Starting phenix.real_space_refine on Sun Mar 24 04:04:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x01_32914/03_2024/7x01_32914_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x01_32914/03_2024/7x01_32914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x01_32914/03_2024/7x01_32914.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x01_32914/03_2024/7x01_32914.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x01_32914/03_2024/7x01_32914_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7x01_32914/03_2024/7x01_32914_updated.pdb" } resolution = 2.62 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= 0.004 sd= 0.085 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 Zn 12 6.06 5 S 324 5.16 5 C 24996 2.51 5 N 6924 2.21 5 O 7464 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 26": "OE1" <-> "OE2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B GLU 412": "OE1" <-> "OE2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "E GLU 412": "OE1" <-> "OE2" Residue "F GLU 26": "OE1" <-> "OE2" Residue "F GLU 91": "OE1" <-> "OE2" Residue "F PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 412": "OE1" <-> "OE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G GLU 353": "OE1" <-> "OE2" Residue "H GLU 349": "OE1" <-> "OE2" Residue "I GLU 26": "OE1" <-> "OE2" Residue "I GLU 202": "OE1" <-> "OE2" Residue "I PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 412": "OE1" <-> "OE2" Residue "J GLU 26": "OE1" <-> "OE2" Residue "J GLU 202": "OE1" <-> "OE2" Residue "J GLU 353": "OE1" <-> "OE2" Residue "J GLU 412": "OE1" <-> "OE2" Residue "K GLU 405": "OE1" <-> "OE2" Residue "K GLU 412": "OE1" <-> "OE2" Residue "L GLU 91": "OE1" <-> "OE2" Residue "L GLU 202": "OE1" <-> "OE2" Residue "L GLU 250": "OE1" <-> "OE2" Residue "L PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 412": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39732 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "B" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "C" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "D" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "E" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "F" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "G" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "H" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "I" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "J" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "K" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "L" Number of atoms: 3289 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Conformer: "B" Number of residues, atoms: 421, 3283 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 399} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 bond proxies already assigned to first conformer: 3344 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' ZN': 1, '7XQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1024 SG CYS A 134 73.126 19.496 59.460 1.00 72.50 S ATOM 1076 SG CYS A 141 69.321 19.950 58.584 1.00 63.16 S ATOM 4313 SG CYS B 134 118.246 16.138 59.431 1.00 70.94 S ATOM 4365 SG CYS B 141 114.724 14.601 58.627 1.00 64.93 S ATOM 7602 SG CYS C 134 159.013 35.783 59.468 1.00 70.38 S ATOM 7654 SG CYS C 141 156.773 32.673 58.593 1.00 66.81 S ATOM 10891 SG CYS D 134 184.506 73.125 59.457 1.00 71.42 S ATOM 10943 SG CYS D 141 184.044 69.322 58.582 1.00 62.34 S ATOM 14180 SG CYS E 134 187.880 118.267 59.413 1.00 70.20 S ATOM 14232 SG CYS E 141 189.407 114.722 58.631 1.00 64.87 S ATOM 17469 SG CYS F 134 168.252 159.044 59.422 1.00 69.59 S ATOM 17521 SG CYS F 141 171.333 156.738 58.607 1.00 65.21 S ATOM 20758 SG CYS G 134 130.867 184.528 59.430 1.00 71.31 S ATOM 20810 SG CYS G 141 134.679 184.075 58.568 1.00 62.60 S ATOM 24047 SG CYS H 134 85.735 187.891 59.405 1.00 70.38 S ATOM 24099 SG CYS H 141 89.279 189.438 58.602 1.00 66.23 S ATOM 27336 SG CYS I 134 44.983 168.220 59.445 1.00 71.14 S ATOM 27388 SG CYS I 141 47.214 171.354 58.544 1.00 66.99 S ATOM 30625 SG CYS J 134 19.496 130.875 59.443 1.00 71.96 S ATOM 30677 SG CYS J 141 19.917 134.678 58.569 1.00 63.38 S ATOM 33914 SG CYS K 134 16.123 85.750 59.417 1.00 70.85 S ATOM 33966 SG CYS K 141 14.587 89.286 58.598 1.00 65.53 S ATOM 37203 SG CYS L 134 35.723 44.931 59.498 1.00 71.32 S ATOM 37255 SG CYS L 141 32.660 47.215 58.574 1.00 66.30 S Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS A 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 236 " occ=0.50 residue: pdb=" N ACYS B 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 236 " occ=0.50 residue: pdb=" N ACYS C 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 236 " occ=0.50 residue: pdb=" N ACYS D 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 236 " occ=0.50 residue: pdb=" N ACYS E 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS E 236 " occ=0.50 residue: pdb=" N ACYS F 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS F 236 " occ=0.50 residue: pdb=" N ACYS G 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS G 236 " occ=0.50 residue: pdb=" N ACYS H 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS H 236 " occ=0.50 residue: pdb=" N ACYS I 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS I 236 " occ=0.50 residue: pdb=" N ACYS J 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS J 236 " occ=0.50 residue: pdb=" N ACYS K 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS K 236 " occ=0.50 residue: pdb=" N ACYS L 236 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS L 236 " occ=0.50 Time building chain proxies: 34.87, per 1000 atoms: 0.88 Number of scatterers: 39732 At special positions: 0 Unit cell: (204.85, 204.85, 88.4, 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) Zn 12 29.99 S 324 16.00 F 12 9.00 O 7464 8.00 N 6924 7.00 C 24996 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: 13.41 Conformation dependent library (CDL) restraints added in 12.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9600 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 60 sheets defined 28.2% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.79 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.570A pdb=" N LYS A 16 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 53 removed outlier: 3.531A pdb=" N PHE A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS A 49 " --> pdb=" O HIS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 103 removed outlier: 3.736A pdb=" N ALA A 103 " --> pdb=" O LYS A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 158 through 168 removed outlier: 3.510A pdb=" N ILE A 167 " --> pdb=" O TYR A 163 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 252 through 258 removed outlier: 4.024A pdb=" N TRP A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 352 through 362 Processing helix chain 'A' and resid 381 through 402 removed outlier: 3.574A pdb=" N ILE A 384 " --> pdb=" O ASN A 381 " (cutoff:3.500A) Proline residue: A 385 - end of helix removed outlier: 3.790A pdb=" N ALA A 388 " --> pdb=" O PRO A 385 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 395 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A 396 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS A 398 " --> pdb=" O ALA A 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 21 removed outlier: 3.564A pdb=" N LYS B 16 " --> pdb=" O ALA B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 53 removed outlier: 3.705A pdb=" N ALA B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 103 Processing helix chain 'B' and resid 112 through 124 Processing helix chain 'B' and resid 158 through 168 removed outlier: 3.515A pdb=" N ILE B 167 " --> pdb=" O TYR B 163 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS B 168 " --> pdb=" O HIS B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 No H-bonds generated for 'chain 'B' and resid 181 through 184' Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 252 through 258 removed outlier: 4.117A pdb=" N TRP B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 345 through 347 No H-bonds generated for 'chain 'B' and resid 345 through 347' Processing helix chain 'B' and resid 352 through 362 Processing helix chain 'B' and resid 381 through 402 Proline residue: B 385 - end of helix removed outlier: 3.770A pdb=" N ALA B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 395 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N CYS B 398 " --> pdb=" O ALA B 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 21 Processing helix chain 'C' and resid 39 through 53 removed outlier: 3.559A pdb=" N PHE C 43 " --> pdb=" O ASN C 39 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE C 48 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 49 " --> pdb=" O HIS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.903A pdb=" N ALA C 103 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 124 Processing helix chain 'C' and resid 158 through 168 removed outlier: 3.527A pdb=" N ILE C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LYS C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 184 No H-bonds generated for 'chain 'C' and resid 181 through 184' Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 252 through 258 removed outlier: 4.076A pdb=" N TRP C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 345 through 347 No H-bonds generated for 'chain 'C' and resid 345 through 347' Processing helix chain 'C' and resid 352 through 362 Processing helix chain 'C' and resid 381 through 402 Proline residue: C 385 - end of helix removed outlier: 3.731A pdb=" N ALA C 388 " --> pdb=" O PRO C 385 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 395 " --> pdb=" O SER C 392 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS C 396 " --> pdb=" O LYS C 393 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS C 398 " --> pdb=" O ALA C 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 21 removed outlier: 3.569A pdb=" N LYS D 16 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 53 removed outlier: 3.527A pdb=" N PHE D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS D 49 " --> pdb=" O HIS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 103 removed outlier: 3.746A pdb=" N ALA D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 124 Processing helix chain 'D' and resid 158 through 168 removed outlier: 3.504A pdb=" N ILE D 167 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LYS D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 184 No H-bonds generated for 'chain 'D' and resid 181 through 184' Processing helix chain 'D' and resid 202 through 204 No H-bonds generated for 'chain 'D' and resid 202 through 204' Processing helix chain 'D' and resid 252 through 258 removed outlier: 4.032A pdb=" N TRP D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 341 Processing helix chain 'D' and resid 345 through 347 No H-bonds generated for 'chain 'D' and resid 345 through 347' Processing helix chain 'D' and resid 352 through 362 Processing helix chain 'D' and resid 381 through 402 removed outlier: 3.533A pdb=" N ILE D 384 " --> pdb=" O ASN D 381 " (cutoff:3.500A) Proline residue: D 385 - end of helix removed outlier: 3.801A pdb=" N ALA D 388 " --> pdb=" O PRO D 385 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 395 " --> pdb=" O SER D 392 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS D 396 " --> pdb=" O LYS D 393 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS D 398 " --> pdb=" O ALA D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 21 Processing helix chain 'E' and resid 38 through 53 removed outlier: 3.723A pdb=" N ALA E 42 " --> pdb=" O ALA E 38 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE E 43 " --> pdb=" O ASN E 39 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS E 49 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 103 removed outlier: 3.619A pdb=" N ALA E 103 " --> pdb=" O LYS E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 124 Processing helix chain 'E' and resid 158 through 168 removed outlier: 3.507A pdb=" N ILE E 167 " --> pdb=" O TYR E 163 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS E 168 " --> pdb=" O HIS E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 184 No H-bonds generated for 'chain 'E' and resid 181 through 184' Processing helix chain 'E' and resid 202 through 204 No H-bonds generated for 'chain 'E' and resid 202 through 204' Processing helix chain 'E' and resid 252 through 258 removed outlier: 4.117A pdb=" N TRP E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 341 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 352 through 362 Processing helix chain 'E' and resid 381 through 402 Proline residue: E 385 - end of helix removed outlier: 3.767A pdb=" N ALA E 388 " --> pdb=" O PRO E 385 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA E 395 " --> pdb=" O SER E 392 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS E 398 " --> pdb=" O ALA E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 39 through 53 removed outlier: 3.561A pdb=" N PHE F 43 " --> pdb=" O ASN F 39 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS F 49 " --> pdb=" O HIS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 103 removed outlier: 3.787A pdb=" N ALA F 103 " --> pdb=" O LYS F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 124 Processing helix chain 'F' and resid 158 through 168 removed outlier: 3.518A pdb=" N ILE F 167 " --> pdb=" O TYR F 163 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LYS F 168 " --> pdb=" O HIS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 184 No H-bonds generated for 'chain 'F' and resid 181 through 184' Processing helix chain 'F' and resid 202 through 204 No H-bonds generated for 'chain 'F' and resid 202 through 204' Processing helix chain 'F' and resid 252 through 258 removed outlier: 4.080A pdb=" N TRP F 258 " --> pdb=" O LEU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 341 Processing helix chain 'F' and resid 345 through 347 No H-bonds generated for 'chain 'F' and resid 345 through 347' Processing helix chain 'F' and resid 352 through 362 Processing helix chain 'F' and resid 381 through 402 Proline residue: F 385 - end of helix removed outlier: 3.732A pdb=" N ALA F 388 " --> pdb=" O PRO F 385 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA F 395 " --> pdb=" O SER F 392 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS F 396 " --> pdb=" O LYS F 393 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS F 398 " --> pdb=" O ALA F 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 21 removed outlier: 3.572A pdb=" N LYS G 16 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 53 removed outlier: 3.695A pdb=" N ALA G 42 " --> pdb=" O ALA G 38 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE G 43 " --> pdb=" O ASN G 39 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS G 49 " --> pdb=" O HIS G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 103 removed outlier: 3.846A pdb=" N ALA G 103 " --> pdb=" O LYS G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 124 Processing helix chain 'G' and resid 158 through 168 removed outlier: 3.535A pdb=" N ILE G 167 " --> pdb=" O TYR G 163 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LYS G 168 " --> pdb=" O HIS G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 184 No H-bonds generated for 'chain 'G' and resid 181 through 184' Processing helix chain 'G' and resid 202 through 204 No H-bonds generated for 'chain 'G' and resid 202 through 204' Processing helix chain 'G' and resid 252 through 258 removed outlier: 4.038A pdb=" N TRP G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 341 Processing helix chain 'G' and resid 345 through 347 No H-bonds generated for 'chain 'G' and resid 345 through 347' Processing helix chain 'G' and resid 352 through 362 Processing helix chain 'G' and resid 381 through 402 removed outlier: 3.554A pdb=" N ILE G 384 " --> pdb=" O ASN G 381 " (cutoff:3.500A) Proline residue: G 385 - end of helix removed outlier: 3.801A pdb=" N ALA G 388 " --> pdb=" O PRO G 385 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA G 395 " --> pdb=" O SER G 392 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS G 396 " --> pdb=" O LYS G 393 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N CYS G 398 " --> pdb=" O ALA G 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 21 Processing helix chain 'H' and resid 39 through 53 removed outlier: 3.561A pdb=" N PHE H 43 " --> pdb=" O ASN H 39 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE H 48 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS H 49 " --> pdb=" O HIS H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 103 Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 158 through 168 removed outlier: 4.782A pdb=" N LYS H 168 " --> pdb=" O HIS H 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 184 No H-bonds generated for 'chain 'H' and resid 181 through 184' Processing helix chain 'H' and resid 202 through 204 No H-bonds generated for 'chain 'H' and resid 202 through 204' Processing helix chain 'H' and resid 252 through 258 removed outlier: 4.096A pdb=" N TRP H 258 " --> pdb=" O LEU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 336 through 341 Processing helix chain 'H' and resid 345 through 347 No H-bonds generated for 'chain 'H' and resid 345 through 347' Processing helix chain 'H' and resid 352 through 362 Processing helix chain 'H' and resid 381 through 402 Proline residue: H 385 - end of helix removed outlier: 3.745A pdb=" N ALA H 388 " --> pdb=" O PRO H 385 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA H 395 " --> pdb=" O SER H 392 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS H 398 " --> pdb=" O ALA H 395 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 21 Processing helix chain 'I' and resid 39 through 53 removed outlier: 3.553A pdb=" N PHE I 43 " --> pdb=" O ASN I 39 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE I 48 " --> pdb=" O SER I 44 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS I 49 " --> pdb=" O HIS I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 103 removed outlier: 3.882A pdb=" N ALA I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 124 Processing helix chain 'I' and resid 158 through 168 removed outlier: 3.512A pdb=" N ILE I 167 " --> pdb=" O TYR I 163 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS I 168 " --> pdb=" O HIS I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 184 No H-bonds generated for 'chain 'I' and resid 181 through 184' Processing helix chain 'I' and resid 202 through 204 No H-bonds generated for 'chain 'I' and resid 202 through 204' Processing helix chain 'I' and resid 252 through 258 removed outlier: 4.088A pdb=" N TRP I 258 " --> pdb=" O LEU I 254 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 341 Processing helix chain 'I' and resid 345 through 347 No H-bonds generated for 'chain 'I' and resid 345 through 347' Processing helix chain 'I' and resid 352 through 362 Processing helix chain 'I' and resid 381 through 402 Proline residue: I 385 - end of helix removed outlier: 3.732A pdb=" N ALA I 388 " --> pdb=" O PRO I 385 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA I 395 " --> pdb=" O SER I 392 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS I 396 " --> pdb=" O LYS I 393 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS I 398 " --> pdb=" O ALA I 395 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 21 removed outlier: 3.566A pdb=" N LYS J 16 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 53 removed outlier: 3.711A pdb=" N ALA J 42 " --> pdb=" O ALA J 38 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE J 43 " --> pdb=" O ASN J 39 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE J 48 " --> pdb=" O SER J 44 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS J 49 " --> pdb=" O HIS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 103 removed outlier: 3.917A pdb=" N ALA J 103 " --> pdb=" O LYS J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 124 Processing helix chain 'J' and resid 158 through 168 removed outlier: 3.521A pdb=" N ILE J 167 " --> pdb=" O TYR J 163 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N LYS J 168 " --> pdb=" O HIS J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 184 No H-bonds generated for 'chain 'J' and resid 181 through 184' Processing helix chain 'J' and resid 202 through 204 No H-bonds generated for 'chain 'J' and resid 202 through 204' Processing helix chain 'J' and resid 252 through 258 removed outlier: 4.037A pdb=" N TRP J 258 " --> pdb=" O LEU J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 341 Processing helix chain 'J' and resid 345 through 347 No H-bonds generated for 'chain 'J' and resid 345 through 347' Processing helix chain 'J' and resid 352 through 362 Processing helix chain 'J' and resid 381 through 402 removed outlier: 3.531A pdb=" N ILE J 384 " --> pdb=" O ASN J 381 " (cutoff:3.500A) Proline residue: J 385 - end of helix removed outlier: 3.799A pdb=" N ALA J 388 " --> pdb=" O PRO J 385 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA J 395 " --> pdb=" O SER J 392 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS J 396 " --> pdb=" O LYS J 393 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS J 398 " --> pdb=" O ALA J 395 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 21 Processing helix chain 'K' and resid 38 through 53 removed outlier: 3.704A pdb=" N ALA K 42 " --> pdb=" O ALA K 38 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE K 48 " --> pdb=" O SER K 44 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS K 49 " --> pdb=" O HIS K 45 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 103 removed outlier: 3.777A pdb=" N ALA K 103 " --> pdb=" O LYS K 99 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 124 Processing helix chain 'K' and resid 158 through 168 removed outlier: 4.786A pdb=" N LYS K 168 " --> pdb=" O HIS K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 184 No H-bonds generated for 'chain 'K' and resid 181 through 184' Processing helix chain 'K' and resid 202 through 204 No H-bonds generated for 'chain 'K' and resid 202 through 204' Processing helix chain 'K' and resid 252 through 258 removed outlier: 4.119A pdb=" N TRP K 258 " --> pdb=" O LEU K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 341 Processing helix chain 'K' and resid 345 through 347 No H-bonds generated for 'chain 'K' and resid 345 through 347' Processing helix chain 'K' and resid 352 through 362 Processing helix chain 'K' and resid 381 through 402 Proline residue: K 385 - end of helix removed outlier: 3.748A pdb=" N ALA K 388 " --> pdb=" O PRO K 385 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA K 395 " --> pdb=" O SER K 392 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N CYS K 398 " --> pdb=" O ALA K 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 21 Processing helix chain 'L' and resid 39 through 53 removed outlier: 3.582A pdb=" N PHE L 43 " --> pdb=" O ASN L 39 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE L 48 " --> pdb=" O SER L 44 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS L 49 " --> pdb=" O HIS L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 103 removed outlier: 3.881A pdb=" N ALA L 103 " --> pdb=" O LYS L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 124 Processing helix chain 'L' and resid 158 through 168 removed outlier: 3.519A pdb=" N ILE L 167 " --> pdb=" O TYR L 163 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS L 168 " --> pdb=" O HIS L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 184 No H-bonds generated for 'chain 'L' and resid 181 through 184' Processing helix chain 'L' and resid 202 through 204 No H-bonds generated for 'chain 'L' and resid 202 through 204' Processing helix chain 'L' and resid 252 through 258 removed outlier: 4.069A pdb=" N TRP L 258 " --> pdb=" O LEU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 341 Processing helix chain 'L' and resid 345 through 347 No H-bonds generated for 'chain 'L' and resid 345 through 347' Processing helix chain 'L' and resid 352 through 362 Processing helix chain 'L' and resid 381 through 402 Proline residue: L 385 - end of helix removed outlier: 3.758A pdb=" N ALA L 388 " --> pdb=" O PRO L 385 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA L 395 " --> pdb=" O SER L 392 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS L 396 " --> pdb=" O LYS L 393 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS L 398 " --> pdb=" O ALA L 395 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.357A pdb=" N GLU A 26 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N VAL A 6 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLU A 28 " --> pdb=" O VAL A 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 77 through 81 removed outlier: 6.854A pdb=" N VAL A 147 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE A 64 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE A 149 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 172 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N TYR A 150 " --> pdb=" O LEU A 172 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR A 174 " --> pdb=" O TYR A 150 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 280 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ARG A 289 " --> pdb=" O THR A 278 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N THR A 278 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR A 291 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N CYS A 276 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N SER A 293 " --> pdb=" O CYS A 274 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N CYS A 274 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 189 through 192 removed outlier: 3.621A pdb=" N THR A 197 " --> pdb=" O TYR A 192 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 303 through 308 removed outlier: 3.906A pdb=" N THR A 437 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 324 through 334 Processing sheet with id= F, first strand: chain 'B' and resid 4 through 6 Processing sheet with id= G, first strand: chain 'B' and resid 77 through 81 removed outlier: 6.855A pdb=" N VAL B 147 " --> pdb=" O LEU B 62 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE B 64 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ILE B 149 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU B 172 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N TYR B 150 " --> pdb=" O LEU B 172 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR B 174 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 280 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ARG B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N THR B 278 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N THR B 291 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N CYS B 276 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N SER B 293 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N CYS B 274 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.615A pdb=" N THR B 197 " --> pdb=" O TYR B 192 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 303 through 308 removed outlier: 3.910A pdb=" N THR B 437 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 324 through 334 Processing sheet with id= K, first strand: chain 'C' and resid 4 through 6 Processing sheet with id= L, first strand: chain 'C' and resid 78 through 81 removed outlier: 6.500A pdb=" N ILE C 61 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL C 81 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ASP C 63 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 147 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N ILE C 64 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE C 149 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU C 172 " --> pdb=" O ALA C 148 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N TYR C 150 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TYR C 174 " --> pdb=" O TYR C 150 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL C 280 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ARG C 289 " --> pdb=" O THR C 278 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N THR C 278 " --> pdb=" O ARG C 289 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N THR C 291 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N CYS C 276 " --> pdb=" O THR C 291 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N SER C 293 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N CYS C 274 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 189 through 192 removed outlier: 3.594A pdb=" N THR C 197 " --> pdb=" O TYR C 192 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 303 through 308 removed outlier: 3.866A pdb=" N THR C 437 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 324 through 334 Processing sheet with id= P, first strand: chain 'D' and resid 3 through 6 removed outlier: 6.257A pdb=" N GLU D 26 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL D 6 " --> pdb=" O GLU D 26 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU D 28 " --> pdb=" O VAL D 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'D' and resid 78 through 81 removed outlier: 6.548A pdb=" N ILE D 61 " --> pdb=" O HIS D 79 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL D 81 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP D 63 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL D 147 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE D 64 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE D 149 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU D 172 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N TYR D 150 " --> pdb=" O LEU D 172 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TYR D 174 " --> pdb=" O TYR D 150 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 280 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG D 289 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N THR D 278 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N THR D 291 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N CYS D 276 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N SER D 293 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N CYS D 274 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 189 through 192 removed outlier: 3.625A pdb=" N THR D 197 " --> pdb=" O TYR D 192 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 303 through 308 removed outlier: 3.905A pdb=" N THR D 437 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 324 through 334 Processing sheet with id= U, first strand: chain 'E' and resid 4 through 6 Processing sheet with id= V, first strand: chain 'E' and resid 77 through 81 removed outlier: 6.854A pdb=" N VAL E 147 " --> pdb=" O LEU E 62 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE E 64 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE E 149 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU E 172 " --> pdb=" O ALA E 148 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N TYR E 150 " --> pdb=" O LEU E 172 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TYR E 174 " --> pdb=" O TYR E 150 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL E 280 " --> pdb=" O VAL E 287 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG E 289 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N THR E 278 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR E 291 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N CYS E 276 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER E 293 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N CYS E 274 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 189 through 192 removed outlier: 3.621A pdb=" N THR E 197 " --> pdb=" O TYR E 192 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 303 through 308 removed outlier: 3.916A pdb=" N THR E 437 " --> pdb=" O HIS E 308 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 324 through 334 Processing sheet with id= Z, first strand: chain 'F' and resid 3 through 6 removed outlier: 6.396A pdb=" N GLU F 26 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N VAL F 6 " --> pdb=" O GLU F 26 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N GLU F 28 " --> pdb=" O VAL F 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 77 through 81 removed outlier: 6.890A pdb=" N VAL F 147 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE F 64 " --> pdb=" O VAL F 147 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ILE F 149 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU F 172 " --> pdb=" O ALA F 148 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N TYR F 150 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR F 174 " --> pdb=" O TYR F 150 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 280 " --> pdb=" O VAL F 287 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG F 289 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N THR F 278 " --> pdb=" O ARG F 289 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N THR F 291 " --> pdb=" O CYS F 276 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N CYS F 276 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N SER F 293 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N CYS F 274 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 189 through 192 removed outlier: 3.591A pdb=" N THR F 197 " --> pdb=" O TYR F 192 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 303 through 308 removed outlier: 3.870A pdb=" N THR F 437 " --> pdb=" O HIS F 308 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 324 through 334 Processing sheet with id= AE, first strand: chain 'G' and resid 4 through 6 Processing sheet with id= AF, first strand: chain 'G' and resid 77 through 81 removed outlier: 6.846A pdb=" N VAL G 147 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE G 64 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE G 149 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU G 172 " --> pdb=" O ALA G 148 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N TYR G 150 " --> pdb=" O LEU G 172 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TYR G 174 " --> pdb=" O TYR G 150 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL G 280 " --> pdb=" O VAL G 287 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG G 289 " --> pdb=" O THR G 278 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N THR G 278 " --> pdb=" O ARG G 289 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR G 291 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N CYS G 276 " --> pdb=" O THR G 291 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N SER G 293 " --> pdb=" O CYS G 274 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N CYS G 274 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 189 through 192 removed outlier: 3.621A pdb=" N THR G 197 " --> pdb=" O TYR G 192 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 303 through 308 removed outlier: 3.904A pdb=" N THR G 437 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 324 through 334 Processing sheet with id= AJ, first strand: chain 'H' and resid 3 through 6 removed outlier: 6.326A pdb=" N GLU H 26 " --> pdb=" O VAL H 4 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL H 6 " --> pdb=" O GLU H 26 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU H 28 " --> pdb=" O VAL H 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'H' and resid 77 through 81 removed outlier: 6.857A pdb=" N VAL H 147 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE H 64 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE H 149 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU H 172 " --> pdb=" O ALA H 148 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N TYR H 150 " --> pdb=" O LEU H 172 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR H 174 " --> pdb=" O TYR H 150 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL H 280 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARG H 289 " --> pdb=" O THR H 278 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N THR H 278 " --> pdb=" O ARG H 289 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N THR H 291 " --> pdb=" O CYS H 276 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N CYS H 276 " --> pdb=" O THR H 291 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER H 293 " --> pdb=" O CYS H 274 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N CYS H 274 " --> pdb=" O SER H 293 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 189 through 192 removed outlier: 3.623A pdb=" N THR H 197 " --> pdb=" O TYR H 192 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 303 through 308 removed outlier: 3.911A pdb=" N THR H 437 " --> pdb=" O HIS H 308 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 324 through 334 Processing sheet with id= AO, first strand: chain 'I' and resid 3 through 6 removed outlier: 6.364A pdb=" N GLU I 26 " --> pdb=" O VAL I 4 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VAL I 6 " --> pdb=" O GLU I 26 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU I 28 " --> pdb=" O VAL I 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'I' and resid 78 through 81 removed outlier: 6.554A pdb=" N ILE I 61 " --> pdb=" O HIS I 79 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N VAL I 81 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP I 63 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL I 147 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N ILE I 64 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE I 149 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU I 172 " --> pdb=" O ALA I 148 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N TYR I 150 " --> pdb=" O LEU I 172 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR I 174 " --> pdb=" O TYR I 150 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL I 280 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARG I 289 " --> pdb=" O THR I 278 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N THR I 278 " --> pdb=" O ARG I 289 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N THR I 291 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N CYS I 276 " --> pdb=" O THR I 291 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N SER I 293 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N CYS I 274 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'I' and resid 189 through 192 removed outlier: 3.594A pdb=" N THR I 197 " --> pdb=" O TYR I 192 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'I' and resid 303 through 308 removed outlier: 3.866A pdb=" N THR I 437 " --> pdb=" O HIS I 308 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'I' and resid 324 through 334 Processing sheet with id= AT, first strand: chain 'J' and resid 3 through 6 removed outlier: 6.340A pdb=" N GLU J 26 " --> pdb=" O VAL J 4 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL J 6 " --> pdb=" O GLU J 26 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU J 28 " --> pdb=" O VAL J 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'J' and resid 78 through 81 removed outlier: 6.595A pdb=" N ILE J 61 " --> pdb=" O HIS J 79 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N VAL J 81 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP J 63 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL J 147 " --> pdb=" O LEU J 62 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ILE J 64 " --> pdb=" O VAL J 147 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE J 149 " --> pdb=" O ILE J 64 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU J 172 " --> pdb=" O ALA J 148 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N TYR J 150 " --> pdb=" O LEU J 172 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N TYR J 174 " --> pdb=" O TYR J 150 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N VAL J 280 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG J 289 " --> pdb=" O THR J 278 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N THR J 278 " --> pdb=" O ARG J 289 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N THR J 291 " --> pdb=" O CYS J 276 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N CYS J 276 " --> pdb=" O THR J 291 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N SER J 293 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N CYS J 274 " --> pdb=" O SER J 293 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'J' and resid 189 through 192 removed outlier: 3.618A pdb=" N THR J 197 " --> pdb=" O TYR J 192 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'J' and resid 303 through 308 removed outlier: 3.904A pdb=" N THR J 437 " --> pdb=" O HIS J 308 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'J' and resid 324 through 334 Processing sheet with id= AY, first strand: chain 'K' and resid 4 through 6 Processing sheet with id= AZ, first strand: chain 'K' and resid 77 through 81 removed outlier: 6.879A pdb=" N VAL K 147 " --> pdb=" O LEU K 62 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE K 64 " --> pdb=" O VAL K 147 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ILE K 149 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU K 172 " --> pdb=" O ALA K 148 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N TYR K 150 " --> pdb=" O LEU K 172 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR K 174 " --> pdb=" O TYR K 150 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL K 280 " --> pdb=" O VAL K 287 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ARG K 289 " --> pdb=" O THR K 278 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N THR K 278 " --> pdb=" O ARG K 289 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N THR K 291 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N CYS K 276 " --> pdb=" O THR K 291 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N SER K 293 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N CYS K 274 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'K' and resid 189 through 192 removed outlier: 3.615A pdb=" N THR K 197 " --> pdb=" O TYR K 192 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'K' and resid 303 through 308 removed outlier: 3.906A pdb=" N THR K 437 " --> pdb=" O HIS K 308 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'K' and resid 324 through 334 Processing sheet with id= BD, first strand: chain 'L' and resid 3 through 6 removed outlier: 6.379A pdb=" N GLU L 26 " --> pdb=" O VAL L 4 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VAL L 6 " --> pdb=" O GLU L 26 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N GLU L 28 " --> pdb=" O VAL L 6 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'L' and resid 78 through 81 removed outlier: 6.554A pdb=" N ILE L 61 " --> pdb=" O HIS L 79 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL L 81 " --> pdb=" O ILE L 61 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ASP L 63 " --> pdb=" O VAL L 81 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL L 147 " --> pdb=" O LEU L 62 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE L 64 " --> pdb=" O VAL L 147 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE L 149 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU L 172 " --> pdb=" O ALA L 148 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N TYR L 150 " --> pdb=" O LEU L 172 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N TYR L 174 " --> pdb=" O TYR L 150 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL L 280 " --> pdb=" O VAL L 287 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ARG L 289 " --> pdb=" O THR L 278 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N THR L 278 " --> pdb=" O ARG L 289 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N THR L 291 " --> pdb=" O CYS L 276 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N CYS L 276 " --> pdb=" O THR L 291 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER L 293 " --> pdb=" O CYS L 274 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N CYS L 274 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'L' and resid 189 through 192 removed outlier: 3.593A pdb=" N THR L 197 " --> pdb=" O TYR L 192 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'L' and resid 303 through 308 removed outlier: 3.867A pdb=" N THR L 437 " --> pdb=" O HIS L 308 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'L' and resid 324 through 334 1320 hydrogen bonds defined for protein. 3309 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: 12.96 Time building geometry restraints manager: 14.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10608 1.33 - 1.45: 6901 1.45 - 1.57: 22523 1.57 - 1.69: 60 1.69 - 1.81: 480 Bond restraints: 40572 Sorted by residual: bond pdb=" C10 7XQ B1002 " pdb=" C11 7XQ B1002 " ideal model delta sigma weight residual 1.536 1.338 0.198 2.00e-02 2.50e+03 9.80e+01 bond pdb=" C10 7XQ C1002 " pdb=" C11 7XQ C1002 " ideal model delta sigma weight residual 1.536 1.338 0.198 2.00e-02 2.50e+03 9.80e+01 bond pdb=" C10 7XQ I1002 " pdb=" C11 7XQ I1002 " ideal model delta sigma weight residual 1.536 1.338 0.198 2.00e-02 2.50e+03 9.80e+01 bond pdb=" C10 7XQ D1002 " pdb=" C11 7XQ D1002 " ideal model delta sigma weight residual 1.536 1.338 0.198 2.00e-02 2.50e+03 9.77e+01 bond pdb=" C10 7XQ F1002 " pdb=" C11 7XQ F1002 " ideal model delta sigma weight residual 1.536 1.338 0.198 2.00e-02 2.50e+03 9.77e+01 ... (remaining 40567 not shown) Histogram of bond angle deviations from ideal: 100.10 - 107.08: 1422 107.08 - 114.07: 22970 114.07 - 121.05: 18105 121.05 - 128.03: 12175 128.03 - 135.02: 324 Bond angle restraints: 54996 Sorted by residual: angle pdb=" C MET D 383 " pdb=" N ILE D 384 " pdb=" CA ILE D 384 " ideal model delta sigma weight residual 120.33 123.75 -3.42 8.00e-01 1.56e+00 1.83e+01 angle pdb=" C MET G 383 " pdb=" N ILE G 384 " pdb=" CA ILE G 384 " ideal model delta sigma weight residual 120.33 123.71 -3.38 8.00e-01 1.56e+00 1.79e+01 angle pdb=" C MET J 383 " pdb=" N ILE J 384 " pdb=" CA ILE J 384 " ideal model delta sigma weight residual 120.33 123.65 -3.32 8.00e-01 1.56e+00 1.72e+01 angle pdb=" C MET A 383 " pdb=" N ILE A 384 " pdb=" CA ILE A 384 " ideal model delta sigma weight residual 120.33 123.44 -3.11 8.00e-01 1.56e+00 1.52e+01 angle pdb=" C MET B 383 " pdb=" N ILE B 384 " pdb=" CA ILE B 384 " ideal model delta sigma weight residual 120.33 123.35 -3.02 8.00e-01 1.56e+00 1.42e+01 ... (remaining 54991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 22256 17.68 - 35.37: 2090 35.37 - 53.05: 423 53.05 - 70.73: 42 70.73 - 88.42: 29 Dihedral angle restraints: 24840 sinusoidal: 9996 harmonic: 14844 Sorted by residual: dihedral pdb=" CA GLY I 298 " pdb=" C GLY I 298 " pdb=" N LYS I 299 " pdb=" CA LYS I 299 " ideal model delta harmonic sigma weight residual 180.00 -161.37 -18.63 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA GLY J 298 " pdb=" C GLY J 298 " pdb=" N LYS J 299 " pdb=" CA LYS J 299 " ideal model delta harmonic sigma weight residual 180.00 -161.75 -18.25 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA GLY C 298 " pdb=" C GLY C 298 " pdb=" N LYS C 299 " pdb=" CA LYS C 299 " ideal model delta harmonic sigma weight residual 180.00 -162.05 -17.95 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 24837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4909 0.053 - 0.106: 1054 0.106 - 0.160: 193 0.160 - 0.213: 12 0.213 - 0.266: 24 Chirality restraints: 6192 Sorted by residual: chirality pdb=" C15 7XQ B1002 " pdb=" C13 7XQ B1002 " pdb=" C16 7XQ B1002 " pdb=" C19 7XQ B1002 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C15 7XQ K1002 " pdb=" C13 7XQ K1002 " pdb=" C16 7XQ K1002 " pdb=" C19 7XQ K1002 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" C15 7XQ D1002 " pdb=" C13 7XQ D1002 " pdb=" C16 7XQ D1002 " pdb=" C19 7XQ D1002 " both_signs ideal model delta sigma weight residual False -2.47 -2.73 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 6189 not shown) Planarity restraints: 7032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 130 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO A 131 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 131 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 131 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 130 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO D 131 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 131 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 131 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 130 " 0.045 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO F 131 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO F 131 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 131 " 0.038 5.00e-02 4.00e+02 ... (remaining 7029 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 6055 2.77 - 3.31: 34392 3.31 - 3.84: 61915 3.84 - 4.37: 73960 4.37 - 4.90: 129766 Nonbonded interactions: 306088 Sorted by model distance: nonbonded pdb=" OE2 GLU L 52 " pdb=" OH TYR L 78 " model vdw 2.242 2.440 nonbonded pdb=" OE2 GLU E 353 " pdb=" NH1 ARG F 399 " model vdw 2.245 2.520 nonbonded pdb=" OD1 ASN C 95 " pdb=" NZ LYS C 99 " model vdw 2.250 2.520 nonbonded pdb=" OE2 GLU I 52 " pdb=" OH TYR I 78 " model vdw 2.253 2.440 nonbonded pdb=" OE2 GLU F 52 " pdb=" OH TYR F 78 " model vdw 2.255 2.440 ... (remaining 306083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 235 or resid 237 through 448 or resid 1001 throu \ gh 1002)) selection = (chain 'B' and (resid 2 through 235 or resid 237 through 448 or resid 1001 throu \ gh 1002)) selection = (chain 'C' and (resid 2 through 235 or resid 237 through 448 or resid 1001 throu \ gh 1002)) selection = (chain 'D' and (resid 2 through 235 or resid 237 through 448 or resid 1001 throu \ gh 1002)) selection = (chain 'E' and (resid 2 through 235 or resid 237 through 448 or resid 1001 throu \ gh 1002)) selection = (chain 'F' and (resid 2 through 235 or resid 237 through 448 or resid 1001 throu \ gh 1002)) selection = (chain 'G' and (resid 2 through 235 or resid 237 through 448 or resid 1001 throu \ gh 1002)) selection = (chain 'H' and (resid 2 through 235 or resid 237 through 448 or resid 1001 throu \ gh 1002)) selection = (chain 'I' and (resid 2 through 235 or resid 237 through 448 or resid 1001 throu \ gh 1002)) selection = (chain 'J' and (resid 2 through 235 or resid 237 through 448 or resid 1001 throu \ gh 1002)) selection = (chain 'K' and (resid 2 through 235 or resid 237 through 448 or resid 1001 throu \ gh 1002)) selection = (chain 'L' and (resid 2 through 235 or resid 237 through 448 or resid 1001 throu \ gh 1002)) } 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=0.50 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: 4.280 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: 24.520 Check model and map are aligned: 0.610 Set scattering table: 0.370 Process input model: 124.330 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.400 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:12.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 169.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 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 : 0.007 0.198 40572 Z= 0.484 Angle : 0.692 7.982 54996 Z= 0.387 Chirality : 0.047 0.266 6192 Planarity : 0.005 0.069 7032 Dihedral : 14.007 88.418 15240 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 0.05 % Favored : 99.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.12), residues: 4992 helix: 1.23 (0.15), residues: 1416 sheet: 0.20 (0.14), residues: 1272 loop : -1.97 (0.11), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 394 HIS 0.010 0.001 HIS F 45 PHE 0.016 0.002 PHE B 25 TYR 0.017 0.001 TYR D 297 ARG 0.006 0.000 ARG K 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 556 time to evaluate : 4.473 Fit side-chains REVERT: A 123 MET cc_start: 0.6304 (mmp) cc_final: 0.5849 (mpm) REVERT: B 30 ARG cc_start: 0.5903 (ttp80) cc_final: 0.5616 (ttp80) REVERT: B 123 MET cc_start: 0.6181 (mmp) cc_final: 0.5689 (mpm) REVERT: C 30 ARG cc_start: 0.5885 (tmm-80) cc_final: 0.5290 (ttp80) REVERT: C 73 MET cc_start: 0.6942 (mmm) cc_final: 0.6681 (mmm) REVERT: D 123 MET cc_start: 0.6248 (mmp) cc_final: 0.5785 (mpm) REVERT: E 30 ARG cc_start: 0.5704 (ttp80) cc_final: 0.5428 (tmm-80) REVERT: E 123 MET cc_start: 0.6191 (mmp) cc_final: 0.5690 (mpm) REVERT: F 91 GLU cc_start: 0.7360 (mp0) cc_final: 0.7072 (mp0) REVERT: G 123 MET cc_start: 0.6308 (mmp) cc_final: 0.5821 (mpm) REVERT: H 30 ARG cc_start: 0.5914 (ttp80) cc_final: 0.5548 (ttp80) REVERT: H 123 MET cc_start: 0.6236 (mmp) cc_final: 0.5700 (mpm) REVERT: I 30 ARG cc_start: 0.5892 (tmm-80) cc_final: 0.5149 (tmm-80) REVERT: I 91 GLU cc_start: 0.7322 (mp0) cc_final: 0.7067 (mp0) REVERT: K 123 MET cc_start: 0.6220 (mmp) cc_final: 0.5728 (mpm) REVERT: L 30 ARG cc_start: 0.5818 (tmm-80) cc_final: 0.5211 (tmm-80) REVERT: L 91 GLU cc_start: 0.7458 (mp0) cc_final: 0.7247 (mp0) outliers start: 0 outliers final: 0 residues processed: 556 average time/residue: 1.8475 time to fit residues: 1207.6701 Evaluate side-chains 385 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 4.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 10.0000 chunk 382 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 130 optimal weight: 8.9990 chunk 257 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 395 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 294 optimal weight: 20.0000 chunk 457 optimal weight: 0.8980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS C 45 HIS D 37 HIS D 45 HIS E 45 HIS F 53 GLN G 37 HIS G 45 HIS H 95 ASN J 37 HIS K 45 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 40572 Z= 0.249 Angle : 0.654 7.057 54996 Z= 0.348 Chirality : 0.048 0.159 6192 Planarity : 0.006 0.067 7032 Dihedral : 5.700 56.495 5856 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.38 % Allowed : 7.42 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.11), residues: 4992 helix: 0.62 (0.15), residues: 1440 sheet: 0.20 (0.15), residues: 1200 loop : -1.94 (0.11), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 394 HIS 0.009 0.001 HIS D 37 PHE 0.019 0.002 PHE G 183 TYR 0.016 0.002 TYR B 297 ARG 0.012 0.001 ARG K 222 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 384 time to evaluate : 5.083 Fit side-chains REVERT: A 99 LYS cc_start: 0.7456 (mptp) cc_final: 0.7112 (mptp) REVERT: A 123 MET cc_start: 0.6323 (mmp) cc_final: 0.5758 (mpm) REVERT: B 91 GLU cc_start: 0.7315 (mp0) cc_final: 0.7085 (mp0) REVERT: B 123 MET cc_start: 0.6257 (mmp) cc_final: 0.5654 (mpm) REVERT: C 30 ARG cc_start: 0.6026 (tmm-80) cc_final: 0.5335 (tmm-80) REVERT: C 53 GLN cc_start: 0.8142 (tt0) cc_final: 0.7931 (tt0) REVERT: C 95 ASN cc_start: 0.8031 (t0) cc_final: 0.7313 (t0) REVERT: C 99 LYS cc_start: 0.7430 (mptp) cc_final: 0.6920 (mptp) REVERT: C 165 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7317 (tp40) REVERT: D 95 ASN cc_start: 0.8136 (t0) cc_final: 0.7883 (t0) REVERT: D 99 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7109 (mptp) REVERT: D 123 MET cc_start: 0.6352 (mmp) cc_final: 0.5788 (mpm) REVERT: E 30 ARG cc_start: 0.5926 (ttp80) cc_final: 0.5652 (ttp80) REVERT: E 95 ASN cc_start: 0.8114 (t0) cc_final: 0.7449 (t0) REVERT: E 123 MET cc_start: 0.6267 (mmp) cc_final: 0.5654 (mpm) REVERT: F 91 GLU cc_start: 0.7337 (mp0) cc_final: 0.7042 (mp0) REVERT: F 165 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7371 (tp40) REVERT: G 73 MET cc_start: 0.7090 (tpp) cc_final: 0.6569 (mmm) REVERT: G 99 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7128 (mptp) REVERT: G 123 MET cc_start: 0.6420 (mmp) cc_final: 0.5818 (mpm) REVERT: G 389 GLN cc_start: 0.7504 (OUTLIER) cc_final: 0.7274 (tm-30) REVERT: H 95 ASN cc_start: 0.8016 (t0) cc_final: 0.7749 (t0) REVERT: H 123 MET cc_start: 0.6224 (mmp) cc_final: 0.5693 (mpm) REVERT: I 30 ARG cc_start: 0.6023 (tmm-80) cc_final: 0.5334 (tmm-80) REVERT: I 91 GLU cc_start: 0.7360 (mp0) cc_final: 0.7045 (mp0) REVERT: I 165 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7359 (tp40) REVERT: J 99 LYS cc_start: 0.7234 (OUTLIER) cc_final: 0.6993 (mptp) REVERT: K 95 ASN cc_start: 0.8189 (t0) cc_final: 0.7697 (t0) REVERT: K 99 LYS cc_start: 0.7651 (mmmm) cc_final: 0.7292 (mptp) REVERT: K 123 MET cc_start: 0.6190 (mmp) cc_final: 0.5609 (mpm) REVERT: L 30 ARG cc_start: 0.5976 (tmm-80) cc_final: 0.5291 (tmm-80) REVERT: L 99 LYS cc_start: 0.7438 (mptp) cc_final: 0.7157 (mttp) REVERT: L 165 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7362 (tp40) REVERT: L 232 LYS cc_start: 0.8465 (mptm) cc_final: 0.7842 (mmmt) outliers start: 59 outliers final: 18 residues processed: 417 average time/residue: 1.7032 time to fit residues: 848.3069 Evaluate side-chains 382 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 356 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 292 MET Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 400 LYS Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 99 LYS Chi-restraints excluded: chain D residue 292 MET Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 165 GLN Chi-restraints excluded: chain F residue 389 GLN Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 389 GLN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain I residue 165 GLN Chi-restraints excluded: chain I residue 389 GLN Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain K residue 389 GLN Chi-restraints excluded: chain L residue 165 GLN Chi-restraints excluded: chain L residue 389 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 0.9980 chunk 142 optimal weight: 4.9990 chunk 380 optimal weight: 6.9990 chunk 311 optimal weight: 5.9990 chunk 126 optimal weight: 20.0000 chunk 458 optimal weight: 0.9980 chunk 495 optimal weight: 5.9990 chunk 408 optimal weight: 9.9990 chunk 454 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 367 optimal weight: 3.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 45 HIS D 45 HIS G 45 HIS I 45 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 40572 Z= 0.302 Angle : 0.681 8.654 54996 Z= 0.364 Chirality : 0.049 0.161 6192 Planarity : 0.006 0.065 7032 Dihedral : 5.801 59.367 5856 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.34 % Allowed : 8.62 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.11), residues: 4992 helix: 0.40 (0.14), residues: 1440 sheet: 0.16 (0.15), residues: 1200 loop : -1.98 (0.11), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 175 HIS 0.008 0.001 HIS C 45 PHE 0.022 0.003 PHE L 183 TYR 0.019 0.002 TYR K 297 ARG 0.006 0.001 ARG I 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 358 time to evaluate : 4.671 Fit side-chains REVERT: A 123 MET cc_start: 0.6439 (mmp) cc_final: 0.5790 (mpm) REVERT: B 30 ARG cc_start: 0.6191 (ttp80) cc_final: 0.5858 (ttp80) REVERT: B 91 GLU cc_start: 0.7356 (mp0) cc_final: 0.7084 (mp0) REVERT: B 123 MET cc_start: 0.6211 (mmp) cc_final: 0.5596 (mpm) REVERT: B 285 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.7416 (m-80) REVERT: C 30 ARG cc_start: 0.6030 (tmm-80) cc_final: 0.5314 (tmm-80) REVERT: C 53 GLN cc_start: 0.8204 (tt0) cc_final: 0.7968 (tt0) REVERT: C 165 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7297 (tp40) REVERT: C 285 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.7311 (m-80) REVERT: D 123 MET cc_start: 0.6484 (mmp) cc_final: 0.5841 (mpm) REVERT: E 95 ASN cc_start: 0.8152 (t0) cc_final: 0.7761 (t0) REVERT: E 99 LYS cc_start: 0.7306 (mptp) cc_final: 0.6877 (mptp) REVERT: E 123 MET cc_start: 0.6225 (mmp) cc_final: 0.5597 (mpm) REVERT: F 91 GLU cc_start: 0.7370 (mp0) cc_final: 0.7051 (mp0) REVERT: F 99 LYS cc_start: 0.7406 (mptp) cc_final: 0.7079 (mttp) REVERT: F 165 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7338 (tp40) REVERT: F 285 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.7293 (m-80) REVERT: G 73 MET cc_start: 0.7021 (tpp) cc_final: 0.6630 (mmm) REVERT: G 95 ASN cc_start: 0.8148 (t0) cc_final: 0.7817 (t0) REVERT: G 99 LYS cc_start: 0.7220 (mptp) cc_final: 0.6901 (mptp) REVERT: G 123 MET cc_start: 0.6460 (mmp) cc_final: 0.5786 (mpm) REVERT: G 389 GLN cc_start: 0.7514 (OUTLIER) cc_final: 0.7244 (tm-30) REVERT: H 95 ASN cc_start: 0.8075 (t0) cc_final: 0.7689 (t0) REVERT: H 232 LYS cc_start: 0.8499 (OUTLIER) cc_final: 0.8175 (mptm) REVERT: I 30 ARG cc_start: 0.6055 (tmm-80) cc_final: 0.5331 (tmm-80) REVERT: I 91 GLU cc_start: 0.7363 (mp0) cc_final: 0.7027 (mp0) REVERT: I 165 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7325 (tp40) REVERT: I 285 TYR cc_start: 0.8923 (OUTLIER) cc_final: 0.7276 (m-80) REVERT: J 99 LYS cc_start: 0.7254 (mptp) cc_final: 0.6924 (mptp) REVERT: J 285 TYR cc_start: 0.8886 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: J 400 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7920 (mttp) REVERT: K 123 MET cc_start: 0.6193 (mmp) cc_final: 0.5606 (mpm) REVERT: K 285 TYR cc_start: 0.8894 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: L 30 ARG cc_start: 0.6024 (tmm-80) cc_final: 0.5404 (tmm-80) REVERT: L 91 GLU cc_start: 0.7540 (mp0) cc_final: 0.7289 (mp0) REVERT: L 165 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7300 (tp40) REVERT: L 285 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.7250 (m-80) outliers start: 57 outliers final: 14 residues processed: 393 average time/residue: 1.6355 time to fit residues: 772.8863 Evaluate side-chains 377 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 349 time to evaluate : 4.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 165 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 389 GLN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain I residue 165 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 400 LYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 389 GLN Chi-restraints excluded: chain L residue 165 GLN Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 0.0970 chunk 344 optimal weight: 8.9990 chunk 237 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 218 optimal weight: 10.0000 chunk 307 optimal weight: 10.0000 chunk 460 optimal weight: 3.9990 chunk 487 optimal weight: 0.8980 chunk 240 optimal weight: 9.9990 chunk 436 optimal weight: 3.9990 chunk 131 optimal weight: 0.3980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 95 ASN A 389 GLN D 45 HIS D 95 ASN D 389 GLN F 95 ASN G 45 HIS I 45 HIS J 389 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40572 Z= 0.196 Angle : 0.582 10.435 54996 Z= 0.307 Chirality : 0.045 0.135 6192 Planarity : 0.005 0.062 7032 Dihedral : 5.378 53.490 5856 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.43 % Allowed : 8.80 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.11), residues: 4992 helix: 0.54 (0.15), residues: 1440 sheet: 0.15 (0.15), residues: 1200 loop : -1.93 (0.11), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 394 HIS 0.006 0.001 HIS C 45 PHE 0.016 0.002 PHE E 423 TYR 0.015 0.001 TYR B 297 ARG 0.005 0.000 ARG K 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 361 time to evaluate : 4.912 Fit side-chains REVERT: A 123 MET cc_start: 0.6412 (mmp) cc_final: 0.6185 (tpp) REVERT: A 285 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.7434 (m-80) REVERT: B 30 ARG cc_start: 0.6158 (ttp80) cc_final: 0.5812 (ttp80) REVERT: B 91 GLU cc_start: 0.7318 (mp0) cc_final: 0.7068 (mp0) REVERT: B 285 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: C 30 ARG cc_start: 0.5940 (tmm-80) cc_final: 0.5339 (ttp80) REVERT: C 53 GLN cc_start: 0.8214 (tt0) cc_final: 0.7987 (tt0) REVERT: C 99 LYS cc_start: 0.7435 (mptp) cc_final: 0.7083 (mttp) REVERT: C 285 TYR cc_start: 0.8873 (OUTLIER) cc_final: 0.7162 (m-80) REVERT: D 95 ASN cc_start: 0.8182 (t0) cc_final: 0.7886 (t0) REVERT: D 123 MET cc_start: 0.6456 (mmp) cc_final: 0.6184 (tpp) REVERT: D 285 TYR cc_start: 0.8776 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: E 30 ARG cc_start: 0.5985 (ttp80) cc_final: 0.5657 (ttp80) REVERT: E 95 ASN cc_start: 0.8109 (t0) cc_final: 0.7683 (t0) REVERT: E 99 LYS cc_start: 0.7356 (mptp) cc_final: 0.7014 (mptp) REVERT: E 285 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.7301 (m-80) REVERT: F 91 GLU cc_start: 0.7336 (mp0) cc_final: 0.7065 (mp0) REVERT: F 95 ASN cc_start: 0.8121 (t0) cc_final: 0.7772 (t0) REVERT: F 285 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: G 73 MET cc_start: 0.6916 (tpp) cc_final: 0.6581 (mmm) REVERT: G 95 ASN cc_start: 0.8102 (t0) cc_final: 0.7740 (t0) REVERT: G 99 LYS cc_start: 0.7155 (mptp) cc_final: 0.6869 (mptp) REVERT: G 123 MET cc_start: 0.6518 (mmp) cc_final: 0.6182 (tpp) REVERT: G 285 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.7431 (m-80) REVERT: G 389 GLN cc_start: 0.7490 (OUTLIER) cc_final: 0.7275 (tm-30) REVERT: H 30 ARG cc_start: 0.6191 (ttp80) cc_final: 0.5836 (ttp80) REVERT: H 95 ASN cc_start: 0.8217 (t0) cc_final: 0.7975 (t0) REVERT: H 99 LYS cc_start: 0.7046 (mptp) cc_final: 0.6728 (mptp) REVERT: H 232 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8135 (mptm) REVERT: H 285 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.7309 (m-80) REVERT: H 389 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7024 (tm-30) REVERT: I 30 ARG cc_start: 0.5949 (tmm-80) cc_final: 0.5201 (tmm-80) REVERT: I 91 GLU cc_start: 0.7358 (mp0) cc_final: 0.7090 (mp0) REVERT: I 285 TYR cc_start: 0.8880 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: J 99 LYS cc_start: 0.7162 (mptp) cc_final: 0.6904 (mptp) REVERT: J 285 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: K 123 MET cc_start: 0.6189 (mmp) cc_final: 0.5541 (mpm) REVERT: K 232 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8209 (mptm) REVERT: K 285 TYR cc_start: 0.8850 (OUTLIER) cc_final: 0.7537 (m-80) REVERT: L 30 ARG cc_start: 0.5928 (tmm-80) cc_final: 0.5252 (tmm-80) REVERT: L 91 GLU cc_start: 0.7551 (mp0) cc_final: 0.7260 (mp0) REVERT: L 285 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.7172 (m-80) outliers start: 61 outliers final: 12 residues processed: 403 average time/residue: 1.6619 time to fit residues: 797.0201 Evaluate side-chains 378 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 350 time to evaluate : 4.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 389 GLN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 232 LYS Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 389 GLN Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 4.9990 chunk 276 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 362 optimal weight: 9.9990 chunk 201 optimal weight: 0.5980 chunk 415 optimal weight: 3.9990 chunk 336 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 248 optimal weight: 0.4980 chunk 437 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 389 GLN C 19 GLN C 165 GLN D 45 HIS D 389 GLN F 19 GLN F 165 GLN G 45 HIS I 19 GLN I 165 GLN J 389 GLN L 19 GLN L 165 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 40572 Z= 0.201 Angle : 0.577 10.370 54996 Z= 0.306 Chirality : 0.045 0.137 6192 Planarity : 0.005 0.060 7032 Dihedral : 5.213 48.782 5856 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.53 % Allowed : 9.30 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.11), residues: 4992 helix: 0.58 (0.15), residues: 1440 sheet: 0.15 (0.15), residues: 1200 loop : -1.91 (0.11), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 175 HIS 0.003 0.001 HIS G 259 PHE 0.016 0.002 PHE K 423 TYR 0.015 0.001 TYR E 297 ARG 0.004 0.000 ARG I 98 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 348 time to evaluate : 4.473 Fit side-chains REVERT: A 123 MET cc_start: 0.6481 (mmp) cc_final: 0.6211 (tpp) REVERT: A 285 TYR cc_start: 0.8782 (OUTLIER) cc_final: 0.7456 (m-80) REVERT: B 30 ARG cc_start: 0.6308 (ttp80) cc_final: 0.5894 (ttp80) REVERT: B 91 GLU cc_start: 0.7300 (mp0) cc_final: 0.7025 (mp0) REVERT: B 285 TYR cc_start: 0.8867 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: C 30 ARG cc_start: 0.5941 (tmm-80) cc_final: 0.5232 (tmm-80) REVERT: C 99 LYS cc_start: 0.7434 (mptp) cc_final: 0.7221 (mttp) REVERT: C 285 TYR cc_start: 0.8872 (OUTLIER) cc_final: 0.7181 (m-80) REVERT: D 123 MET cc_start: 0.6449 (mmp) cc_final: 0.6142 (tpp) REVERT: D 285 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.7460 (m-80) REVERT: E 30 ARG cc_start: 0.6006 (ttp80) cc_final: 0.5660 (ttp80) REVERT: E 95 ASN cc_start: 0.8088 (t0) cc_final: 0.7672 (t0) REVERT: E 99 LYS cc_start: 0.7279 (mptp) cc_final: 0.6936 (mptp) REVERT: E 285 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: F 91 GLU cc_start: 0.7310 (mp0) cc_final: 0.7021 (mp0) REVERT: F 285 TYR cc_start: 0.8876 (OUTLIER) cc_final: 0.7191 (m-80) REVERT: G 26 GLU cc_start: 0.6353 (OUTLIER) cc_final: 0.5899 (pt0) REVERT: G 95 ASN cc_start: 0.8085 (t0) cc_final: 0.7669 (t0) REVERT: G 99 LYS cc_start: 0.7127 (mptp) cc_final: 0.6863 (mptp) REVERT: G 123 MET cc_start: 0.6413 (mmp) cc_final: 0.6046 (tpp) REVERT: G 285 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: G 389 GLN cc_start: 0.7482 (OUTLIER) cc_final: 0.7257 (tm-30) REVERT: H 30 ARG cc_start: 0.6266 (ttp80) cc_final: 0.5897 (ttp80) REVERT: H 285 TYR cc_start: 0.8836 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: H 389 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7014 (tm-30) REVERT: I 30 ARG cc_start: 0.5976 (tmm-80) cc_final: 0.5210 (tmm-80) REVERT: I 91 GLU cc_start: 0.7342 (mp0) cc_final: 0.7018 (mp0) REVERT: I 285 TYR cc_start: 0.8878 (OUTLIER) cc_final: 0.7194 (m-80) REVERT: J 285 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7470 (m-80) REVERT: K 123 MET cc_start: 0.6158 (mmp) cc_final: 0.5505 (mpm) REVERT: K 232 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8190 (mptm) REVERT: K 285 TYR cc_start: 0.8860 (OUTLIER) cc_final: 0.7442 (m-80) REVERT: L 30 ARG cc_start: 0.5925 (tmm-80) cc_final: 0.5238 (tmm-80) REVERT: L 91 GLU cc_start: 0.7544 (mp0) cc_final: 0.7319 (mp0) REVERT: L 285 TYR cc_start: 0.8881 (OUTLIER) cc_final: 0.7189 (m-80) outliers start: 65 outliers final: 15 residues processed: 394 average time/residue: 1.6190 time to fit residues: 765.0899 Evaluate side-chains 377 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 346 time to evaluate : 4.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 389 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 127 ASP Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain G residue 389 GLN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 15 LEU Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain K residue 389 GLN Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 3.9990 chunk 438 optimal weight: 0.0770 chunk 96 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 120 optimal weight: 0.0770 chunk 487 optimal weight: 9.9990 chunk 404 optimal weight: 0.7980 chunk 225 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 chunk 256 optimal weight: 0.3980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 95 ASN A 389 GLN B 95 ASN C 19 GLN C 165 GLN D 45 HIS D 95 ASN D 389 GLN E 19 GLN F 19 GLN F 53 GLN F 165 GLN G 45 HIS I 19 GLN I 53 GLN I 165 GLN J 95 ASN J 389 GLN K 19 GLN L 19 GLN L 53 GLN L 165 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40572 Z= 0.142 Angle : 0.522 11.786 54996 Z= 0.271 Chirality : 0.043 0.129 6192 Planarity : 0.005 0.058 7032 Dihedral : 4.815 43.661 5856 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.38 % Allowed : 9.67 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.12), residues: 4992 helix: 0.74 (0.15), residues: 1440 sheet: 0.18 (0.15), residues: 1200 loop : -1.85 (0.11), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 394 HIS 0.002 0.001 HIS A 45 PHE 0.016 0.001 PHE I 423 TYR 0.013 0.001 TYR A 297 ARG 0.004 0.000 ARG E 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 352 time to evaluate : 4.180 Fit side-chains REVERT: A 95 ASN cc_start: 0.8178 (t0) cc_final: 0.7882 (t0) REVERT: A 99 LYS cc_start: 0.7450 (mptp) cc_final: 0.7244 (mptp) REVERT: A 123 MET cc_start: 0.6433 (mmp) cc_final: 0.6143 (tpp) REVERT: A 285 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.7467 (m-80) REVERT: B 30 ARG cc_start: 0.6315 (ttp80) cc_final: 0.5877 (ttp80) REVERT: B 91 GLU cc_start: 0.7254 (mp0) cc_final: 0.7014 (mp0) REVERT: B 232 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7928 (tptm) REVERT: B 285 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7601 (m-80) REVERT: C 30 ARG cc_start: 0.5817 (tmm-80) cc_final: 0.5379 (ttp80) REVERT: C 285 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.7159 (m-80) REVERT: D 95 ASN cc_start: 0.8146 (t0) cc_final: 0.7930 (t0) REVERT: D 99 LYS cc_start: 0.7366 (mptp) cc_final: 0.7035 (mptp) REVERT: D 123 MET cc_start: 0.6406 (mmp) cc_final: 0.6082 (tpp) REVERT: D 285 TYR cc_start: 0.8725 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: E 26 GLU cc_start: 0.6040 (OUTLIER) cc_final: 0.5458 (pt0) REVERT: E 30 ARG cc_start: 0.5987 (ttp80) cc_final: 0.5605 (ttp80) REVERT: E 53 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7594 (tt0) REVERT: E 95 ASN cc_start: 0.8054 (t0) cc_final: 0.7604 (t0) REVERT: E 99 LYS cc_start: 0.7238 (mptp) cc_final: 0.6894 (mptp) REVERT: E 232 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8160 (tptm) REVERT: E 285 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7430 (m-80) REVERT: F 91 GLU cc_start: 0.7312 (mp0) cc_final: 0.7026 (mp0) REVERT: F 285 TYR cc_start: 0.8809 (OUTLIER) cc_final: 0.7172 (m-80) REVERT: G 26 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5822 (pt0) REVERT: G 99 LYS cc_start: 0.7064 (mptp) cc_final: 0.6760 (mptp) REVERT: G 123 MET cc_start: 0.6500 (mmp) cc_final: 0.6100 (tpp) REVERT: G 285 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: H 30 ARG cc_start: 0.6222 (ttp80) cc_final: 0.5841 (ttp80) REVERT: H 53 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: H 95 ASN cc_start: 0.8033 (t0) cc_final: 0.7783 (t0) REVERT: H 99 LYS cc_start: 0.6784 (mptp) cc_final: 0.6409 (mptp) REVERT: H 285 TYR cc_start: 0.8769 (OUTLIER) cc_final: 0.7437 (m-80) REVERT: H 389 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7044 (tm-30) REVERT: I 30 ARG cc_start: 0.5836 (tmm-80) cc_final: 0.5122 (ttp80) REVERT: I 91 GLU cc_start: 0.7322 (mp0) cc_final: 0.7059 (mp0) REVERT: I 285 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.7165 (m-80) REVERT: J 285 TYR cc_start: 0.8751 (OUTLIER) cc_final: 0.7494 (m-80) REVERT: K 123 MET cc_start: 0.6222 (mmp) cc_final: 0.5541 (mpm) REVERT: K 232 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7982 (tptm) REVERT: K 285 TYR cc_start: 0.8806 (OUTLIER) cc_final: 0.7484 (m-80) REVERT: L 30 ARG cc_start: 0.5895 (tmm-80) cc_final: 0.5184 (tmm-80) REVERT: L 91 GLU cc_start: 0.7546 (mp0) cc_final: 0.7293 (mp0) REVERT: L 232 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8169 (tptm) REVERT: L 285 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.7129 (m-80) outliers start: 59 outliers final: 9 residues processed: 393 average time/residue: 1.6512 time to fit residues: 775.0260 Evaluate side-chains 373 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 343 time to evaluate : 4.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 19 GLN Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 232 LYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 19 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 53 GLN Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 19 GLN Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 19 GLN Chi-restraints excluded: chain L residue 232 LYS Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 277 optimal weight: 10.0000 chunk 356 optimal weight: 0.7980 chunk 275 optimal weight: 7.9990 chunk 410 optimal weight: 0.7980 chunk 272 optimal weight: 3.9990 chunk 485 optimal weight: 1.9990 chunk 304 optimal weight: 20.0000 chunk 296 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS A 389 GLN B 389 GLN C 19 GLN C 165 GLN D 45 HIS D 389 GLN E 19 GLN F 19 GLN F 53 GLN F 165 GLN G 45 HIS H 95 ASN I 19 GLN I 165 GLN J 389 GLN K 19 GLN L 19 GLN L 53 GLN L 165 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 40572 Z= 0.162 Angle : 0.538 11.369 54996 Z= 0.279 Chirality : 0.044 0.133 6192 Planarity : 0.005 0.058 7032 Dihedral : 4.758 41.549 5856 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.27 % Allowed : 9.91 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.12), residues: 4992 helix: 0.76 (0.15), residues: 1440 sheet: 0.22 (0.15), residues: 1200 loop : -1.84 (0.11), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 394 HIS 0.002 0.001 HIS H 259 PHE 0.016 0.002 PHE E 423 TYR 0.014 0.001 TYR E 297 ARG 0.003 0.000 ARG I 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9984 Ramachandran restraints generated. 4992 Oldfield, 0 Emsley, 4992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 345 time to evaluate : 4.524 Fit side-chains REVERT: A 95 ASN cc_start: 0.8187 (t0) cc_final: 0.7972 (t0) REVERT: A 99 LYS cc_start: 0.7434 (mptp) cc_final: 0.7079 (mptp) REVERT: A 123 MET cc_start: 0.6410 (mmp) cc_final: 0.6113 (tpp) REVERT: A 285 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.7474 (m-80) REVERT: B 26 GLU cc_start: 0.6071 (OUTLIER) cc_final: 0.5544 (pt0) REVERT: B 30 ARG cc_start: 0.6272 (ttp80) cc_final: 0.5814 (ttp80) REVERT: B 91 GLU cc_start: 0.7257 (mp0) cc_final: 0.7007 (mp0) REVERT: B 232 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7946 (tptm) REVERT: B 285 TYR cc_start: 0.8814 (OUTLIER) cc_final: 0.7498 (m-80) REVERT: C 30 ARG cc_start: 0.5822 (tmm-80) cc_final: 0.5383 (ttp80) REVERT: C 285 TYR cc_start: 0.8807 (OUTLIER) cc_final: 0.7151 (m-80) REVERT: D 73 MET cc_start: 0.7025 (tpp) cc_final: 0.6650 (mmm) REVERT: D 95 ASN cc_start: 0.8198 (t0) cc_final: 0.7967 (t0) REVERT: D 99 LYS cc_start: 0.7328 (mptp) cc_final: 0.6995 (mptp) REVERT: D 123 MET cc_start: 0.6462 (mmp) cc_final: 0.6135 (tpp) REVERT: D 285 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: E 26 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5428 (pt0) REVERT: E 30 ARG cc_start: 0.5993 (ttp80) cc_final: 0.5608 (ttp80) REVERT: E 53 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7612 (tt0) REVERT: E 95 ASN cc_start: 0.8068 (t0) cc_final: 0.7622 (t0) REVERT: E 99 LYS cc_start: 0.7224 (mptp) cc_final: 0.6894 (mptp) REVERT: E 285 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: F 30 ARG cc_start: 0.5797 (tmm-80) cc_final: 0.5086 (tmm-80) REVERT: F 91 GLU cc_start: 0.7321 (mp0) cc_final: 0.7102 (mp0) REVERT: F 285 TYR cc_start: 0.8811 (OUTLIER) cc_final: 0.7157 (m-80) REVERT: G 26 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5813 (pt0) REVERT: G 73 MET cc_start: 0.6901 (tpp) cc_final: 0.6465 (mmm) REVERT: G 123 MET cc_start: 0.6498 (mmp) cc_final: 0.6088 (tpp) REVERT: G 285 TYR cc_start: 0.8735 (OUTLIER) cc_final: 0.7465 (m-80) REVERT: H 30 ARG cc_start: 0.6262 (ttp80) cc_final: 0.5846 (ttp80) REVERT: H 53 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7602 (tt0) REVERT: H 285 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.7352 (m-80) REVERT: H 389 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: I 30 ARG cc_start: 0.5824 (tmm-80) cc_final: 0.5109 (ttp80) REVERT: I 91 GLU cc_start: 0.7298 (mp0) cc_final: 0.7037 (mp0) REVERT: I 285 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.7155 (m-80) REVERT: J 285 TYR cc_start: 0.8774 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: K 123 MET cc_start: 0.6256 (mmp) cc_final: 0.5570 (mpm) REVERT: K 232 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7969 (tptm) REVERT: K 285 TYR cc_start: 0.8813 (OUTLIER) cc_final: 0.7394 (m-80) REVERT: L 30 ARG cc_start: 0.5899 (tmm-80) cc_final: 0.5184 (tmm-80) REVERT: L 91 GLU cc_start: 0.7555 (mp0) cc_final: 0.7298 (mp0) REVERT: L 232 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8140 (tptm) REVERT: L 285 TYR cc_start: 0.8826 (OUTLIER) cc_final: 0.7182 (m-80) outliers start: 54 outliers final: 8 residues processed: 388 average time/residue: 1.6619 time to fit residues: 770.0062 Evaluate side-chains 374 residues out of total 4308 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 345 time to evaluate : 4.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain B residue 232 LYS Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 53 GLN Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain F residue 19 GLN Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 53 GLN Chi-restraints excluded: chain H residue 285 TYR Chi-restraints excluded: chain H residue 389 GLN Chi-restraints excluded: chain I residue 19 GLN Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 45 HIS Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain K residue 285 TYR Chi-restraints excluded: chain L residue 19 GLN Chi-restraints excluded: chain L residue 232 LYS Chi-restraints excluded: chain L residue 285 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.5006 > 50: distance: 29 - 36: 35.723 distance: 37 - 38: 6.922 distance: 37 - 40: 55.479 distance: 38 - 39: 51.953 distance: 38 - 45: 40.122 distance: 40 - 41: 57.809 distance: 42 - 43: 41.052 distance: 42 - 44: 56.036 distance: 45 - 46: 40.693 distance: 46 - 47: 40.951 distance: 46 - 49: 57.007 distance: 47 - 48: 39.763 distance: 47 - 52: 4.219 distance: 49 - 50: 69.856 distance: 49 - 51: 67.849 distance: 52 - 53: 6.878 distance: 53 - 54: 56.509 distance: 53 - 56: 41.232 distance: 54 - 55: 56.623 distance: 54 - 59: 57.120 distance: 56 - 57: 55.768 distance: 56 - 58: 56.989 distance: 59 - 60: 44.004 distance: 59 - 65: 17.616 distance: 60 - 61: 44.980 distance: 60 - 63: 43.613 distance: 61 - 66: 55.414 distance: 64 - 65: 21.629 distance: 67 - 70: 56.610 distance: 68 - 69: 39.374 distance: 70 - 71: 13.362 distance: 71 - 72: 31.427 distance: 71 - 73: 18.615 distance: 74 - 75: 7.997 distance: 75 - 76: 7.086 distance: 75 - 78: 50.745 distance: 76 - 77: 40.281 distance: 76 - 82: 39.046 distance: 78 - 79: 39.696 distance: 79 - 81: 39.298 distance: 82 - 83: 39.845 distance: 83 - 84: 53.032 distance: 83 - 86: 26.957 distance: 84 - 85: 6.395 distance: 84 - 92: 45.943 distance: 86 - 87: 42.229 distance: 87 - 88: 12.084 distance: 87 - 89: 44.777 distance: 88 - 90: 42.792 distance: 89 - 91: 22.466 distance: 90 - 91: 61.285 distance: 92 - 93: 13.843 distance: 93 - 94: 19.698 distance: 93 - 96: 55.871 distance: 94 - 95: 37.424 distance: 94 - 97: 37.325 distance: 97 - 98: 17.634 distance: 98 - 99: 21.471 distance: 98 - 101: 17.201 distance: 101 - 102: 10.573 distance: 102 - 103: 46.178 distance: 102 - 104: 41.348 distance: 105 - 106: 16.196 distance: 106 - 107: 21.228 distance: 106 - 109: 35.050 distance: 107 - 108: 40.663 distance: 107 - 110: 28.418 distance: 108 - 130: 36.290