 251 LEU Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 314 SER Chi-restraints excluded: chain Q residue 344 LEU Chi-restraints excluded: chain Q residue 412 CYS Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 534 ASP Chi-restraints excluded: chain Q residue 550 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain S residue 371 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 326 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 chunk 315 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 103 optimal weight: 0.7980 chunk 102 optimal weight: 0.5980 chunk 335 optimal weight: 0.6980 chunk 359 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 415 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 141 GLN ** G 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 259 GLN R 141 GLN S 348 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 42908 Z= 0.180 Angle : 0.532 9.588 58416 Z= 0.267 Chirality : 0.042 0.188 6800 Planarity : 0.004 0.078 7516 Dihedral : 6.960 89.315 6323 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.93 % Allowed : 15.07 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: 0.17 (0.11), residues: 5448 helix: 0.40 (0.11), residues: 2272 sheet: 0.59 (0.15), residues: 1128 loop : -0.32 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP P 440 HIS 0.004 0.001 HIS M 143 PHE 0.015 0.001 PHE E 458 TYR 0.013 0.001 TYR M 154 ARG 0.017 0.000 ARG K 416 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 503 time to evaluate : 5.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7091 (mm-30) REVERT: D 267 TRP cc_start: 0.7501 (m100) cc_final: 0.6792 (m100) REVERT: D 277 MET cc_start: 0.8031 (mtp) cc_final: 0.7643 (mtm) REVERT: D 335 LEU cc_start: 0.5923 (OUTLIER) cc_final: 0.5528 (mp) REVERT: E 227 ASP cc_start: 0.6947 (t0) cc_final: 0.6642 (t0) REVERT: E 267 TRP cc_start: 0.8348 (m100) cc_final: 0.7848 (m100) REVERT: E 272 ARG cc_start: 0.7620 (mtt180) cc_final: 0.7314 (mtm-85) REVERT: E 392 VAL cc_start: 0.7151 (t) cc_final: 0.6870 (p) REVERT: E 449 GLN cc_start: 0.7291 (mm-40) cc_final: 0.6884 (mm-40) REVERT: E 543 MET cc_start: 0.7253 (mtt) cc_final: 0.6992 (mtt) REVERT: G 348 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8292 (mm-40) REVERT: G 380 GLN cc_start: 0.8236 (tp40) cc_final: 0.7981 (tm-30) REVERT: G 400 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8089 (tm-30) REVERT: G 462 GLU cc_start: 0.8141 (pt0) cc_final: 0.7918 (pt0) REVERT: H 203 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7814 (p) REVERT: H 267 TRP cc_start: 0.7552 (m100) cc_final: 0.6789 (m100) REVERT: H 335 LEU cc_start: 0.5954 (OUTLIER) cc_final: 0.5466 (mp) REVERT: H 572 MET cc_start: 0.4618 (ttp) cc_final: 0.4252 (tmm) REVERT: I 392 VAL cc_start: 0.7148 (t) cc_final: 0.6854 (p) REVERT: J 123 ARG cc_start: 0.7869 (ttm110) cc_final: 0.7567 (ptt90) REVERT: J 217 GLU cc_start: 0.8470 (tt0) cc_final: 0.8112 (pt0) REVERT: K 348 GLN cc_start: 0.8639 (mm-40) cc_final: 0.8144 (mt0) REVERT: K 380 GLN cc_start: 0.8095 (tp-100) cc_final: 0.7836 (tm-30) REVERT: K 400 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7965 (tm-30) REVERT: K 462 GLU cc_start: 0.8086 (pt0) cc_final: 0.7767 (pt0) REVERT: L 280 MET cc_start: 0.7443 (mtp) cc_final: 0.6598 (mpp) REVERT: L 601 MET cc_start: 0.8871 (mmt) cc_final: 0.8554 (mmt) REVERT: M 322 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8066 (mm-30) REVERT: M 429 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7526 (mpt-90) REVERT: N 191 ARG cc_start: 0.8685 (ttm-80) cc_final: 0.8392 (ttt180) REVERT: N 217 GLU cc_start: 0.8542 (tt0) cc_final: 0.8033 (pt0) REVERT: O 348 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8253 (mm-40) REVERT: O 380 GLN cc_start: 0.8208 (tp40) cc_final: 0.7888 (tm-30) REVERT: O 400 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7930 (tm-30) REVERT: P 105 GLU cc_start: 0.7720 (tt0) cc_final: 0.7319 (mm-30) REVERT: P 227 ASP cc_start: 0.7665 (OUTLIER) cc_final: 0.7328 (p0) REVERT: P 546 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.6448 (pp30) REVERT: P 572 MET cc_start: 0.4760 (ttp) cc_final: 0.4519 (tmm) REVERT: Q 227 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.6856 (t70) REVERT: Q 322 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8077 (mm-30) REVERT: Q 534 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6409 (m-30) REVERT: R 165 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: R 217 GLU cc_start: 0.8467 (tt0) cc_final: 0.7984 (pt0) REVERT: S 380 GLN cc_start: 0.8175 (tp40) cc_final: 0.7868 (tm-30) REVERT: S 389 GLU cc_start: 0.8139 (pt0) cc_final: 0.7896 (pt0) REVERT: S 400 GLU cc_start: 0.8341 (tm-30) cc_final: 0.7930 (tm-30) outliers start: 125 outliers final: 101 residues processed: 600 average time/residue: 0.4915 time to fit residues: 500.5414 Evaluate side-chains 594 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 483 time to evaluate : 4.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 507 SER Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 372 GLU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain H residue 124 MET Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 507 SER Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain I residue 550 THR Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain K residue 383 LYS Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain M residue 550 THR Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain O residue 370 THR Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain O residue 372 GLU Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 227 ASP Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 254 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 491 TRP Chi-restraints excluded: chain P residue 546 GLN Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 167 THR Chi-restraints excluded: chain Q residue 227 ASP Chi-restraints excluded: chain Q residue 251 LEU Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 314 SER Chi-restraints excluded: chain Q residue 344 LEU Chi-restraints excluded: chain Q residue 412 CYS Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 534 ASP Chi-restraints excluded: chain Q residue 550 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 372 GLU Chi-restraints excluded: chain S residue 375 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 480 optimal weight: 0.8980 chunk 506 optimal weight: 1.9990 chunk 461 optimal weight: 5.9990 chunk 492 optimal weight: 20.0000 chunk 505 optimal weight: 0.6980 chunk 296 optimal weight: 0.3980 chunk 214 optimal weight: 10.0000 chunk 386 optimal weight: 0.9990 chunk 151 optimal weight: 0.0470 chunk 444 optimal weight: 5.9990 chunk 465 optimal weight: 0.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 141 GLN M 449 GLN M 489 GLN N 140 GLN ** N 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 600 ASN S 348 GLN ** S 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 42908 Z= 0.150 Angle : 0.522 9.638 58416 Z= 0.261 Chirality : 0.042 0.178 6800 Planarity : 0.004 0.066 7516 Dihedral : 6.834 85.985 6323 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.46 % Allowed : 15.73 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: 0.33 (0.11), residues: 5448 helix: 0.55 (0.11), residues: 2264 sheet: 0.68 (0.15), residues: 1128 loop : -0.26 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP P 440 HIS 0.005 0.000 HIS M 143 PHE 0.014 0.001 PHE E 515 TYR 0.021 0.001 TYR M 466 ARG 0.016 0.000 ARG K 416 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 517 time to evaluate : 4.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.8064 (mt-10) cc_final: 0.7097 (mm-30) REVERT: D 267 TRP cc_start: 0.7468 (m100) cc_final: 0.6803 (m100) REVERT: D 277 MET cc_start: 0.8017 (mtp) cc_final: 0.7637 (mtm) REVERT: D 335 LEU cc_start: 0.5936 (OUTLIER) cc_final: 0.5562 (mp) REVERT: E 227 ASP cc_start: 0.6928 (t0) cc_final: 0.6602 (t0) REVERT: E 267 TRP cc_start: 0.8297 (m100) cc_final: 0.7816 (m100) REVERT: E 392 VAL cc_start: 0.7140 (t) cc_final: 0.6853 (p) REVERT: E 442 ASN cc_start: 0.9200 (t0) cc_final: 0.8945 (p0) REVERT: E 449 GLN cc_start: 0.7300 (mm-40) cc_final: 0.6897 (mm-40) REVERT: G 348 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8305 (mm-40) REVERT: G 400 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8104 (tm-30) REVERT: G 462 GLU cc_start: 0.8075 (pt0) cc_final: 0.7806 (pt0) REVERT: H 105 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7028 (mm-30) REVERT: H 203 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7780 (p) REVERT: H 267 TRP cc_start: 0.7516 (m100) cc_final: 0.6797 (m100) REVERT: H 335 LEU cc_start: 0.5910 (OUTLIER) cc_final: 0.5421 (mp) REVERT: H 572 MET cc_start: 0.4645 (ttp) cc_final: 0.4160 (tmm) REVERT: I 267 TRP cc_start: 0.8320 (m100) cc_final: 0.7861 (m100) REVERT: I 392 VAL cc_start: 0.7169 (t) cc_final: 0.6878 (p) REVERT: J 123 ARG cc_start: 0.7876 (ttm110) cc_final: 0.7576 (ptt90) REVERT: J 217 GLU cc_start: 0.8457 (tt0) cc_final: 0.8017 (pt0) REVERT: K 348 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8134 (mt0) REVERT: K 380 GLN cc_start: 0.8039 (tp-100) cc_final: 0.7811 (tm-30) REVERT: K 400 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7924 (tm-30) REVERT: K 462 GLU cc_start: 0.8073 (pt0) cc_final: 0.7777 (pt0) REVERT: L 105 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7319 (mm-30) REVERT: L 280 MET cc_start: 0.7428 (mtp) cc_final: 0.6603 (mpp) REVERT: M 322 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8049 (mm-30) REVERT: M 429 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7529 (mpt-90) REVERT: N 191 ARG cc_start: 0.8661 (ttm-80) cc_final: 0.8370 (ttt180) REVERT: N 217 GLU cc_start: 0.8533 (tt0) cc_final: 0.8018 (pt0) REVERT: O 348 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8282 (mm-40) REVERT: O 380 GLN cc_start: 0.8154 (tp40) cc_final: 0.7875 (tm-30) REVERT: O 400 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7913 (tm-30) REVERT: P 105 GLU cc_start: 0.7707 (tt0) cc_final: 0.7313 (mm-30) REVERT: P 227 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7336 (p0) REVERT: P 546 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6457 (pp30) REVERT: P 572 MET cc_start: 0.4933 (ttp) cc_final: 0.4612 (tmm) REVERT: Q 322 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8039 (mm-30) REVERT: Q 534 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6478 (m-30) REVERT: R 165 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8310 (tm-30) REVERT: S 380 GLN cc_start: 0.8142 (tp40) cc_final: 0.7886 (tm-30) REVERT: S 389 GLU cc_start: 0.8118 (pt0) cc_final: 0.7875 (pt0) REVERT: S 400 GLU cc_start: 0.8342 (tm-30) cc_final: 0.7939 (tm-30) outliers start: 105 outliers final: 92 residues processed: 598 average time/residue: 0.5236 time to fit residues: 531.5872 Evaluate side-chains 580 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 479 time to evaluate : 5.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 372 GLU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain H residue 124 MET Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain I residue 88 ILE Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 200 HIS Chi-restraints excluded: chain K residue 383 LYS Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain L residue 163 ILE Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain O residue 370 THR Chi-restraints excluded: chain O residue 371 ASP Chi-restraints excluded: chain O residue 372 GLU Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain O residue 438 THR Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 227 ASP Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 254 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 546 GLN Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 167 THR Chi-restraints excluded: chain Q residue 251 LEU Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 314 SER Chi-restraints excluded: chain Q residue 344 LEU Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 534 ASP Chi-restraints excluded: chain Q residue 550 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 372 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 490 optimal weight: 9.9990 chunk 323 optimal weight: 9.9990 chunk 520 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 246 optimal weight: 1.9990 chunk 361 optimal weight: 9.9990 chunk 545 optimal weight: 3.9990 chunk 502 optimal weight: 6.9990 chunk 434 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 335 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 141 GLN M 489 GLN ** N 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 452 GLN Q 259 GLN R 151 ASN S 348 GLN ** S 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 452 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 42908 Z= 0.395 Angle : 0.646 10.033 58416 Z= 0.329 Chirality : 0.046 0.203 6800 Planarity : 0.005 0.078 7516 Dihedral : 7.198 78.607 6323 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.86 % Allowed : 15.64 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: -0.21 (0.11), residues: 5448 helix: 0.11 (0.11), residues: 2288 sheet: 0.29 (0.15), residues: 1148 loop : -0.47 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 574 HIS 0.016 0.001 HIS I 143 PHE 0.017 0.001 PHE J 223 TYR 0.027 0.002 TYR I 154 ARG 0.014 0.001 ARG K 416 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10896 Ramachandran restraints generated. 5448 Oldfield, 0 Emsley, 5448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 479 time to evaluate : 4.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 267 TRP cc_start: 0.7657 (m100) cc_final: 0.6815 (m100) REVERT: D 277 MET cc_start: 0.8098 (mtp) cc_final: 0.7658 (mtm) REVERT: D 335 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.5663 (mp) REVERT: E 267 TRP cc_start: 0.8389 (m100) cc_final: 0.7867 (m100) REVERT: E 392 VAL cc_start: 0.7143 (t) cc_final: 0.6881 (p) REVERT: E 449 GLN cc_start: 0.7303 (mm-40) cc_final: 0.6892 (mm-40) REVERT: G 348 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8239 (mm-40) REVERT: G 400 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8102 (tm-30) REVERT: G 462 GLU cc_start: 0.8151 (pt0) cc_final: 0.7837 (pt0) REVERT: H 105 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7082 (mm-30) REVERT: H 203 THR cc_start: 0.8072 (OUTLIER) cc_final: 0.7815 (p) REVERT: H 267 TRP cc_start: 0.7665 (m100) cc_final: 0.6808 (m100) REVERT: H 335 LEU cc_start: 0.6037 (OUTLIER) cc_final: 0.5486 (mp) REVERT: H 572 MET cc_start: 0.4801 (ttp) cc_final: 0.4519 (tmm) REVERT: I 267 TRP cc_start: 0.8415 (m100) cc_final: 0.7869 (m100) REVERT: I 392 VAL cc_start: 0.7137 (t) cc_final: 0.6870 (p) REVERT: J 123 ARG cc_start: 0.7814 (ttm110) cc_final: 0.7534 (ptt90) REVERT: J 217 GLU cc_start: 0.8439 (tt0) cc_final: 0.8068 (pt0) REVERT: K 380 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7864 (tm-30) REVERT: K 400 GLU cc_start: 0.8397 (tm-30) cc_final: 0.7987 (tm-30) REVERT: K 416 ARG cc_start: 0.8629 (mmm160) cc_final: 0.8307 (mmm160) REVERT: L 280 MET cc_start: 0.7425 (mtp) cc_final: 0.6522 (mpp) REVERT: L 323 LEU cc_start: 0.7542 (mt) cc_final: 0.7305 (tt) REVERT: L 601 MET cc_start: 0.8871 (mmt) cc_final: 0.8501 (mmt) REVERT: M 322 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8014 (mm-30) REVERT: N 217 GLU cc_start: 0.8475 (tt0) cc_final: 0.8119 (pt0) REVERT: O 348 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8236 (mm-40) REVERT: O 400 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7974 (tm-30) REVERT: P 105 GLU cc_start: 0.7662 (tt0) cc_final: 0.7371 (mm-30) REVERT: P 227 ASP cc_start: 0.7692 (t70) cc_final: 0.7321 (p0) REVERT: P 546 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7144 (pm20) REVERT: P 572 MET cc_start: 0.5015 (ttp) cc_final: 0.4702 (tmm) REVERT: P 601 MET cc_start: 0.8866 (mmt) cc_final: 0.8448 (mmt) REVERT: Q 322 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8013 (mm-30) REVERT: R 165 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: R 217 GLU cc_start: 0.8433 (tt0) cc_final: 0.7936 (pt0) REVERT: R 227 GLU cc_start: 0.7198 (mm-30) cc_final: 0.6958 (mm-30) REVERT: S 380 GLN cc_start: 0.8219 (tp40) cc_final: 0.7957 (tm-30) REVERT: S 400 GLU cc_start: 0.8394 (tm-30) cc_final: 0.7961 (tm-30) REVERT: S 416 ARG cc_start: 0.8340 (mmm160) cc_final: 0.8116 (mmm160) outliers start: 122 outliers final: 110 residues processed: 574 average time/residue: 0.5044 time to fit residues: 491.3045 Evaluate side-chains 573 residues out of total 4628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 456 time to evaluate : 4.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 167 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 335 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 556 LEU Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain E residue 167 THR Chi-restraints excluded: chain E residue 181 ASP Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 372 VAL Chi-restraints excluded: chain E residue 412 CYS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 135 THR Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 164 VAL Chi-restraints excluded: chain F residue 200 HIS Chi-restraints excluded: chain F residue 229 VAL Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain G residue 348 GLN Chi-restraints excluded: chain G residue 357 THR Chi-restraints excluded: chain G residue 370 THR Chi-restraints excluded: chain G residue 371 ASP Chi-restraints excluded: chain G residue 372 GLU Chi-restraints excluded: chain G residue 375 SER Chi-restraints excluded: chain H residue 124 MET Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain H residue 167 THR Chi-restraints excluded: chain H residue 203 THR Chi-restraints excluded: chain H residue 226 MET Chi-restraints excluded: chain H residue 228 VAL Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 335 LEU Chi-restraints excluded: chain H residue 525 VAL Chi-restraints excluded: chain H residue 556 LEU Chi-restraints excluded: chain I residue 114 THR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 163 ILE Chi-restraints excluded: chain I residue 167 THR Chi-restraints excluded: chain I residue 181 ASP Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain I residue 271 MET Chi-restraints excluded: chain I residue 372 VAL Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 88 THR Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 130 ILE Chi-restraints excluded: chain J residue 135 THR Chi-restraints excluded: chain J residue 139 LEU Chi-restraints excluded: chain J residue 164 VAL Chi-restraints excluded: chain J residue 229 VAL Chi-restraints excluded: chain K residue 383 LYS Chi-restraints excluded: chain K residue 417 ASP Chi-restraints excluded: chain L residue 167 THR Chi-restraints excluded: chain L residue 228 VAL Chi-restraints excluded: chain L residue 254 VAL Chi-restraints excluded: chain L residue 335 LEU Chi-restraints excluded: chain L residue 491 TRP Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain M residue 88 ILE Chi-restraints excluded: chain M residue 163 ILE Chi-restraints excluded: chain M residue 181 ASP Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 344 LEU Chi-restraints excluded: chain M residue 372 VAL Chi-restraints excluded: chain M residue 412 CYS Chi-restraints excluded: chain M residue 471 LEU Chi-restraints excluded: chain N residue 88 THR Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 127 LEU Chi-restraints excluded: chain N residue 130 ILE Chi-restraints excluded: chain N residue 135 THR Chi-restraints excluded: chain N residue 139 LEU Chi-restraints excluded: chain N residue 160 SER Chi-restraints excluded: chain N residue 164 VAL Chi-restraints excluded: chain N residue 229 VAL Chi-restraints excluded: chain O residue 348 GLN Chi-restraints excluded: chain O residue 370 THR Chi-restraints excluded: chain O residue 372 GLU Chi-restraints excluded: chain O residue 417 ASP Chi-restraints excluded: chain O residue 438 THR Chi-restraints excluded: chain O residue 452 GLN Chi-restraints excluded: chain P residue 163 ILE Chi-restraints excluded: chain P residue 167 THR Chi-restraints excluded: chain P residue 228 VAL Chi-restraints excluded: chain P residue 243 THR Chi-restraints excluded: chain P residue 254 VAL Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain P residue 546 GLN Chi-restraints excluded: chain Q residue 88 ILE Chi-restraints excluded: chain Q residue 167 THR Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain Q residue 251 LEU Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain Q residue 344 LEU Chi-restraints excluded: chain Q residue 471 LEU Chi-restraints excluded: chain Q residue 550 THR Chi-restraints excluded: chain R residue 88 THR Chi-restraints excluded: chain R residue 127 LEU Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 164 VAL Chi-restraints excluded: chain R residue 165 GLU Chi-restraints excluded: chain R residue 229 VAL Chi-restraints excluded: chain S residue 357 THR Chi-restraints excluded: chain S residue 371 ASP Chi-restraints excluded: chain S residue 372 GLU Chi-restraints excluded: chain S residue 438 THR Chi-restraints excluded: chain S residue 452 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 266 optimal weight: 0.9990 chunk 345 optimal weight: 0.9980 chunk 463 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 400 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 435 optimal weight: 8.9990 chunk 182 optimal weight: 0.9980 chunk 447 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 GLN ** N 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 151 ASN ** O 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 452 GLN Q 449 GLN R 151 ASN S 348 GLN ** S 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 452 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.157859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.119766 restraints weight = 77164.693| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.18 r_work: 0.3543 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 42908 Z= 0.176 Angle : 0.558 9.356 58416 Z= 0.279 Chirality : 0.043 0.184 6800 Planarity : 0.004 0.068 7516 Dihedral : 6.958 73.176 6323 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.43 % Allowed : 16.20 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % 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: 0.03 (0.11), residues: 5448 helix: 0.34 (0.11), residues: 2280 sheet: 0.49 (0.16), residues: 1108 loop : -0.43 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 440 HIS 0.005 0.001 HIS I 143 PHE 0.010 0.001 PHE E 458 TYR 0.021 0.001 TYR M 466 ARG 0.014 0.000 ARG K 416 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11150.55 seconds wall clock time: 202 minutes 8.76 seconds (12128.76 seconds total)