Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 19 01:09:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4m_25680/10_2023/7t4m_25680.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4m_25680/10_2023/7t4m_25680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4m_25680/10_2023/7t4m_25680.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4m_25680/10_2023/7t4m_25680.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4m_25680/10_2023/7t4m_25680.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4m_25680/10_2023/7t4m_25680.pdb" } resolution = 2.48 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= 0.002 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 264 5.16 5 C 25002 2.51 5 N 6576 2.21 5 O 7212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 123": "OE1" <-> "OE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A GLU 441": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B ASP 379": "OD1" <-> "OD2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "C GLU 123": "OE1" <-> "OE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 376": "OE1" <-> "OE2" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C GLU 547": "OE1" <-> "OE2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "D TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 199": "OD1" <-> "OD2" Residue "D TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "D ASP 379": "OD1" <-> "OD2" Residue "D GLU 440": "OE1" <-> "OE2" Residue "D GLU 501": "OE1" <-> "OE2" Residue "E GLU 123": "OE1" <-> "OE2" Residue "E TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 376": "OE1" <-> "OE2" Residue "E GLU 441": "OE1" <-> "OE2" Residue "E GLU 547": "OE1" <-> "OE2" Residue "F GLU 149": "OE1" <-> "OE2" Residue "F TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 199": "OD1" <-> "OD2" Residue "F TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 376": "OE1" <-> "OE2" Residue "F ASP 379": "OD1" <-> "OD2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F GLU 501": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "G TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 376": "OE1" <-> "OE2" Residue "G GLU 441": "OE1" <-> "OE2" Residue "G GLU 547": "OE1" <-> "OE2" Residue "H GLU 149": "OE1" <-> "OE2" Residue "H TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 199": "OD1" <-> "OD2" Residue "H TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 376": "OE1" <-> "OE2" Residue "H ASP 379": "OD1" <-> "OD2" Residue "H GLU 440": "OE1" <-> "OE2" Residue "H GLU 501": "OE1" <-> "OE2" Residue "I GLU 123": "OE1" <-> "OE2" Residue "I TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 376": "OE1" <-> "OE2" Residue "I GLU 441": "OE1" <-> "OE2" Residue "I GLU 547": "OE1" <-> "OE2" Residue "J GLU 149": "OE1" <-> "OE2" Residue "J TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 199": "OD1" <-> "OD2" Residue "J TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 376": "OE1" <-> "OE2" Residue "J ASP 379": "OD1" <-> "OD2" Residue "J GLU 440": "OE1" <-> "OE2" Residue "J GLU 501": "OE1" <-> "OE2" Residue "K GLU 123": "OE1" <-> "OE2" Residue "K TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 376": "OE1" <-> "OE2" Residue "K GLU 441": "OE1" <-> "OE2" Residue "K GLU 547": "OE1" <-> "OE2" Residue "L GLU 149": "OE1" <-> "OE2" Residue "L TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 199": "OD1" <-> "OD2" Residue "L TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 376": "OE1" <-> "OE2" Residue "L ASP 379": "OD1" <-> "OD2" Residue "L GLU 440": "OE1" <-> "OE2" Residue "L GLU 501": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 39054 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3331 Chain: "B" Number of atoms: 3222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3265 Chain: "C" Number of atoms: 3287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3331 Chain: "D" Number of atoms: 3222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3265 Chain: "E" Number of atoms: 3287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3331 Chain: "F" Number of atoms: 3222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3265 Chain: "G" Number of atoms: 3287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3331 Chain: "H" Number of atoms: 3222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3265 Chain: "I" Number of atoms: 3287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3331 Chain: "J" Number of atoms: 3222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3265 Chain: "K" Number of atoms: 3287 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 Conformer: "B" Number of residues, atoms: 408, 3278 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 389} Chain breaks: 4 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 18 bond proxies already assigned to first conformer: 3331 Chain: "L" Number of atoms: 3222 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 401, 3213 Classifications: {'peptide': 401} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 18, 'TRANS': 382} Chain breaks: 4 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 3265 Time building chain proxies: 35.81, per 1000 atoms: 0.92 Number of scatterers: 39054 At special positions: 0 Unit cell: (164.101, 162.435, 124.117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 264 16.00 O 7212 8.00 N 6576 7.00 C 25002 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.14 Conformation dependent library (CDL) restraints added in 10.7 seconds 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9444 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 48 sheets defined 45.7% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'A' and resid 119 through 137 Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 307 through 328 removed outlier: 3.631A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 357 through 361 removed outlier: 4.529A pdb=" N CYS A 360 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 406 through 420 removed outlier: 3.533A pdb=" N ALA A 414 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 471 through 485 Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.770A pdb=" N LEU A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 517 removed outlier: 3.503A pdb=" N LYS A 512 " --> pdb=" O CYS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 557 through 574 removed outlier: 3.945A pdb=" N HIS A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 137 removed outlier: 4.396A pdb=" N GLY B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.636A pdb=" N HIS B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 4.465A pdb=" N CYS B 360 " --> pdb=" O ALA B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.597A pdb=" N GLY B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA B 414 " --> pdb=" O TRP B 410 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 471 through 485 Processing helix chain 'B' and resid 486 through 491 removed outlier: 3.573A pdb=" N LEU B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 516 Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 557 through 574 Processing helix chain 'C' and resid 119 through 137 Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 203 through 215 Processing helix chain 'C' and resid 229 through 233 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 307 through 328 removed outlier: 3.630A pdb=" N HIS C 328 " --> pdb=" O HIS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 338 No H-bonds generated for 'chain 'C' and resid 336 through 338' Processing helix chain 'C' and resid 357 through 361 removed outlier: 4.528A pdb=" N CYS C 360 " --> pdb=" O ALA C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 393 Processing helix chain 'C' and resid 406 through 420 removed outlier: 3.532A pdb=" N ALA C 414 " --> pdb=" O TRP C 410 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU C 418 " --> pdb=" O ALA C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 462 Processing helix chain 'C' and resid 471 through 485 Processing helix chain 'C' and resid 486 through 491 removed outlier: 3.769A pdb=" N LEU C 490 " --> pdb=" O PRO C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 517 removed outlier: 3.502A pdb=" N LYS C 512 " --> pdb=" O CYS C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 554 Processing helix chain 'C' and resid 557 through 574 removed outlier: 3.945A pdb=" N HIS C 572 " --> pdb=" O ILE C 568 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 137 removed outlier: 4.395A pdb=" N GLY D 126 " --> pdb=" O ASP D 122 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 203 through 215 Processing helix chain 'D' and resid 297 through 304 Processing helix chain 'D' and resid 307 through 328 removed outlier: 3.636A pdb=" N HIS D 328 " --> pdb=" O HIS D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 357 through 361 removed outlier: 4.466A pdb=" N CYS D 360 " --> pdb=" O ALA D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 393 Processing helix chain 'D' and resid 406 through 420 removed outlier: 3.598A pdb=" N GLY D 413 " --> pdb=" O LEU D 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA D 414 " --> pdb=" O TRP D 410 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR D 417 " --> pdb=" O GLY D 413 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 451 through 462 Processing helix chain 'D' and resid 471 through 485 Processing helix chain 'D' and resid 486 through 491 removed outlier: 3.573A pdb=" N LEU D 490 " --> pdb=" O PRO D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 516 Processing helix chain 'D' and resid 542 through 554 Processing helix chain 'D' and resid 557 through 574 Processing helix chain 'E' and resid 119 through 137 Processing helix chain 'E' and resid 148 through 152 Processing helix chain 'E' and resid 155 through 159 Processing helix chain 'E' and resid 203 through 215 Processing helix chain 'E' and resid 229 through 233 Processing helix chain 'E' and resid 297 through 304 Processing helix chain 'E' and resid 307 through 328 removed outlier: 3.630A pdb=" N HIS E 328 " --> pdb=" O HIS E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 338 No H-bonds generated for 'chain 'E' and resid 336 through 338' Processing helix chain 'E' and resid 357 through 361 removed outlier: 4.527A pdb=" N CYS E 360 " --> pdb=" O ALA E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 393 Processing helix chain 'E' and resid 406 through 420 removed outlier: 3.533A pdb=" N ALA E 414 " --> pdb=" O TRP E 410 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR E 417 " --> pdb=" O GLY E 413 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU E 418 " --> pdb=" O ALA E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 462 Processing helix chain 'E' and resid 471 through 485 Processing helix chain 'E' and resid 486 through 491 removed outlier: 3.770A pdb=" N LEU E 490 " --> pdb=" O PRO E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 517 removed outlier: 3.502A pdb=" N LYS E 512 " --> pdb=" O CYS E 508 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 554 Processing helix chain 'E' and resid 557 through 574 removed outlier: 3.945A pdb=" N HIS E 572 " --> pdb=" O ILE E 568 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 137 removed outlier: 4.395A pdb=" N GLY F 126 " --> pdb=" O ASP F 122 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE F 127 " --> pdb=" O GLU F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 152 Processing helix chain 'F' and resid 155 through 159 Processing helix chain 'F' and resid 203 through 215 Processing helix chain 'F' and resid 297 through 304 Processing helix chain 'F' and resid 307 through 328 removed outlier: 3.635A pdb=" N HIS F 328 " --> pdb=" O HIS F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 361 removed outlier: 4.465A pdb=" N CYS F 360 " --> pdb=" O ALA F 357 " (cutoff:3.500A) Processing helix chain 'F' and resid 388 through 393 Processing helix chain 'F' and resid 406 through 420 removed outlier: 3.598A pdb=" N GLY F 413 " --> pdb=" O LEU F 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA F 414 " --> pdb=" O TRP F 410 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR F 417 " --> pdb=" O GLY F 413 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU F 418 " --> pdb=" O ALA F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 451 through 462 Processing helix chain 'F' and resid 471 through 485 Processing helix chain 'F' and resid 486 through 491 removed outlier: 3.572A pdb=" N LEU F 490 " --> pdb=" O PRO F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 516 Processing helix chain 'F' and resid 542 through 554 Processing helix chain 'F' and resid 557 through 574 Processing helix chain 'G' and resid 119 through 137 Processing helix chain 'G' and resid 148 through 152 Processing helix chain 'G' and resid 155 through 159 Processing helix chain 'G' and resid 203 through 215 Processing helix chain 'G' and resid 229 through 233 Processing helix chain 'G' and resid 297 through 304 Processing helix chain 'G' and resid 307 through 328 removed outlier: 3.631A pdb=" N HIS G 328 " --> pdb=" O HIS G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 338 No H-bonds generated for 'chain 'G' and resid 336 through 338' Processing helix chain 'G' and resid 357 through 361 removed outlier: 4.528A pdb=" N CYS G 360 " --> pdb=" O ALA G 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 393 Processing helix chain 'G' and resid 406 through 420 removed outlier: 3.532A pdb=" N ALA G 414 " --> pdb=" O TRP G 410 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR G 417 " --> pdb=" O GLY G 413 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 462 Processing helix chain 'G' and resid 471 through 485 Processing helix chain 'G' and resid 486 through 491 removed outlier: 3.770A pdb=" N LEU G 490 " --> pdb=" O PRO G 486 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 517 removed outlier: 3.503A pdb=" N LYS G 512 " --> pdb=" O CYS G 508 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 554 Processing helix chain 'G' and resid 557 through 574 removed outlier: 3.945A pdb=" N HIS G 572 " --> pdb=" O ILE G 568 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 137 removed outlier: 4.395A pdb=" N GLY H 126 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ILE H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 152 Processing helix chain 'H' and resid 155 through 159 Processing helix chain 'H' and resid 203 through 215 Processing helix chain 'H' and resid 297 through 304 Processing helix chain 'H' and resid 307 through 328 removed outlier: 3.636A pdb=" N HIS H 328 " --> pdb=" O HIS H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 361 removed outlier: 4.465A pdb=" N CYS H 360 " --> pdb=" O ALA H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 393 Processing helix chain 'H' and resid 406 through 420 removed outlier: 3.599A pdb=" N GLY H 413 " --> pdb=" O LEU H 409 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA H 414 " --> pdb=" O TRP H 410 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR H 417 " --> pdb=" O GLY H 413 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU H 418 " --> pdb=" O ALA H 414 " (cutoff:3.500A) Processing helix chain 'H' and resid 451 through 462 Processing helix chain 'H' and resid 471 through 485 Processing helix chain 'H' and resid 486 through 491 removed outlier: 3.573A pdb=" N LEU H 490 " --> pdb=" O PRO H 486 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 516 Processing helix chain 'H' and resid 542 through 554 Processing helix chain 'H' and resid 557 through 574 Processing helix chain 'I' and resid 119 through 137 Processing helix chain 'I' and resid 148 through 152 Processing helix chain 'I' and resid 155 through 159 Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 229 through 233 Processing helix chain 'I' and resid 297 through 304 Processing helix chain 'I' and resid 307 through 328 removed outlier: 3.630A pdb=" N HIS I 328 " --> pdb=" O HIS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 336 through 338 No H-bonds generated for 'chain 'I' and resid 336 through 338' Processing helix chain 'I' and resid 357 through 361 removed outlier: 4.528A pdb=" N CYS I 360 " --> pdb=" O ALA I 357 " (cutoff:3.500A) Processing helix chain 'I' and resid 388 through 393 Processing helix chain 'I' and resid 406 through 420 removed outlier: 3.533A pdb=" N ALA I 414 " --> pdb=" O TRP I 410 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR I 417 " --> pdb=" O GLY I 413 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU I 418 " --> pdb=" O ALA I 414 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 462 Processing helix chain 'I' and resid 471 through 485 Processing helix chain 'I' and resid 486 through 491 removed outlier: 3.770A pdb=" N LEU I 490 " --> pdb=" O PRO I 486 " (cutoff:3.500A) Processing helix chain 'I' and resid 498 through 517 removed outlier: 3.502A pdb=" N LYS I 512 " --> pdb=" O CYS I 508 " (cutoff:3.500A) Processing helix chain 'I' and resid 542 through 554 Processing helix chain 'I' and resid 557 through 574 removed outlier: 3.945A pdb=" N HIS I 572 " --> pdb=" O ILE I 568 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 137 removed outlier: 4.395A pdb=" N GLY J 126 " --> pdb=" O ASP J 122 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE J 127 " --> pdb=" O GLU J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 152 Processing helix chain 'J' and resid 155 through 159 Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 297 through 304 Processing helix chain 'J' and resid 307 through 328 removed outlier: 3.636A pdb=" N HIS J 328 " --> pdb=" O HIS J 324 " (cutoff:3.500A) Processing helix chain 'J' and resid 357 through 361 removed outlier: 4.465A pdb=" N CYS J 360 " --> pdb=" O ALA J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 388 through 393 Processing helix chain 'J' and resid 406 through 420 removed outlier: 3.597A pdb=" N GLY J 413 " --> pdb=" O LEU J 409 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA J 414 " --> pdb=" O TRP J 410 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR J 417 " --> pdb=" O GLY J 413 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU J 418 " --> pdb=" O ALA J 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 451 through 462 Processing helix chain 'J' and resid 471 through 485 Processing helix chain 'J' and resid 486 through 491 removed outlier: 3.572A pdb=" N LEU J 490 " --> pdb=" O PRO J 486 " (cutoff:3.500A) Processing helix chain 'J' and resid 498 through 516 Processing helix chain 'J' and resid 542 through 554 Processing helix chain 'J' and resid 557 through 574 Processing helix chain 'K' and resid 119 through 137 Processing helix chain 'K' and resid 148 through 152 Processing helix chain 'K' and resid 155 through 159 Processing helix chain 'K' and resid 203 through 215 Processing helix chain 'K' and resid 229 through 233 Processing helix chain 'K' and resid 297 through 304 Processing helix chain 'K' and resid 307 through 328 removed outlier: 3.630A pdb=" N HIS K 328 " --> pdb=" O HIS K 324 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 338 No H-bonds generated for 'chain 'K' and resid 336 through 338' Processing helix chain 'K' and resid 357 through 361 removed outlier: 4.528A pdb=" N CYS K 360 " --> pdb=" O ALA K 357 " (cutoff:3.500A) Processing helix chain 'K' and resid 388 through 393 Processing helix chain 'K' and resid 406 through 420 removed outlier: 3.533A pdb=" N ALA K 414 " --> pdb=" O TRP K 410 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR K 417 " --> pdb=" O GLY K 413 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU K 418 " --> pdb=" O ALA K 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 451 through 462 Processing helix chain 'K' and resid 471 through 485 Processing helix chain 'K' and resid 486 through 491 removed outlier: 3.770A pdb=" N LEU K 490 " --> pdb=" O PRO K 486 " (cutoff:3.500A) Processing helix chain 'K' and resid 498 through 517 removed outlier: 3.503A pdb=" N LYS K 512 " --> pdb=" O CYS K 508 " (cutoff:3.500A) Processing helix chain 'K' and resid 542 through 554 Processing helix chain 'K' and resid 557 through 574 removed outlier: 3.945A pdb=" N HIS K 572 " --> pdb=" O ILE K 568 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 137 removed outlier: 4.395A pdb=" N GLY L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE L 127 " --> pdb=" O GLU L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 152 Processing helix chain 'L' and resid 155 through 159 Processing helix chain 'L' and resid 203 through 215 Processing helix chain 'L' and resid 297 through 304 Processing helix chain 'L' and resid 307 through 328 removed outlier: 3.635A pdb=" N HIS L 328 " --> pdb=" O HIS L 324 " (cutoff:3.500A) Processing helix chain 'L' and resid 357 through 361 removed outlier: 4.466A pdb=" N CYS L 360 " --> pdb=" O ALA L 357 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 393 Processing helix chain 'L' and resid 406 through 420 removed outlier: 3.597A pdb=" N GLY L 413 " --> pdb=" O LEU L 409 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA L 414 " --> pdb=" O TRP L 410 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR L 417 " --> pdb=" O GLY L 413 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU L 418 " --> pdb=" O ALA L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 462 Processing helix chain 'L' and resid 471 through 485 Processing helix chain 'L' and resid 486 through 491 removed outlier: 3.573A pdb=" N LEU L 490 " --> pdb=" O PRO L 486 " (cutoff:3.500A) Processing helix chain 'L' and resid 498 through 516 Processing helix chain 'L' and resid 542 through 554 Processing helix chain 'L' and resid 557 through 574 Processing sheet with id=AA1, first strand: chain 'A' and resid 165 through 166 removed outlier: 3.541A pdb=" N SER A 251 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS A 291 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET A 249 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 254 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 295 through 296 removed outlier: 3.577A pdb=" N CYS A 295 " --> pdb=" O VAL A 342 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 372 Processing sheet with id=AA5, first strand: chain 'B' and resid 165 through 167 removed outlier: 3.589A pdb=" N SER B 251 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS B 291 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET B 249 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 254 " --> pdb=" O PHE B 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AA7, first strand: chain 'B' and resid 330 through 331 Processing sheet with id=AA8, first strand: chain 'B' and resid 370 through 372 Processing sheet with id=AA9, first strand: chain 'C' and resid 165 through 166 removed outlier: 3.541A pdb=" N SER C 251 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS C 291 " --> pdb=" O MET C 249 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET C 249 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 254 " --> pdb=" O PHE C 222 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 295 through 296 removed outlier: 3.576A pdb=" N CYS C 295 " --> pdb=" O VAL C 342 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 330 through 331 Processing sheet with id=AB3, first strand: chain 'C' and resid 370 through 372 Processing sheet with id=AB4, first strand: chain 'D' and resid 165 through 167 removed outlier: 3.589A pdb=" N SER D 251 " --> pdb=" O VAL D 289 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS D 291 " --> pdb=" O MET D 249 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET D 249 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA D 254 " --> pdb=" O PHE D 222 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 295 through 296 Processing sheet with id=AB6, first strand: chain 'D' and resid 330 through 331 Processing sheet with id=AB7, first strand: chain 'D' and resid 370 through 372 Processing sheet with id=AB8, first strand: chain 'E' and resid 165 through 166 removed outlier: 3.541A pdb=" N SER E 251 " --> pdb=" O VAL E 289 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N LYS E 291 " --> pdb=" O MET E 249 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET E 249 " --> pdb=" O LYS E 291 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 254 " --> pdb=" O PHE E 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 295 through 296 removed outlier: 3.576A pdb=" N CYS E 295 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 330 through 331 Processing sheet with id=AC2, first strand: chain 'E' and resid 370 through 372 Processing sheet with id=AC3, first strand: chain 'F' and resid 165 through 167 removed outlier: 3.589A pdb=" N SER F 251 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS F 291 " --> pdb=" O MET F 249 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET F 249 " --> pdb=" O LYS F 291 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA F 254 " --> pdb=" O PHE F 222 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 295 through 296 Processing sheet with id=AC5, first strand: chain 'F' and resid 330 through 331 Processing sheet with id=AC6, first strand: chain 'F' and resid 370 through 372 Processing sheet with id=AC7, first strand: chain 'G' and resid 165 through 166 removed outlier: 3.541A pdb=" N SER G 251 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LYS G 291 " --> pdb=" O MET G 249 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET G 249 " --> pdb=" O LYS G 291 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA G 254 " --> pdb=" O PHE G 222 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 295 through 296 removed outlier: 3.577A pdb=" N CYS G 295 " --> pdb=" O VAL G 342 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 330 through 331 Processing sheet with id=AD1, first strand: chain 'G' and resid 370 through 372 Processing sheet with id=AD2, first strand: chain 'H' and resid 165 through 167 removed outlier: 3.589A pdb=" N SER H 251 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS H 291 " --> pdb=" O MET H 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET H 249 " --> pdb=" O LYS H 291 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA H 254 " --> pdb=" O PHE H 222 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 295 through 296 Processing sheet with id=AD4, first strand: chain 'H' and resid 330 through 331 Processing sheet with id=AD5, first strand: chain 'H' and resid 370 through 372 Processing sheet with id=AD6, first strand: chain 'I' and resid 165 through 166 removed outlier: 3.540A pdb=" N SER I 251 " --> pdb=" O VAL I 289 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS I 291 " --> pdb=" O MET I 249 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET I 249 " --> pdb=" O LYS I 291 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA I 254 " --> pdb=" O PHE I 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 295 through 296 removed outlier: 3.577A pdb=" N CYS I 295 " --> pdb=" O VAL I 342 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 330 through 331 Processing sheet with id=AD9, first strand: chain 'I' and resid 370 through 372 Processing sheet with id=AE1, first strand: chain 'J' and resid 165 through 167 removed outlier: 3.589A pdb=" N SER J 251 " --> pdb=" O VAL J 289 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS J 291 " --> pdb=" O MET J 249 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET J 249 " --> pdb=" O LYS J 291 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA J 254 " --> pdb=" O PHE J 222 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 295 through 296 Processing sheet with id=AE3, first strand: chain 'J' and resid 330 through 331 Processing sheet with id=AE4, first strand: chain 'J' and resid 370 through 372 Processing sheet with id=AE5, first strand: chain 'K' and resid 165 through 166 removed outlier: 3.541A pdb=" N SER K 251 " --> pdb=" O VAL K 289 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS K 291 " --> pdb=" O MET K 249 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET K 249 " --> pdb=" O LYS K 291 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA K 254 " --> pdb=" O PHE K 222 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 295 through 296 removed outlier: 3.576A pdb=" N CYS K 295 " --> pdb=" O VAL K 342 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 330 through 331 Processing sheet with id=AE8, first strand: chain 'K' and resid 370 through 372 Processing sheet with id=AE9, first strand: chain 'L' and resid 165 through 167 removed outlier: 3.590A pdb=" N SER L 251 " --> pdb=" O VAL L 289 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LYS L 291 " --> pdb=" O MET L 249 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N MET L 249 " --> pdb=" O LYS L 291 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA L 254 " --> pdb=" O PHE L 222 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 295 through 296 Processing sheet with id=AF2, first strand: chain 'L' and resid 330 through 331 Processing sheet with id=AF3, first strand: chain 'L' and resid 370 through 372 1770 hydrogen bonds defined for protein. 4920 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: 13.90 Time building geometry restraints manager: 15.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 12606 1.34 - 1.46: 8664 1.46 - 1.58: 18162 1.58 - 1.69: 0 1.69 - 1.81: 408 Bond restraints: 39840 Sorted by residual: bond pdb=" C GLU F 346 " pdb=" N GLY F 347 " ideal model delta sigma weight residual 1.321 1.331 -0.009 1.24e-02 6.50e+03 5.55e-01 bond pdb=" C GLU B 346 " pdb=" N GLY B 347 " ideal model delta sigma weight residual 1.321 1.330 -0.009 1.24e-02 6.50e+03 5.34e-01 bond pdb=" C GLU H 346 " pdb=" N GLY H 347 " ideal model delta sigma weight residual 1.321 1.330 -0.009 1.24e-02 6.50e+03 5.23e-01 bond pdb=" C GLU J 346 " pdb=" N GLY J 347 " ideal model delta sigma weight residual 1.321 1.330 -0.009 1.24e-02 6.50e+03 5.05e-01 bond pdb=" C GLU D 346 " pdb=" N GLY D 347 " ideal model delta sigma weight residual 1.321 1.330 -0.009 1.24e-02 6.50e+03 4.98e-01 ... (remaining 39835 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.09: 1176 107.09 - 113.82: 22429 113.82 - 120.54: 15783 120.54 - 127.27: 14114 127.27 - 133.99: 444 Bond angle restraints: 53946 Sorted by residual: angle pdb=" N ILE L 257 " pdb=" CA ILE L 257 " pdb=" C ILE L 257 " ideal model delta sigma weight residual 107.60 109.64 -2.04 1.07e+00 8.73e-01 3.65e+00 angle pdb=" N ILE B 257 " pdb=" CA ILE B 257 " pdb=" C ILE B 257 " ideal model delta sigma weight residual 107.60 109.62 -2.02 1.07e+00 8.73e-01 3.56e+00 angle pdb=" N ILE F 257 " pdb=" CA ILE F 257 " pdb=" C ILE F 257 " ideal model delta sigma weight residual 107.60 109.62 -2.02 1.07e+00 8.73e-01 3.55e+00 angle pdb=" N ILE H 257 " pdb=" CA ILE H 257 " pdb=" C ILE H 257 " ideal model delta sigma weight residual 107.60 109.60 -2.00 1.07e+00 8.73e-01 3.49e+00 angle pdb=" N ILE D 257 " pdb=" CA ILE D 257 " pdb=" C ILE D 257 " ideal model delta sigma weight residual 107.60 109.57 -1.97 1.07e+00 8.73e-01 3.39e+00 ... (remaining 53941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 23448 17.61 - 35.21: 798 35.21 - 52.82: 102 52.82 - 70.42: 42 70.42 - 88.03: 24 Dihedral angle restraints: 24414 sinusoidal: 9930 harmonic: 14484 Sorted by residual: dihedral pdb=" CB GLU G 123 " pdb=" CG GLU G 123 " pdb=" CD GLU G 123 " pdb=" OE1 GLU G 123 " ideal model delta sinusoidal sigma weight residual 0.00 88.03 -88.03 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU C 123 " pdb=" CG GLU C 123 " pdb=" CD GLU C 123 " pdb=" OE1 GLU C 123 " ideal model delta sinusoidal sigma weight residual 0.00 88.02 -88.02 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU E 123 " pdb=" CG GLU E 123 " pdb=" CD GLU E 123 " pdb=" OE1 GLU E 123 " ideal model delta sinusoidal sigma weight residual 0.00 88.01 -88.01 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 24411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3970 0.029 - 0.057: 1478 0.057 - 0.086: 360 0.086 - 0.114: 218 0.114 - 0.143: 58 Chirality restraints: 6084 Sorted by residual: chirality pdb=" CA ILE J 450 " pdb=" N ILE J 450 " pdb=" C ILE J 450 " pdb=" CB ILE J 450 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA ILE B 450 " pdb=" N ILE B 450 " pdb=" C ILE B 450 " pdb=" CB ILE B 450 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.82e-01 chirality pdb=" CA ILE L 450 " pdb=" N ILE L 450 " pdb=" C ILE L 450 " pdb=" CB ILE L 450 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 6081 not shown) Planarity restraints: 6846 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE K 450 " -0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO K 451 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO K 451 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO K 451 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE I 450 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO I 451 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO I 451 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO I 451 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 450 " -0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO D 451 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 451 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 451 " -0.018 5.00e-02 4.00e+02 ... (remaining 6843 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 7896 2.78 - 3.31: 37699 3.31 - 3.84: 65046 3.84 - 4.37: 81568 4.37 - 4.90: 137599 Nonbonded interactions: 329808 Sorted by model distance: nonbonded pdb=" O THR G 215 " pdb=" OH TYR G 221 " model vdw 2.253 2.440 nonbonded pdb=" O THR A 215 " pdb=" OH TYR A 221 " model vdw 2.253 2.440 nonbonded pdb=" O THR K 215 " pdb=" OH TYR K 221 " model vdw 2.254 2.440 nonbonded pdb=" O THR E 215 " pdb=" OH TYR E 221 " model vdw 2.254 2.440 nonbonded pdb=" O THR I 215 " pdb=" OH TYR I 221 " model vdw 2.254 2.440 ... (remaining 329803 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 120 and (name N or name CA or name C or name O or name CB \ )) or resid 121 through 179 or resid 188 through 211 or resid 213 through 267 o \ r (resid 282 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 83 through 515 or (resid 516 through 540 and (name N or name CA or name C or nam \ e O or name CB )) or resid 542 through 573 or (resid 574 and (name N or name CA \ or name C or name O or name CB )))) selection = (chain 'B' and (resid 120 through 211 or resid 213 through 540 or (resid 541 and \ (name N or name CA or name C or name O or name CB )) or resid 542 through 574)) \ selection = (chain 'C' and ((resid 120 and (name N or name CA or name C or name O or name CB \ )) or resid 121 through 179 or resid 188 through 211 or resid 213 through 267 o \ r (resid 282 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 83 through 515 or (resid 516 through 540 and (name N or name CA or name C or nam \ e O or name CB )) or resid 542 through 573 or (resid 574 and (name N or name CA \ or name C or name O or name CB )))) selection = (chain 'D' and (resid 120 through 211 or resid 213 through 540 or (resid 541 and \ (name N or name CA or name C or name O or name CB )) or resid 542 through 574)) \ selection = (chain 'E' and ((resid 120 and (name N or name CA or name C or name O or name CB \ )) or resid 121 through 179 or resid 188 through 211 or resid 213 through 267 o \ r (resid 282 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 83 through 515 or (resid 516 through 540 and (name N or name CA or name C or nam \ e O or name CB )) or resid 542 through 573 or (resid 574 and (name N or name CA \ or name C or name O or name CB )))) selection = (chain 'F' and (resid 120 through 211 or resid 213 through 540 or (resid 541 and \ (name N or name CA or name C or name O or name CB )) or resid 542 through 574)) \ selection = (chain 'G' and ((resid 120 and (name N or name CA or name C or name O or name CB \ )) or resid 121 through 179 or resid 188 through 211 or resid 213 through 267 o \ r (resid 282 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 83 through 515 or (resid 516 through 540 and (name N or name CA or name C or nam \ e O or name CB )) or resid 542 through 573 or (resid 574 and (name N or name CA \ or name C or name O or name CB )))) selection = (chain 'H' and (resid 120 through 211 or resid 213 through 540 or (resid 541 and \ (name N or name CA or name C or name O or name CB )) or resid 542 through 574)) \ selection = (chain 'I' and ((resid 120 and (name N or name CA or name C or name O or name CB \ )) or resid 121 through 179 or resid 188 through 211 or resid 213 through 267 o \ r (resid 282 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 83 through 515 or (resid 516 through 540 and (name N or name CA or name C or nam \ e O or name CB )) or resid 542 through 573 or (resid 574 and (name N or name CA \ or name C or name O or name CB )))) selection = (chain 'J' and (resid 120 through 211 or resid 213 through 540 or (resid 541 and \ (name N or name CA or name C or name O or name CB )) or resid 542 through 574)) \ selection = (chain 'K' and ((resid 120 and (name N or name CA or name C or name O or name CB \ )) or resid 121 through 179 or resid 188 through 211 or resid 213 through 267 o \ r (resid 282 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 83 through 515 or (resid 516 through 540 and (name N or name CA or name C or nam \ e O or name CB )) or resid 542 through 573 or (resid 574 and (name N or name CA \ or name C or name O or name CB )))) selection = (chain 'L' and (resid 120 through 211 or resid 213 through 540 or (resid 541 and \ (name N or name CA or name C or name O or name CB )) or resid 542 through 574)) \ } 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 13.070 Check model and map are aligned: 0.560 Set scattering table: 0.320 Process input model: 118.960 Find NCS groups from input model: 3.090 Set up NCS constraints: 0.230 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 151.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.001 0.026 39840 Z= 0.092 Angle : 0.375 4.708 53946 Z= 0.198 Chirality : 0.036 0.143 6084 Planarity : 0.003 0.033 6846 Dihedral : 9.690 88.027 14970 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.97 % Allowed : 3.90 % Favored : 95.13 % 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: 1.34 (0.12), residues: 4746 helix: 1.99 (0.12), residues: 1896 sheet: -0.21 (0.18), residues: 786 loop : 0.42 (0.13), residues: 2064 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 641 time to evaluate : 4.764 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 8 residues processed: 652 average time/residue: 1.6053 time to fit residues: 1249.7847 Evaluate side-chains 521 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 513 time to evaluate : 4.227 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 4 average time/residue: 0.4379 time to fit residues: 8.8135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 405 optimal weight: 0.0670 chunk 363 optimal weight: 6.9990 chunk 201 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 245 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 376 optimal weight: 0.9990 chunk 145 optimal weight: 0.0670 chunk 228 optimal weight: 4.9990 chunk 280 optimal weight: 1.9990 chunk 435 optimal weight: 4.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 170 ASN A 189 GLN B 197 ASN B 366 GLN C 152 GLN C 170 ASN C 189 GLN D 366 GLN D 559 HIS E 170 ASN E 189 GLN F 197 ASN F 224 ASN F 559 HIS G 152 GLN G 170 ASN G 189 GLN H 197 ASN H 366 GLN H 559 HIS I 152 GLN I 170 ASN I 189 GLN J 197 ASN J 224 ASN J 559 HIS K 152 GLN K 170 ASN K 189 GLN L 197 ASN L 366 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39840 Z= 0.195 Angle : 0.519 6.302 53946 Z= 0.269 Chirality : 0.041 0.152 6084 Planarity : 0.004 0.042 6846 Dihedral : 3.546 13.951 5274 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.25 % Allowed : 7.18 % Favored : 91.57 % 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: 1.41 (0.12), residues: 4746 helix: 2.05 (0.11), residues: 2016 sheet: -0.15 (0.18), residues: 726 loop : 0.32 (0.13), residues: 2004 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 554 time to evaluate : 4.473 Fit side-chains outliers start: 54 outliers final: 24 residues processed: 578 average time/residue: 1.6465 time to fit residues: 1149.2342 Evaluate side-chains 534 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 510 time to evaluate : 4.783 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 12 residues processed: 12 average time/residue: 1.2151 time to fit residues: 25.2072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 242 optimal weight: 6.9990 chunk 135 optimal weight: 0.0060 chunk 362 optimal weight: 5.9990 chunk 296 optimal weight: 0.7980 chunk 120 optimal weight: 0.0030 chunk 436 optimal weight: 1.9990 chunk 471 optimal weight: 5.9990 chunk 388 optimal weight: 1.9990 chunk 433 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 350 optimal weight: 2.9990 overall best weight: 0.9610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 189 GLN A 504 GLN B 197 ASN B 366 GLN C 152 GLN C 189 GLN D 224 ASN D 366 GLN E 152 GLN E 189 GLN E 504 GLN F 197 ASN F 224 ASN G 152 GLN G 189 GLN H 366 GLN H 559 HIS I 152 GLN I 189 GLN J 197 ASN J 224 ASN K 152 GLN K 189 GLN L 197 ASN L 366 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 39840 Z= 0.162 Angle : 0.462 5.134 53946 Z= 0.241 Chirality : 0.039 0.132 6084 Planarity : 0.004 0.041 6846 Dihedral : 3.601 14.053 5274 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.22 % Allowed : 8.24 % Favored : 90.54 % 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: 1.53 (0.12), residues: 4746 helix: 2.20 (0.11), residues: 2016 sheet: 0.15 (0.18), residues: 660 loop : 0.21 (0.13), residues: 2070 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 529 time to evaluate : 4.704 Fit side-chains outliers start: 53 outliers final: 34 residues processed: 547 average time/residue: 1.6391 time to fit residues: 1079.7075 Evaluate side-chains 521 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 487 time to evaluate : 4.525 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 18 residues processed: 18 average time/residue: 1.0729 time to fit residues: 31.5597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 431 optimal weight: 5.9990 chunk 328 optimal weight: 0.9980 chunk 226 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 293 optimal weight: 10.0000 chunk 438 optimal weight: 0.9980 chunk 463 optimal weight: 0.0770 chunk 228 optimal weight: 5.9990 chunk 415 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 overall best weight: 0.8138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN A 569 GLN B 197 ASN C 152 GLN C 504 GLN D 366 GLN E 189 GLN E 504 GLN F 224 ASN G 152 GLN G 366 GLN G 504 GLN H 366 GLN I 189 GLN J 224 ASN K 152 GLN K 189 GLN K 366 GLN L 197 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 39840 Z= 0.148 Angle : 0.455 5.242 53946 Z= 0.235 Chirality : 0.039 0.132 6084 Planarity : 0.004 0.051 6846 Dihedral : 3.589 14.171 5274 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.15 % Allowed : 9.10 % Favored : 89.75 % 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: 1.54 (0.12), residues: 4746 helix: 2.28 (0.11), residues: 2016 sheet: 0.06 (0.18), residues: 660 loop : 0.17 (0.13), residues: 2070 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 515 time to evaluate : 4.490 Fit side-chains revert: symmetry clash outliers start: 50 outliers final: 30 residues processed: 537 average time/residue: 1.7404 time to fit residues: 1124.6636 Evaluate side-chains 517 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 487 time to evaluate : 4.351 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 23 residues processed: 9 average time/residue: 0.7160 time to fit residues: 15.4303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 386 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 345 optimal weight: 2.9990 chunk 191 optimal weight: 0.6980 chunk 395 optimal weight: 0.3980 chunk 320 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 236 optimal weight: 0.9980 chunk 416 optimal weight: 2.9990 chunk 117 optimal weight: 0.1980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 189 GLN A 366 GLN C 152 GLN C 366 GLN C 504 GLN D 366 GLN D 504 GLN E 189 GLN E 504 GLN F 224 ASN F 366 GLN G 152 GLN G 366 GLN G 504 GLN H 366 GLN I 504 GLN J 224 ASN J 366 GLN K 152 GLN ** K 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 366 GLN K 504 GLN K 569 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 39840 Z= 0.152 Angle : 0.456 8.667 53946 Z= 0.235 Chirality : 0.039 0.132 6084 Planarity : 0.004 0.045 6846 Dihedral : 3.597 14.285 5274 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.27 % Allowed : 9.26 % Favored : 89.47 % 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: 1.54 (0.12), residues: 4746 helix: 2.31 (0.11), residues: 2016 sheet: -0.03 (0.18), residues: 660 loop : 0.16 (0.13), residues: 2070 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 502 time to evaluate : 4.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 34 residues processed: 525 average time/residue: 1.6794 time to fit residues: 1068.1140 Evaluate side-chains 519 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 485 time to evaluate : 4.536 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 19 residues processed: 17 average time/residue: 0.9056 time to fit residues: 27.3229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 156 optimal weight: 0.8980 chunk 417 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 272 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 464 optimal weight: 5.9990 chunk 385 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 243 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 189 GLN A 366 GLN C 152 GLN C 366 GLN C 504 GLN D 366 GLN D 504 GLN E 366 GLN E 504 GLN E 569 GLN F 224 ASN F 366 GLN G 152 GLN G 366 GLN G 504 GLN H 366 GLN I 504 GLN I 569 GLN J 224 ASN J 366 GLN K 152 GLN ** K 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 366 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 39840 Z= 0.227 Angle : 0.504 8.341 53946 Z= 0.260 Chirality : 0.041 0.135 6084 Planarity : 0.004 0.048 6846 Dihedral : 3.841 14.248 5274 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.41 % Allowed : 9.46 % Favored : 89.13 % 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: 1.37 (0.12), residues: 4746 helix: 2.24 (0.11), residues: 1980 sheet: -0.30 (0.18), residues: 690 loop : 0.12 (0.13), residues: 2076 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 519 time to evaluate : 4.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 33 residues processed: 546 average time/residue: 1.6525 time to fit residues: 1087.4912 Evaluate side-chains 536 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 503 time to evaluate : 4.265 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 18 residues processed: 17 average time/residue: 1.0301 time to fit residues: 29.0858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 447 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 264 optimal weight: 1.9990 chunk 339 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 390 optimal weight: 0.9990 chunk 259 optimal weight: 1.9990 chunk 462 optimal weight: 0.5980 chunk 289 optimal weight: 5.9990 chunk 282 optimal weight: 7.9990 chunk 213 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 189 GLN A 366 GLN B 197 ASN C 152 GLN C 366 GLN C 504 GLN C 569 GLN D 366 GLN E 504 GLN F 224 ASN F 366 GLN G 152 GLN G 366 GLN G 504 GLN G 569 GLN H 366 GLN H 572 HIS I 504 GLN J 224 ASN J 366 GLN K 152 GLN K 189 GLN K 366 GLN L 197 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 39840 Z= 0.173 Angle : 0.473 8.261 53946 Z= 0.244 Chirality : 0.039 0.135 6084 Planarity : 0.004 0.044 6846 Dihedral : 3.774 14.483 5274 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.04 % Allowed : 10.18 % Favored : 88.78 % 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: 1.46 (0.12), residues: 4746 helix: 2.30 (0.11), residues: 1980 sheet: -0.07 (0.18), residues: 660 loop : 0.10 (0.13), residues: 2106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 515 time to evaluate : 4.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 32 residues processed: 539 average time/residue: 1.7023 time to fit residues: 1104.6449 Evaluate side-chains 528 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 496 time to evaluate : 4.441 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 27 residues processed: 8 average time/residue: 1.1638 time to fit residues: 18.1456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 286 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 276 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 294 optimal weight: 5.9990 chunk 315 optimal weight: 0.8980 chunk 228 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 363 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 189 GLN A 366 GLN B 572 HIS C 152 GLN C 189 GLN C 366 GLN C 504 GLN D 366 GLN D 572 HIS E 504 GLN F 224 ASN F 366 GLN G 152 GLN G 366 GLN G 504 GLN H 366 GLN H 572 HIS I 152 GLN I 504 GLN J 224 ASN J 366 GLN K 152 GLN K 366 GLN L 197 ASN L 366 GLN L 572 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 39840 Z= 0.244 Angle : 0.515 8.402 53946 Z= 0.266 Chirality : 0.041 0.138 6084 Planarity : 0.004 0.047 6846 Dihedral : 3.948 15.618 5274 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.13 % Allowed : 10.18 % Favored : 88.69 % 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: 1.27 (0.12), residues: 4746 helix: 2.13 (0.11), residues: 1980 sheet: -0.33 (0.18), residues: 690 loop : 0.08 (0.13), residues: 2076 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 523 time to evaluate : 4.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 28 residues processed: 545 average time/residue: 1.6502 time to fit residues: 1087.3549 Evaluate side-chains 540 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 512 time to evaluate : 4.552 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 18 residues processed: 11 average time/residue: 0.6003 time to fit residues: 16.2667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 420 optimal weight: 3.9990 chunk 443 optimal weight: 5.9990 chunk 404 optimal weight: 0.9990 chunk 431 optimal weight: 0.6980 chunk 259 optimal weight: 0.0070 chunk 187 optimal weight: 0.9980 chunk 338 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 389 optimal weight: 0.9990 chunk 407 optimal weight: 5.9990 chunk 429 optimal weight: 4.9990 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 189 GLN A 366 GLN B 197 ASN B 366 GLN B 572 HIS C 152 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 GLN C 504 GLN D 366 GLN D 572 HIS E 152 GLN E 504 GLN F 224 ASN F 366 GLN G 152 GLN ** G 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 366 GLN G 504 GLN H 366 GLN I 504 GLN J 224 ASN J 366 GLN K 152 GLN K 366 GLN L 366 GLN L 572 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39840 Z= 0.145 Angle : 0.467 8.080 53946 Z= 0.240 Chirality : 0.039 0.190 6084 Planarity : 0.004 0.042 6846 Dihedral : 3.743 15.930 5274 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.69 % Allowed : 11.06 % Favored : 88.25 % 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: 1.49 (0.12), residues: 4746 helix: 2.36 (0.12), residues: 1980 sheet: -0.33 (0.18), residues: 708 loop : 0.20 (0.13), residues: 2058 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 542 time to evaluate : 4.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 23 residues processed: 559 average time/residue: 1.6270 time to fit residues: 1105.6815 Evaluate side-chains 539 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 516 time to evaluate : 4.410 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 6 average time/residue: 0.7006 time to fit residues: 12.3257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 283 optimal weight: 5.9990 chunk 455 optimal weight: 0.1980 chunk 278 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 316 optimal weight: 5.9990 chunk 478 optimal weight: 0.9980 chunk 440 optimal weight: 1.9990 chunk 380 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 294 optimal weight: 3.9990 chunk 233 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 189 GLN A 366 GLN B 366 GLN B 572 HIS C 152 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 GLN C 504 GLN D 366 GLN D 572 HIS E 366 GLN E 504 GLN F 224 ASN F 366 GLN G 152 GLN G 189 GLN G 366 GLN G 504 GLN H 366 GLN H 572 HIS I 504 GLN J 224 ASN J 366 GLN J 572 HIS K 152 GLN K 366 GLN L 366 GLN L 572 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 39840 Z= 0.153 Angle : 0.472 8.254 53946 Z= 0.242 Chirality : 0.039 0.151 6084 Planarity : 0.004 0.043 6846 Dihedral : 3.708 17.011 5274 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.62 % Allowed : 11.38 % Favored : 88.00 % 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: 1.52 (0.12), residues: 4746 helix: 2.40 (0.11), residues: 1986 sheet: -0.12 (0.19), residues: 648 loop : 0.10 (0.13), residues: 2112 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9492 Ramachandran restraints generated. 4746 Oldfield, 0 Emsley, 4746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 533 time to evaluate : 4.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 21 residues processed: 550 average time/residue: 1.6069 time to fit residues: 1071.8163 Evaluate side-chains 538 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 517 time to evaluate : 4.464 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 5 average time/residue: 0.6123 time to fit residues: 11.0113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 480 random chunks: chunk 302 optimal weight: 0.8980 chunk 405 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 351 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 381 optimal weight: 0.4980 chunk 159 optimal weight: 1.9990 chunk 391 optimal weight: 0.0470 chunk 48 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 189 GLN A 366 GLN B 366 GLN B 572 HIS C 152 GLN ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 366 GLN C 504 GLN D 366 GLN D 504 GLN D 572 HIS E 366 GLN E 504 GLN F 224 ASN F 366 GLN G 152 GLN ** G 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 366 GLN G 504 GLN H 366 GLN H 504 GLN I 152 GLN I 504 GLN J 224 ASN J 366 GLN K 152 GLN K 366 GLN L 366 GLN L 572 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.146796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108951 restraints weight = 85755.465| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.59 r_work: 0.3180 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 39840 Z= 0.134 Angle : 0.463 8.250 53946 Z= 0.237 Chirality : 0.038 0.157 6084 Planarity : 0.004 0.042 6846 Dihedral : 3.626 14.304 5274 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.69 % Allowed : 11.40 % Favored : 87.90 % 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: 1.57 (0.12), residues: 4746 helix: 2.44 (0.12), residues: 1998 sheet: -0.08 (0.19), residues: 660 loop : 0.10 (0.13), residues: 2088 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16897.63 seconds wall clock time: 299 minutes 20.68 seconds (17960.68 seconds total)