Starting phenix.real_space_refine on Fri Mar 22 10:03:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/03_2024/8ab6_15312_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/03_2024/8ab6_15312.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/03_2024/8ab6_15312_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/03_2024/8ab6_15312_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/03_2024/8ab6_15312_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/03_2024/8ab6_15312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/03_2024/8ab6_15312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/03_2024/8ab6_15312_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/03_2024/8ab6_15312_updated.pdb" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 6 7.16 5 P 30 5.49 5 S 96 5.16 5 C 20428 2.51 5 N 5128 2.21 5 O 7226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 4": "NH1" <-> "NH2" Residue "C ARG 70": "NH1" <-> "NH2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 110": "NH1" <-> "NH2" Residue "C ARG 283": "NH1" <-> "NH2" Residue "C ARG 310": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "P ARG 56": "NH1" <-> "NH2" Residue "G GLU 12": "OE1" <-> "OE2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 61": "NH1" <-> "NH2" Residue "G GLU 66": "OE1" <-> "OE2" Residue "G ARG 70": "NH1" <-> "NH2" Residue "G ARG 73": "NH1" <-> "NH2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 110": "OE1" <-> "OE2" Residue "G GLU 123": "OE1" <-> "OE2" Residue "F GLU 88": "OE1" <-> "OE2" Residue "F GLU 118": "OE1" <-> "OE2" Residue "F GLU 121": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A GLU 354": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A GLU 424": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ARG 234": "NH1" <-> "NH2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D GLU 164": "OE1" <-> "OE2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "D ARG 189": "NH1" <-> "NH2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ARG 321": "NH1" <-> "NH2" Residue "I GLU 34": "OE1" <-> "OE2" Residue "J TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 70": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" Residue "N TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 110": "NH1" <-> "NH2" Residue "N ARG 283": "NH1" <-> "NH2" Residue "N ARG 310": "NH1" <-> "NH2" Residue "N ARG 314": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R GLU 50": "OE1" <-> "OE2" Residue "R GLU 51": "OE1" <-> "OE2" Residue "R ARG 60": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R GLU 66": "OE1" <-> "OE2" Residue "R ARG 70": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R GLU 96": "OE1" <-> "OE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R GLU 112": "OE1" <-> "OE2" Residue "R GLU 123": "OE1" <-> "OE2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q GLU 118": "OE1" <-> "OE2" Residue "Q GLU 121": "OE1" <-> "OE2" Residue "Q GLU 126": "OE1" <-> "OE2" Residue "L GLU 141": "OE1" <-> "OE2" Residue "L ARG 188": "NH1" <-> "NH2" Residue "L GLU 354": "OE1" <-> "OE2" Residue "L ARG 384": "NH1" <-> "NH2" Residue "L GLU 424": "OE1" <-> "OE2" Residue "M GLU 76": "OE1" <-> "OE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M GLU 117": "OE1" <-> "OE2" Residue "M PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 140": "NH1" <-> "NH2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M ARG 234": "NH1" <-> "NH2" Residue "M ARG 236": "NH1" <-> "NH2" Residue "M GLU 313": "OE1" <-> "OE2" Residue "M GLU 350": "OE1" <-> "OE2" Residue "M GLU 365": "OE1" <-> "OE2" Residue "M GLU 376": "OE1" <-> "OE2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 132": "NH1" <-> "NH2" Residue "O ARG 136": "NH1" <-> "NH2" Residue "O GLU 164": "OE1" <-> "OE2" Residue "O ARG 170": "NH1" <-> "NH2" Residue "O ARG 189": "NH1" <-> "NH2" Residue "O ARG 207": "NH1" <-> "NH2" Residue "O ARG 250": "NH1" <-> "NH2" Residue "O GLU 260": "OE1" <-> "OE2" Residue "O ARG 289": "NH1" <-> "NH2" Residue "O ARG 321": "NH1" <-> "NH2" Residue "T GLU 34": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 32914 Number of models: 1 Model: "" Number of chains: 53 Chain: "C" Number of atoms: 3055 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Conformer: "B" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} bond proxies already assigned to first conformer: 3149 Chain: "P" Number of atoms: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 478 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "F" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "B" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "D" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "H" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "I" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "J" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "N" Number of atoms: 3052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3052 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 481 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 63, 478 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Conformer: "B" Number of residues, atoms: 63, 478 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} bond proxies already assigned to first conformer: 483 Chain: "R" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 7, 'TRANS': 116} Chain: "Q" Number of atoms: 579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 579 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "L" Number of atoms: 3446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3446 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 13, 'TRANS': 424} Chain breaks: 1 Chain: "M" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3008 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 20, 'TRANS': 381} Chain: "O" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1893 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 22, 'TRANS': 221} Chain: "S" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 5, 'TRANS': 79} Chain: "T" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 452 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "U" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 8, 'TRANS': 66} Chain: "C" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'LMT': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "J" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 248 Unusual residues: {'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 41 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "C" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "P" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "G" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 81 Classifications: {'water': 81} Link IDs: {None: 80} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 165 Classifications: {'water': 165} Link IDs: {None: 164} Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "D" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "J" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "N" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 138 Classifications: {'water': 138} Link IDs: {None: 137} Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 157 Classifications: {'water': 157} Link IDs: {None: 156} Chain: "M" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "O" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "S" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Chain: "T" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "U" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 17.63, per 1000 atoms: 0.54 Number of scatterers: 32914 At special positions: 0 Unit cell: (119.691, 129.735, 164.052, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 S 96 16.00 P 30 15.00 O 7226 8.00 N 5128 7.00 C 20428 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS F 91 " - pdb=" SG CYS F 133 " distance=2.05 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.06 Simple disulfide: pdb=" SG CYS Q 91 " - pdb=" SG CYS Q 133 " distance=2.05 Simple disulfide: pdb=" SG CYS Q 101 " - pdb=" SG CYS Q 123 " distance=2.05 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.68 Conformation dependent library (CDL) restraints added in 5.6 seconds 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7272 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 181 helices and 12 sheets defined 55.7% alpha, 7.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.06 Creating SS restraints... Processing helix chain 'C' and resid 3 through 6 No H-bonds generated for 'chain 'C' and resid 3 through 6' Processing helix chain 'C' and resid 8 through 17 Processing helix chain 'C' and resid 28 through 52 removed outlier: 3.870A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE C 48 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 70 Processing helix chain 'C' and resid 75 through 102 removed outlier: 3.744A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 3.526A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 3.555A pdb=" N LEU C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 166 Processing helix chain 'C' and resid 173 through 203 Proline residue: C 187 - end of helix removed outlier: 4.039A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.912A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR C 232 " --> pdb=" O LYS C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 257 Processing helix chain 'C' and resid 273 through 284 Proline residue: C 277 - end of helix Processing helix chain 'C' and resid 288 through 308 removed outlier: 3.837A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU C 305 " --> pdb=" O ILE C 301 " (cutoff:3.500A) Proline residue: C 306 - end of helix Processing helix chain 'C' and resid 320 through 340 Processing helix chain 'C' and resid 348 through 364 removed outlier: 4.113A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 381 Processing helix chain 'P' and resid 59 through 91 removed outlier: 3.593A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N MET P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 100 removed outlier: 3.627A pdb=" N MET P 100 " --> pdb=" O ASP P 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 16 Processing helix chain 'G' and resid 18 through 35 Proline residue: G 26 - end of helix Processing helix chain 'G' and resid 37 through 40 Processing helix chain 'G' and resid 44 through 47 Processing helix chain 'G' and resid 53 through 60 Processing helix chain 'G' and resid 64 through 82 Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 95 through 97 No H-bonds generated for 'chain 'G' and resid 95 through 97' Processing helix chain 'G' and resid 103 through 121 removed outlier: 3.671A pdb=" N ASN G 121 " --> pdb=" O ASP G 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 88 Processing helix chain 'F' and resid 92 through 110 Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.598A pdb=" N VAL F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 72 through 81 removed outlier: 3.520A pdb=" N HIS A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE A 81 " --> pdb=" O GLU A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 99 Processing helix chain 'A' and resid 120 through 135 removed outlier: 3.833A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.823A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 155 removed outlier: 4.033A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 196 through 206 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 222 through 232 Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.525A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.002A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 359 through 375 removed outlier: 3.565A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 374 " --> pdb=" O TRP A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 395 removed outlier: 3.509A pdb=" N ARG A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 432 through 442 Processing helix chain 'A' and resid 462 through 469 removed outlier: 3.657A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET A 469 " --> pdb=" O ILE A 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 70 through 79 Processing helix chain 'B' and resid 101 through 117 Proline residue: B 105 - end of helix removed outlier: 3.636A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU B 117 " --> pdb=" O VAL B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 129 through 141 Processing helix chain 'B' and resid 144 through 157 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 200 through 210 Processing helix chain 'B' and resid 254 through 263 removed outlier: 3.699A pdb=" N LEU B 263 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 removed outlier: 3.840A pdb=" N THR B 282 " --> pdb=" O LEU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 330 Processing helix chain 'B' and resid 334 through 353 Processing helix chain 'B' and resid 355 through 367 removed outlier: 3.619A pdb=" N SER B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 383 through 394 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'D' and resid 87 through 90 No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 124 through 126 No H-bonds generated for 'chain 'D' and resid 124 through 126' Processing helix chain 'D' and resid 135 through 138 Processing helix chain 'D' and resid 145 through 153 Processing helix chain 'D' and resid 185 through 192 Processing helix chain 'D' and resid 210 through 218 removed outlier: 3.551A pdb=" N PHE D 215 " --> pdb=" O ASP D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 282 Processing helix chain 'D' and resid 286 through 319 Proline residue: D 317 - end of helix Processing helix chain 'H' and resid 40 through 81 removed outlier: 4.432A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL H 59 " --> pdb=" O GLN H 55 " (cutoff:3.500A) Proline residue: H 62 - end of helix Processing helix chain 'H' and resid 86 through 92 Processing helix chain 'I' and resid 5 through 11 Processing helix chain 'I' and resid 15 through 44 Processing helix chain 'I' and resid 50 through 56 removed outlier: 5.162A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.507A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP J 31 " --> pdb=" O THR J 27 " (cutoff:3.500A) Proline residue: J 33 - end of helix Processing helix chain 'J' and resid 54 through 59 Processing helix chain 'J' and resid 61 through 63 No H-bonds generated for 'chain 'J' and resid 61 through 63' Processing helix chain 'J' and resid 67 through 71 Processing helix chain 'J' and resid 77 through 79 No H-bonds generated for 'chain 'J' and resid 77 through 79' Processing helix chain 'N' and resid 3 through 6 No H-bonds generated for 'chain 'N' and resid 3 through 6' Processing helix chain 'N' and resid 8 through 17 Processing helix chain 'N' and resid 28 through 52 removed outlier: 3.872A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE N 48 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 70 Processing helix chain 'N' and resid 75 through 102 removed outlier: 3.736A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 3.559A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 3.559A pdb=" N LEU N 150 " --> pdb=" O VAL N 146 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA N 153 " --> pdb=" O ASN N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 166 Processing helix chain 'N' and resid 173 through 203 Proline residue: N 187 - end of helix removed outlier: 4.040A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.932A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR N 232 " --> pdb=" O LYS N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 254 through 257 Processing helix chain 'N' and resid 273 through 284 Proline residue: N 277 - end of helix Processing helix chain 'N' and resid 288 through 308 removed outlier: 3.842A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU N 305 " --> pdb=" O ILE N 301 " (cutoff:3.500A) Proline residue: N 306 - end of helix Processing helix chain 'N' and resid 320 through 340 Processing helix chain 'N' and resid 348 through 364 removed outlier: 4.112A pdb=" N PHE N 363 " --> pdb=" O TYR N 359 " (cutoff:3.500A) Processing helix chain 'N' and resid 366 through 382 Processing helix chain 'E' and resid 59 through 91 removed outlier: 3.681A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N MET E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 100 removed outlier: 3.631A pdb=" N MET E 100 " --> pdb=" O ASP E 96 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 35 Proline residue: R 26 - end of helix Processing helix chain 'R' and resid 37 through 40 Processing helix chain 'R' and resid 44 through 47 Processing helix chain 'R' and resid 53 through 61 Processing helix chain 'R' and resid 64 through 82 Processing helix chain 'R' and resid 89 through 91 No H-bonds generated for 'chain 'R' and resid 89 through 91' Processing helix chain 'R' and resid 95 through 97 No H-bonds generated for 'chain 'R' and resid 95 through 97' Processing helix chain 'R' and resid 103 through 121 removed outlier: 3.648A pdb=" N ASN R 121 " --> pdb=" O ASP R 117 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 88 Processing helix chain 'Q' and resid 92 through 110 Processing helix chain 'Q' and resid 124 through 137 Processing helix chain 'Q' and resid 139 through 145 removed outlier: 3.602A pdb=" N VAL Q 145 " --> pdb=" O LYS Q 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 72 through 79 removed outlier: 3.515A pdb=" N HIS L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 99 Processing helix chain 'L' and resid 120 through 135 removed outlier: 3.835A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.822A pdb=" N VAL L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 156 removed outlier: 4.042A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU L 156 " --> pdb=" O THR L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 160 No H-bonds generated for 'chain 'L' and resid 158 through 160' Processing helix chain 'L' and resid 162 through 174 Processing helix chain 'L' and resid 179 through 181 No H-bonds generated for 'chain 'L' and resid 179 through 181' Processing helix chain 'L' and resid 188 through 191 No H-bonds generated for 'chain 'L' and resid 188 through 191' Processing helix chain 'L' and resid 196 through 206 Processing helix chain 'L' and resid 209 through 211 No H-bonds generated for 'chain 'L' and resid 209 through 211' Processing helix chain 'L' and resid 222 through 232 Processing helix chain 'L' and resid 294 through 304 removed outlier: 3.523A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 316 removed outlier: 4.003A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 327 Processing helix chain 'L' and resid 359 through 375 removed outlier: 3.557A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.745A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU L 394 " --> pdb=" O LYS L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 413 Processing helix chain 'L' and resid 420 through 428 Processing helix chain 'L' and resid 432 through 442 Processing helix chain 'L' and resid 462 through 469 removed outlier: 3.660A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N MET L 469 " --> pdb=" O ILE L 465 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 47 No H-bonds generated for 'chain 'M' and resid 45 through 47' Processing helix chain 'M' and resid 53 through 59 Processing helix chain 'M' and resid 70 through 79 Processing helix chain 'M' and resid 101 through 117 Proline residue: M 105 - end of helix removed outlier: 3.670A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU M 117 " --> pdb=" O VAL M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 127 Processing helix chain 'M' and resid 129 through 141 Processing helix chain 'M' and resid 144 through 157 Processing helix chain 'M' and resid 160 through 162 No H-bonds generated for 'chain 'M' and resid 160 through 162' Processing helix chain 'M' and resid 175 through 185 Processing helix chain 'M' and resid 188 through 190 No H-bonds generated for 'chain 'M' and resid 188 through 190' Processing helix chain 'M' and resid 200 through 210 Processing helix chain 'M' and resid 254 through 263 removed outlier: 3.683A pdb=" N LEU M 263 " --> pdb=" O ALA M 260 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 334 through 353 Processing helix chain 'M' and resid 355 through 367 removed outlier: 3.969A pdb=" N SER M 360 " --> pdb=" O ASP M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 375 through 377 No H-bonds generated for 'chain 'M' and resid 375 through 377' Processing helix chain 'M' and resid 383 through 394 removed outlier: 3.503A pdb=" N LEU M 393 " --> pdb=" O ALA M 389 " (cutoff:3.500A) Processing helix chain 'M' and resid 407 through 409 No H-bonds generated for 'chain 'M' and resid 407 through 409' Processing helix chain 'M' and resid 413 through 415 No H-bonds generated for 'chain 'M' and resid 413 through 415' Processing helix chain 'O' and resid 87 through 90 No H-bonds generated for 'chain 'O' and resid 87 through 90' Processing helix chain 'O' and resid 110 through 122 Processing helix chain 'O' and resid 124 through 126 No H-bonds generated for 'chain 'O' and resid 124 through 126' Processing helix chain 'O' and resid 135 through 138 Processing helix chain 'O' and resid 145 through 153 Processing helix chain 'O' and resid 185 through 192 Processing helix chain 'O' and resid 210 through 218 removed outlier: 3.556A pdb=" N PHE O 215 " --> pdb=" O ASP O 212 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 282 Processing helix chain 'O' and resid 286 through 319 Proline residue: O 317 - end of helix Processing helix chain 'S' and resid 40 through 81 removed outlier: 4.380A pdb=" N THR S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU S 57 " --> pdb=" O LYS S 53 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL S 59 " --> pdb=" O GLN S 55 " (cutoff:3.500A) Proline residue: S 62 - end of helix Processing helix chain 'S' and resid 86 through 92 Processing helix chain 'T' and resid 5 through 11 Processing helix chain 'T' and resid 15 through 44 Processing helix chain 'T' and resid 50 through 56 removed outlier: 5.165A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.610A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP U 31 " --> pdb=" O THR U 27 " (cutoff:3.500A) Proline residue: U 33 - end of helix Processing helix chain 'U' and resid 54 through 59 Processing helix chain 'U' and resid 61 through 63 No H-bonds generated for 'chain 'U' and resid 61 through 63' Processing helix chain 'U' and resid 67 through 71 Processing helix chain 'U' and resid 77 through 79 No H-bonds generated for 'chain 'U' and resid 77 through 79' Processing sheet with id= A, first strand: chain 'C' and resid 21 through 23 Processing sheet with id= B, first strand: chain 'A' and resid 31 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 266 through 271 Processing sheet with id= D, first strand: chain 'B' and resid 16 through 20 removed outlier: 4.186A pdb=" N LYS B 24 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.598A pdb=" N ASN B 241 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 156 through 158 Processing sheet with id= G, first strand: chain 'N' and resid 21 through 23 Processing sheet with id= H, first strand: chain 'L' and resid 31 through 34 Processing sheet with id= I, first strand: chain 'L' and resid 266 through 271 Processing sheet with id= J, first strand: chain 'M' and resid 16 through 20 removed outlier: 4.236A pdb=" N LYS M 24 " --> pdb=" O VAL M 191 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'M' and resid 231 through 235 removed outlier: 3.576A pdb=" N ASN M 241 " --> pdb=" O GLY M 308 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 156 through 158 1562 hydrogen bonds defined for protein. 4269 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: 10.36 Time building geometry restraints manager: 15.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.35: 9758 1.35 - 1.54: 21936 1.54 - 1.73: 504 1.73 - 1.93: 174 1.93 - 2.12: 20 Bond restraints: 32392 Sorted by residual: bond pdb=" CB HIS A 433 " pdb=" CG HIS A 433 " ideal model delta sigma weight residual 1.497 1.368 0.129 1.40e-02 5.10e+03 8.51e+01 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.470 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.470 -0.136 2.00e-02 2.50e+03 4.63e+01 bond pdb=" CA HIS A 433 " pdb=" CB HIS A 433 " ideal model delta sigma weight residual 1.532 1.425 0.107 1.65e-02 3.67e+03 4.20e+01 bond pdb=" C2A HEC O 401 " pdb=" C3A HEC O 401 " ideal model delta sigma weight residual 1.334 1.456 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 32387 not shown) Histogram of bond angle deviations from ideal: 85.31 - 104.04: 611 104.04 - 122.77: 38411 122.77 - 141.50: 4996 141.50 - 160.23: 0 160.23 - 178.97: 12 Bond angle restraints: 44030 Sorted by residual: angle pdb=" N HIS A 433 " pdb=" CA HIS A 433 " pdb=" CB HIS A 433 " ideal model delta sigma weight residual 110.44 85.31 25.13 1.56e+00 4.11e-01 2.60e+02 angle pdb=" C HIS L 433 " pdb=" CA HIS L 433 " pdb=" CB HIS L 433 " ideal model delta sigma weight residual 110.85 91.10 19.75 1.70e+00 3.46e-01 1.35e+02 angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 97.11 14.16 1.47e+00 4.63e-01 9.28e+01 angle pdb=" CG ARG D 289 " pdb=" CD ARG D 289 " pdb=" NE ARG D 289 " ideal model delta sigma weight residual 112.00 91.97 20.03 2.20e+00 2.07e-01 8.29e+01 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 97.90 13.37 1.47e+00 4.63e-01 8.27e+01 ... (remaining 44025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.47: 18381 31.47 - 62.93: 908 62.93 - 94.40: 89 94.40 - 125.87: 1 125.87 - 157.33: 3 Dihedral angle restraints: 19382 sinusoidal: 8096 harmonic: 11286 Sorted by residual: dihedral pdb=" N HIS A 433 " pdb=" C HIS A 433 " pdb=" CA HIS A 433 " pdb=" CB HIS A 433 " ideal model delta harmonic sigma weight residual 122.80 93.92 28.88 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" C ASN L 379 " pdb=" N ASN L 379 " pdb=" CA ASN L 379 " pdb=" CB ASN L 379 " ideal model delta harmonic sigma weight residual -122.60 -145.78 23.18 0 2.50e+00 1.60e-01 8.60e+01 dihedral pdb=" N ASN L 379 " pdb=" C ASN L 379 " pdb=" CA ASN L 379 " pdb=" CB ASN L 379 " ideal model delta harmonic sigma weight residual 122.80 144.61 -21.81 0 2.50e+00 1.60e-01 7.61e+01 ... (remaining 19379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.199: 4556 0.199 - 0.399: 251 0.399 - 0.598: 8 0.598 - 0.798: 4 0.798 - 0.997: 1 Chirality restraints: 4820 Sorted by residual: chirality pdb=" CA ASN L 379 " pdb=" N ASN L 379 " pdb=" C ASN L 379 " pdb=" CB ASN L 379 " both_signs ideal model delta sigma weight residual False 2.51 1.51 1.00 2.00e-01 2.50e+01 2.49e+01 chirality pdb=" CB4 CDL S 702 " pdb=" CB3 CDL S 702 " pdb=" CB6 CDL S 702 " pdb=" OB6 CDL S 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.86 -0.71 2.00e-01 2.50e+01 1.27e+01 chirality pdb=" CB4 CDL H 702 " pdb=" CB3 CDL H 702 " pdb=" CB6 CDL H 702 " pdb=" OB6 CDL H 702 " both_signs ideal model delta sigma weight residual False -2.57 -1.87 -0.71 2.00e-01 2.50e+01 1.24e+01 ... (remaining 4817 not shown) Planarity restraints: 5526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 433 " 0.105 2.00e-02 2.50e+03 7.86e-02 9.28e+01 pdb=" CG HIS A 433 " -0.084 2.00e-02 2.50e+03 pdb=" ND1 HIS A 433 " -0.069 2.00e-02 2.50e+03 pdb=" CD2 HIS A 433 " -0.077 2.00e-02 2.50e+03 pdb=" CE1 HIS A 433 " 0.048 2.00e-02 2.50e+03 pdb=" NE2 HIS A 433 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 120 " -0.050 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR D 120 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 120 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR D 120 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR D 120 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR D 120 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 120 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 120 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEC D 401 " 0.002 2.00e-02 2.50e+03 2.34e-02 1.23e+01 pdb=" C1B HEC D 401 " 0.004 2.00e-02 2.50e+03 pdb=" C2B HEC D 401 " 0.012 2.00e-02 2.50e+03 pdb=" C3B HEC D 401 " 0.007 2.00e-02 2.50e+03 pdb=" C4B HEC D 401 " -0.012 2.00e-02 2.50e+03 pdb=" CAB HEC D 401 " -0.043 2.00e-02 2.50e+03 pdb=" CHB HEC D 401 " -0.030 2.00e-02 2.50e+03 pdb=" CHC HEC D 401 " 0.031 2.00e-02 2.50e+03 pdb=" CMB HEC D 401 " 0.029 2.00e-02 2.50e+03 ... (remaining 5523 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 780 2.65 - 3.21: 31471 3.21 - 3.78: 58368 3.78 - 4.34: 84776 4.34 - 4.90: 126708 Nonbonded interactions: 302103 Sorted by model distance: nonbonded pdb=" OD2 ASP A 461 " pdb=" O HOH A3101 " model vdw 2.091 2.440 nonbonded pdb=" NE2 HIS N 82 " pdb="FE HEM N 501 " model vdw 2.100 3.080 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.103 3.080 nonbonded pdb=" OD2 ASP L 461 " pdb=" O HOH L3101 " model vdw 2.107 2.440 nonbonded pdb=" O2D HEM C 502 " pdb=" O HOH C 601 " model vdw 2.113 2.440 ... (remaining 302098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'M' } ncs_group { reference = (chain 'C' and (resid 1 through 321 or resid 323 through 383 or resid 501 throug \ h 506)) selection = (chain 'N' and (resid 1 through 321 or resid 323 through 383 or resid 501 throug \ h 506)) } ncs_group { reference = chain 'D' selection = chain 'O' } ncs_group { reference = (chain 'E' and (resid 39 through 64 or resid 66 through 101)) selection = (chain 'P' and (resid 39 through 64 or resid 66 through 101)) } ncs_group { reference = chain 'F' selection = chain 'Q' } ncs_group { reference = chain 'G' selection = chain 'R' } ncs_group { reference = chain 'H' selection = chain 'S' } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = (chain 'J' and resid 8 through 82) selection = chain 'U' } 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: 2.380 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: 11.960 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 84.990 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.300 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:14.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 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 : 0.010 0.179 32392 Z= 0.635 Angle : 1.597 25.133 44030 Z= 0.996 Chirality : 0.105 0.997 4820 Planarity : 0.006 0.079 5526 Dihedral : 17.506 157.334 12098 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.32 % Favored : 97.65 % Rotamer: Outliers : 1.89 % Allowed : 5.99 % Favored : 92.12 % Cbeta Deviations : 0.77 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.12), residues: 3836 helix: -0.63 (0.10), residues: 2154 sheet: 0.44 (0.25), residues: 330 loop : -0.34 (0.17), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.006 TRP O 280 HIS 0.029 0.004 HIS A 433 PHE 0.047 0.006 PHE M 107 TYR 0.050 0.006 TYR D 120 ARG 0.027 0.002 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 595 time to evaluate : 3.806 Fit side-chains REVERT: C 152 SER cc_start: 0.8240 (m) cc_final: 0.7994 (p) REVERT: C 159 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7086 (pm20) REVERT: C 165 LEU cc_start: 0.8315 (mt) cc_final: 0.8038 (tp) REVERT: C 250 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7801 (tppt) REVERT: C 288 LYS cc_start: 0.7116 (tttt) cc_final: 0.6817 (tttt) REVERT: G 9 LYS cc_start: 0.8010 (mttp) cc_final: 0.7520 (mmmt) REVERT: G 23 ILE cc_start: 0.7734 (mt) cc_final: 0.7407 (mm) REVERT: G 32 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8748 (t) REVERT: G 33 LYS cc_start: 0.8020 (tttt) cc_final: 0.7775 (tttt) REVERT: G 44 MET cc_start: 0.8839 (tmm) cc_final: 0.8620 (tmm) REVERT: G 66 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7859 (mm-30) REVERT: G 117 ASP cc_start: 0.7808 (m-30) cc_final: 0.7575 (m-30) REVERT: F 144 ARG cc_start: 0.7144 (mtm-85) cc_final: 0.6761 (mtt90) REVERT: A 29 LYS cc_start: 0.7058 (tttm) cc_final: 0.6856 (tttm) REVERT: A 32 THR cc_start: 0.8258 (m) cc_final: 0.7684 (p) REVERT: A 36 LYS cc_start: 0.6728 (mmtt) cc_final: 0.6523 (ttmm) REVERT: A 68 TYR cc_start: 0.6797 (m-80) cc_final: 0.6503 (m-80) REVERT: A 87 ARG cc_start: 0.7654 (OUTLIER) cc_final: 0.7327 (ptp90) REVERT: A 93 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6633 (mt-10) REVERT: A 98 ASN cc_start: 0.7429 (m-40) cc_final: 0.7220 (m-40) REVERT: A 125 LYS cc_start: 0.7152 (mttp) cc_final: 0.6567 (ttmm) REVERT: A 128 GLU cc_start: 0.7465 (tm-30) cc_final: 0.7211 (tm-30) REVERT: A 147 GLU cc_start: 0.6816 (mm-30) cc_final: 0.6531 (tp30) REVERT: A 149 GLU cc_start: 0.6053 (mt-10) cc_final: 0.5808 (tm-30) REVERT: A 153 ARG cc_start: 0.6223 (ttp-110) cc_final: 0.5864 (ttt90) REVERT: A 176 MET cc_start: 0.8871 (ttm) cc_final: 0.8670 (ttm) REVERT: A 198 GLU cc_start: 0.6813 (pt0) cc_final: 0.6085 (tp30) REVERT: A 201 LYS cc_start: 0.7864 (tttm) cc_final: 0.7659 (tttt) REVERT: A 205 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6841 (mm-30) REVERT: A 220 VAL cc_start: 0.7956 (t) cc_final: 0.7640 (p) REVERT: A 231 LYS cc_start: 0.7355 (tttt) cc_final: 0.7033 (tttp) REVERT: A 292 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7109 (pm20) REVERT: A 390 LYS cc_start: 0.7331 (tptt) cc_final: 0.6821 (mtmt) REVERT: A 422 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6555 (mt-10) REVERT: A 426 LYS cc_start: 0.7906 (mttt) cc_final: 0.7705 (mmtp) REVERT: A 436 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8209 (mtm-85) REVERT: B 19 GLU cc_start: 0.7065 (tp30) cc_final: 0.6838 (mm-30) REVERT: B 72 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8590 (tpp-160) REVERT: B 83 LYS cc_start: 0.8315 (mmtm) cc_final: 0.8023 (mmmm) REVERT: B 139 LYS cc_start: 0.7454 (tttt) cc_final: 0.7125 (ttpt) REVERT: B 180 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6754 (tp30) REVERT: B 251 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5891 (pm20) REVERT: B 269 MET cc_start: 0.8072 (ttp) cc_final: 0.7749 (ttp) REVERT: B 339 ARG cc_start: 0.7520 (ttp80) cc_final: 0.7129 (ttp-110) REVERT: B 353 GLU cc_start: 0.6173 (mt-10) cc_final: 0.5938 (mt-10) REVERT: B 364 MET cc_start: 0.7437 (tpp) cc_final: 0.7215 (tpp) REVERT: B 376 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.6340 (pt0) REVERT: B 379 GLN cc_start: 0.6903 (tt0) cc_final: 0.6575 (tt0) REVERT: B 380 LYS cc_start: 0.7115 (tttm) cc_final: 0.6894 (tttt) REVERT: D 86 THR cc_start: 0.7638 (m) cc_final: 0.7159 (p) REVERT: D 89 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7835 (mt-10) REVERT: D 96 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7246 (mp0) REVERT: D 154 GLU cc_start: 0.7602 (mt-10) cc_final: 0.7016 (pt0) REVERT: D 164 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6456 (mp0) REVERT: D 166 ASN cc_start: 0.7533 (m110) cc_final: 0.7327 (m-40) REVERT: D 224 GLU cc_start: 0.6941 (tt0) cc_final: 0.6691 (pm20) REVERT: D 230 VAL cc_start: 0.6979 (t) cc_final: 0.6666 (m) REVERT: H 35 ARG cc_start: 0.8040 (mtm-85) cc_final: 0.7780 (mtm110) REVERT: H 78 GLU cc_start: 0.7722 (tt0) cc_final: 0.7260 (mt-10) REVERT: J 10 LYS cc_start: 0.7271 (tttm) cc_final: 0.6543 (tptp) REVERT: J 11 LYS cc_start: 0.6085 (OUTLIER) cc_final: 0.5602 (mmtm) REVERT: J 20 PHE cc_start: 0.7586 (t80) cc_final: 0.7266 (t80) REVERT: J 55 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.7982 (ttp-110) REVERT: J 58 GLN cc_start: 0.7439 (tp40) cc_final: 0.7225 (tt0) REVERT: N 159 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7106 (pm20) REVERT: N 165 LEU cc_start: 0.8311 (mt) cc_final: 0.8036 (tp) REVERT: N 250 LYS cc_start: 0.8006 (ttmt) cc_final: 0.7786 (tppt) REVERT: N 288 LYS cc_start: 0.6918 (tttt) cc_final: 0.6708 (tttm) REVERT: E 54 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7130 (mmpt) REVERT: R 9 LYS cc_start: 0.8042 (mttp) cc_final: 0.7544 (mmmt) REVERT: R 22 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.5806 (ptpt) REVERT: R 23 ILE cc_start: 0.7817 (mt) cc_final: 0.7440 (mm) REVERT: R 33 LYS cc_start: 0.8021 (tttt) cc_final: 0.7765 (tttt) REVERT: R 66 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7845 (mm-30) REVERT: R 117 ASP cc_start: 0.7799 (m-30) cc_final: 0.7567 (m-30) REVERT: L 32 THR cc_start: 0.8230 (m) cc_final: 0.7663 (p) REVERT: L 36 LYS cc_start: 0.6724 (mmtt) cc_final: 0.6522 (ttmm) REVERT: L 68 TYR cc_start: 0.6787 (m-80) cc_final: 0.6495 (m-80) REVERT: L 93 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6623 (mt-10) REVERT: L 97 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6614 (mm-30) REVERT: L 98 ASN cc_start: 0.7444 (m-40) cc_final: 0.7112 (m-40) REVERT: L 120 LYS cc_start: 0.6574 (tttt) cc_final: 0.6210 (ptmt) REVERT: L 125 LYS cc_start: 0.7155 (mttp) cc_final: 0.6897 (mtmm) REVERT: L 128 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7182 (tm-30) REVERT: L 147 GLU cc_start: 0.6723 (mm-30) cc_final: 0.6521 (tp30) REVERT: L 153 ARG cc_start: 0.6194 (ttp-110) cc_final: 0.5848 (ttt90) REVERT: L 176 MET cc_start: 0.8874 (ttm) cc_final: 0.8615 (ttm) REVERT: L 198 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6555 (tp30) REVERT: L 201 LYS cc_start: 0.7875 (tttm) cc_final: 0.7644 (tttt) REVERT: L 220 VAL cc_start: 0.7926 (t) cc_final: 0.7601 (p) REVERT: L 231 LYS cc_start: 0.7387 (tttt) cc_final: 0.7077 (tttp) REVERT: L 292 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7108 (pm20) REVERT: L 390 LYS cc_start: 0.7289 (tptt) cc_final: 0.6596 (mtpt) REVERT: L 422 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6556 (mt-10) REVERT: L 433 HIS cc_start: 0.7698 (m-70) cc_final: 0.6708 (t-90) REVERT: L 436 ARG cc_start: 0.8505 (mtp85) cc_final: 0.8235 (mtm-85) REVERT: M 24 LYS cc_start: 0.7420 (mttt) cc_final: 0.7101 (mmtp) REVERT: M 72 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8607 (tpp-160) REVERT: M 83 LYS cc_start: 0.8331 (mmtm) cc_final: 0.8044 (mmmm) REVERT: M 139 LYS cc_start: 0.7454 (tttt) cc_final: 0.7127 (ttpt) REVERT: M 180 GLU cc_start: 0.7065 (tp30) cc_final: 0.6856 (tp30) REVERT: M 269 MET cc_start: 0.8234 (ptt) cc_final: 0.7884 (ptt) REVERT: M 335 GLU cc_start: 0.6058 (tm-30) cc_final: 0.5671 (tp30) REVERT: M 379 GLN cc_start: 0.6896 (tt0) cc_final: 0.6569 (tt0) REVERT: M 380 LYS cc_start: 0.7114 (tttm) cc_final: 0.6865 (tttt) REVERT: O 164 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6451 (mp0) REVERT: O 166 ASN cc_start: 0.7536 (m110) cc_final: 0.7330 (m-40) REVERT: S 35 ARG cc_start: 0.8033 (mtm-85) cc_final: 0.7776 (mtm110) REVERT: S 53 LYS cc_start: 0.8361 (ttpt) cc_final: 0.8147 (ttpp) REVERT: S 78 GLU cc_start: 0.7721 (tt0) cc_final: 0.7260 (mt-10) REVERT: U 10 LYS cc_start: 0.7451 (tttm) cc_final: 0.6655 (tptp) REVERT: U 20 PHE cc_start: 0.7613 (t80) cc_final: 0.7291 (t80) REVERT: U 58 GLN cc_start: 0.7472 (tp40) cc_final: 0.7253 (tt0) REVERT: U 73 ARG cc_start: 0.6244 (OUTLIER) cc_final: 0.5838 (mpt180) outliers start: 60 outliers final: 8 residues processed: 633 average time/residue: 1.7737 time to fit residues: 1297.4923 Evaluate side-chains 467 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 448 time to evaluate : 3.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 32 VAL Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain R residue 22 LYS Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 72 ARG Chi-restraints excluded: chain U residue 73 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 7.9990 chunk 288 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 153 optimal weight: 5.9990 chunk 297 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 181 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 345 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 22 GLN C 173 ASN C 202 HIS C 332 ASN ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 90 ASN F 96 HIS A 74 HIS A 89 GLN A 222 HIS A 371 ASN A 410 GLN B 197 ASN B 319 HIS D 93 HIS I 55 HIS N 14 ASN N 22 GLN N 202 HIS N 332 ASN ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 ASN L 89 GLN L 192 GLN L 371 ASN L 410 GLN M 197 ASN M 241 ASN M 319 HIS M 354 ASN O 93 HIS T 55 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 32392 Z= 0.184 Angle : 0.604 10.649 44030 Z= 0.310 Chirality : 0.042 0.167 4820 Planarity : 0.004 0.033 5526 Dihedral : 14.381 162.953 5181 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.18 % Allowed : 7.41 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 1.21 (0.13), residues: 3836 helix: 1.15 (0.11), residues: 2138 sheet: 0.83 (0.26), residues: 336 loop : 0.43 (0.17), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 156 HIS 0.017 0.001 HIS A 433 PHE 0.025 0.002 PHE L 334 TYR 0.022 0.002 TYR O 237 ARG 0.005 0.001 ARG M 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 498 time to evaluate : 3.725 Fit side-chains REVERT: C 159 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7126 (pm20) REVERT: C 165 LEU cc_start: 0.8294 (mt) cc_final: 0.8053 (tp) REVERT: C 250 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7710 (tppt) REVERT: C 288 LYS cc_start: 0.7029 (tttt) cc_final: 0.6773 (tttt) REVERT: P 54 LYS cc_start: 0.7622 (ttpt) cc_final: 0.7355 (ttmt) REVERT: G 9 LYS cc_start: 0.8134 (mttp) cc_final: 0.7399 (tptp) REVERT: G 19 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5720 (pp) REVERT: G 23 ILE cc_start: 0.7712 (mt) cc_final: 0.7459 (mm) REVERT: G 33 LYS cc_start: 0.8065 (tttt) cc_final: 0.7835 (tttt) REVERT: G 44 MET cc_start: 0.8727 (tmm) cc_final: 0.8492 (tmm) REVERT: G 117 ASP cc_start: 0.7801 (m-30) cc_final: 0.7577 (m-30) REVERT: F 138 THR cc_start: 0.7975 (m) cc_final: 0.7714 (p) REVERT: F 144 ARG cc_start: 0.7219 (mtm-85) cc_final: 0.6793 (mtt90) REVERT: A 29 LYS cc_start: 0.7047 (tttm) cc_final: 0.6661 (mttp) REVERT: A 32 THR cc_start: 0.8306 (m) cc_final: 0.7743 (p) REVERT: A 33 SER cc_start: 0.8336 (m) cc_final: 0.7894 (p) REVERT: A 36 LYS cc_start: 0.6515 (mmtt) cc_final: 0.6242 (mmtm) REVERT: A 48 LEU cc_start: 0.5340 (OUTLIER) cc_final: 0.5058 (tp) REVERT: A 50 GLN cc_start: 0.7131 (mm-40) cc_final: 0.6713 (mm-40) REVERT: A 87 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7424 (ptp90) REVERT: A 98 ASN cc_start: 0.7395 (m-40) cc_final: 0.7005 (m110) REVERT: A 125 LYS cc_start: 0.7071 (mttp) cc_final: 0.6793 (mtmm) REVERT: A 128 GLU cc_start: 0.7220 (tm-30) cc_final: 0.7011 (tm-30) REVERT: A 153 ARG cc_start: 0.6472 (ttp-110) cc_final: 0.6163 (ttt90) REVERT: A 198 GLU cc_start: 0.6691 (pt0) cc_final: 0.5867 (tm-30) REVERT: A 205 GLU cc_start: 0.7188 (tt0) cc_final: 0.6920 (tt0) REVERT: A 231 LYS cc_start: 0.7245 (tttt) cc_final: 0.6978 (tttp) REVERT: A 292 GLU cc_start: 0.7606 (mt-10) cc_final: 0.7167 (pm20) REVERT: A 390 LYS cc_start: 0.7258 (tptt) cc_final: 0.6877 (ttmt) REVERT: A 422 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6470 (tt0) REVERT: A 436 ARG cc_start: 0.8449 (mtp85) cc_final: 0.8171 (mtm-85) REVERT: B 16 SER cc_start: 0.7387 (m) cc_final: 0.7042 (t) REVERT: B 19 GLU cc_start: 0.7082 (tp30) cc_final: 0.6836 (mm-30) REVERT: B 28 GLN cc_start: 0.7595 (tt0) cc_final: 0.7086 (tt0) REVERT: B 83 LYS cc_start: 0.8152 (mmtm) cc_final: 0.7779 (mmmm) REVERT: B 139 LYS cc_start: 0.7556 (tttt) cc_final: 0.7197 (ttpt) REVERT: B 180 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6623 (pp20) REVERT: B 251 GLU cc_start: 0.6163 (mt-10) cc_final: 0.5927 (pm20) REVERT: B 316 GLN cc_start: 0.7084 (tt0) cc_final: 0.6809 (tt0) REVERT: B 339 ARG cc_start: 0.7609 (ttp80) cc_final: 0.7177 (ttm110) REVERT: B 364 MET cc_start: 0.7499 (tpp) cc_final: 0.7156 (tpp) REVERT: B 376 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.6142 (pt0) REVERT: B 379 GLN cc_start: 0.6795 (tt0) cc_final: 0.6483 (tt0) REVERT: B 380 LYS cc_start: 0.7168 (tttm) cc_final: 0.6944 (tttp) REVERT: D 96 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7212 (mp0) REVERT: D 154 GLU cc_start: 0.7488 (mt-10) cc_final: 0.7097 (pt0) REVERT: D 164 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6375 (mp0) REVERT: D 256 VAL cc_start: 0.8181 (m) cc_final: 0.7885 (p) REVERT: H 35 ARG cc_start: 0.7995 (mtm-85) cc_final: 0.7744 (mtm110) REVERT: H 78 GLU cc_start: 0.7698 (tt0) cc_final: 0.7258 (mt-10) REVERT: J 10 LYS cc_start: 0.7290 (tttm) cc_final: 0.6413 (tptp) REVERT: J 20 PHE cc_start: 0.7627 (t80) cc_final: 0.7322 (t80) REVERT: J 55 ARG cc_start: 0.8228 (ttm-80) cc_final: 0.7989 (ttp-170) REVERT: N 159 GLU cc_start: 0.7417 (mm-30) cc_final: 0.7148 (pm20) REVERT: N 160 ASP cc_start: 0.8037 (m-30) cc_final: 0.7815 (m-30) REVERT: N 165 LEU cc_start: 0.8302 (mt) cc_final: 0.8057 (tp) REVERT: N 250 LYS cc_start: 0.7946 (ttmt) cc_final: 0.7710 (tppt) REVERT: N 288 LYS cc_start: 0.6987 (tttt) cc_final: 0.6719 (tttt) REVERT: E 54 LYS cc_start: 0.7379 (tttm) cc_final: 0.7113 (mmpt) REVERT: R 9 LYS cc_start: 0.8144 (mttp) cc_final: 0.7418 (tptp) REVERT: R 23 ILE cc_start: 0.7793 (mt) cc_final: 0.7464 (mm) REVERT: R 33 LYS cc_start: 0.8091 (tttt) cc_final: 0.7866 (tttt) REVERT: R 117 ASP cc_start: 0.7803 (m-30) cc_final: 0.7575 (m-30) REVERT: Q 144 ARG cc_start: 0.7226 (mtm-85) cc_final: 0.6799 (mtt90) REVERT: L 32 THR cc_start: 0.8223 (m) cc_final: 0.7655 (p) REVERT: L 36 LYS cc_start: 0.6435 (mmtt) cc_final: 0.6183 (mmtm) REVERT: L 50 GLN cc_start: 0.6978 (mm-40) cc_final: 0.6465 (mm-40) REVERT: L 125 LYS cc_start: 0.7079 (mttp) cc_final: 0.6795 (mtmm) REVERT: L 128 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6995 (tm-30) REVERT: L 153 ARG cc_start: 0.6448 (ttp-110) cc_final: 0.6153 (ttt180) REVERT: L 231 LYS cc_start: 0.7259 (tttt) cc_final: 0.6987 (tttp) REVERT: L 292 GLU cc_start: 0.7619 (mt-10) cc_final: 0.7183 (pm20) REVERT: L 390 LYS cc_start: 0.7245 (OUTLIER) cc_final: 0.6947 (ttmt) REVERT: L 422 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6547 (mt-10) REVERT: L 426 LYS cc_start: 0.7907 (mttt) cc_final: 0.7704 (mmtp) REVERT: L 436 ARG cc_start: 0.8456 (mtp85) cc_final: 0.8182 (mtm-85) REVERT: M 28 GLN cc_start: 0.7587 (tt0) cc_final: 0.7130 (tt0) REVERT: M 83 LYS cc_start: 0.8198 (mmtm) cc_final: 0.7829 (mmmm) REVERT: M 139 LYS cc_start: 0.7558 (tttt) cc_final: 0.7204 (ttpt) REVERT: M 180 GLU cc_start: 0.7054 (tp30) cc_final: 0.6756 (pp20) REVERT: M 269 MET cc_start: 0.8196 (ptt) cc_final: 0.7894 (ptt) REVERT: M 273 VAL cc_start: 0.6926 (OUTLIER) cc_final: 0.6621 (p) REVERT: M 316 GLN cc_start: 0.7104 (tt0) cc_final: 0.6809 (tt0) REVERT: M 364 MET cc_start: 0.7521 (tpp) cc_final: 0.7158 (tpt) REVERT: M 379 GLN cc_start: 0.6802 (tt0) cc_final: 0.6496 (tt0) REVERT: M 380 LYS cc_start: 0.7089 (tttm) cc_final: 0.6865 (tttp) REVERT: O 96 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7211 (mp0) REVERT: O 164 GLU cc_start: 0.6910 (mm-30) cc_final: 0.6385 (mp0) REVERT: O 166 ASN cc_start: 0.7505 (m110) cc_final: 0.7301 (m-40) REVERT: O 230 VAL cc_start: 0.6998 (t) cc_final: 0.6648 (m) REVERT: O 256 VAL cc_start: 0.8202 (m) cc_final: 0.7902 (p) REVERT: S 35 ARG cc_start: 0.7989 (mtm-85) cc_final: 0.7739 (mtm110) REVERT: S 78 GLU cc_start: 0.7699 (tt0) cc_final: 0.7258 (mt-10) REVERT: U 10 LYS cc_start: 0.7411 (tttm) cc_final: 0.6461 (tptp) REVERT: U 20 PHE cc_start: 0.7629 (t80) cc_final: 0.7320 (t80) REVERT: U 55 ARG cc_start: 0.8261 (ttm-80) cc_final: 0.8011 (ttp-170) outliers start: 37 outliers final: 13 residues processed: 520 average time/residue: 1.7542 time to fit residues: 1054.7676 Evaluate side-chains 461 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 442 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 8.9990 chunk 107 optimal weight: 0.3980 chunk 287 optimal weight: 0.6980 chunk 234 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 345 optimal weight: 5.9990 chunk 373 optimal weight: 10.0000 chunk 307 optimal weight: 5.9990 chunk 342 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 277 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN A 135 GLN A 192 GLN B 205 GLN B 316 GLN B 319 HIS D 93 HIS ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 316 GLN M 319 HIS O 93 HIS U 58 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 32392 Z= 0.136 Angle : 0.502 11.977 44030 Z= 0.251 Chirality : 0.039 0.148 4820 Planarity : 0.004 0.038 5526 Dihedral : 13.124 159.865 5150 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.96 % Allowed : 8.31 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 1.87 (0.14), residues: 3836 helix: 1.69 (0.11), residues: 2124 sheet: 1.06 (0.27), residues: 340 loop : 0.75 (0.18), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 156 HIS 0.007 0.001 HIS C 197 PHE 0.020 0.001 PHE L 334 TYR 0.014 0.001 TYR O 237 ARG 0.003 0.000 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 469 time to evaluate : 3.741 Fit side-chains REVERT: C 159 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7100 (pm20) REVERT: C 165 LEU cc_start: 0.8302 (mt) cc_final: 0.8056 (tp) REVERT: C 186 MET cc_start: 0.8419 (tpp) cc_final: 0.8183 (mmp) REVERT: C 250 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7678 (tppt) REVERT: C 288 LYS cc_start: 0.7024 (tttt) cc_final: 0.6697 (tttt) REVERT: P 54 LYS cc_start: 0.7636 (ttpt) cc_final: 0.7352 (ttmt) REVERT: P 74 MET cc_start: 0.8283 (tmm) cc_final: 0.7926 (tmm) REVERT: G 9 LYS cc_start: 0.8156 (mttp) cc_final: 0.7401 (tptp) REVERT: G 13 LEU cc_start: 0.7914 (tp) cc_final: 0.7709 (tp) REVERT: G 33 LYS cc_start: 0.8055 (tttt) cc_final: 0.7834 (tttt) REVERT: G 44 MET cc_start: 0.8619 (tmm) cc_final: 0.8417 (tmm) REVERT: F 138 THR cc_start: 0.7942 (m) cc_final: 0.7679 (p) REVERT: F 144 ARG cc_start: 0.7257 (mtm-85) cc_final: 0.6845 (mtt90) REVERT: A 32 THR cc_start: 0.8245 (m) cc_final: 0.7683 (p) REVERT: A 34 ASN cc_start: 0.7868 (m110) cc_final: 0.7604 (m-40) REVERT: A 36 LYS cc_start: 0.6636 (mmtt) cc_final: 0.6328 (mmtm) REVERT: A 50 GLN cc_start: 0.7062 (mm-40) cc_final: 0.6596 (mm-40) REVERT: A 98 ASN cc_start: 0.7368 (m-40) cc_final: 0.7079 (m110) REVERT: A 125 LYS cc_start: 0.7061 (mttp) cc_final: 0.6830 (mtmm) REVERT: A 153 ARG cc_start: 0.6506 (ttp-110) cc_final: 0.6284 (ttt90) REVERT: A 194 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.6066 (mm) REVERT: A 198 GLU cc_start: 0.6711 (pt0) cc_final: 0.6049 (tm-30) REVERT: A 231 LYS cc_start: 0.7247 (tttt) cc_final: 0.6986 (tttp) REVERT: A 292 GLU cc_start: 0.7641 (mt-10) cc_final: 0.7269 (pm20) REVERT: A 390 LYS cc_start: 0.7229 (OUTLIER) cc_final: 0.6937 (ttmt) REVERT: A 422 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6556 (mt-10) REVERT: A 436 ARG cc_start: 0.8399 (mtp85) cc_final: 0.8110 (mtm-85) REVERT: A 471 MET cc_start: 0.8326 (mtt) cc_final: 0.8055 (mtm) REVERT: B 16 SER cc_start: 0.7482 (m) cc_final: 0.7162 (t) REVERT: B 19 GLU cc_start: 0.7067 (tp30) cc_final: 0.6845 (mm-30) REVERT: B 28 GLN cc_start: 0.7606 (tt0) cc_final: 0.7160 (tt0) REVERT: B 83 LYS cc_start: 0.8140 (mmtm) cc_final: 0.7800 (mmmm) REVERT: B 139 LYS cc_start: 0.7548 (tttt) cc_final: 0.7190 (ttpt) REVERT: B 180 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6705 (tt0) REVERT: B 183 ARG cc_start: 0.7000 (mtm110) cc_final: 0.6466 (ttp80) REVERT: B 251 GLU cc_start: 0.6206 (mt-10) cc_final: 0.5943 (pm20) REVERT: B 353 GLU cc_start: 0.5949 (pp20) cc_final: 0.5738 (pp20) REVERT: B 364 MET cc_start: 0.7532 (tpp) cc_final: 0.7100 (tpp) REVERT: D 96 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7202 (mp0) REVERT: D 154 GLU cc_start: 0.7460 (mt-10) cc_final: 0.7127 (pt0) REVERT: D 164 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6543 (mp0) REVERT: D 230 VAL cc_start: 0.7025 (t) cc_final: 0.6609 (m) REVERT: D 256 VAL cc_start: 0.8121 (m) cc_final: 0.7862 (p) REVERT: H 35 ARG cc_start: 0.7983 (mtm-85) cc_final: 0.7711 (mtm110) REVERT: H 78 GLU cc_start: 0.7680 (tt0) cc_final: 0.7230 (mt-10) REVERT: J 10 LYS cc_start: 0.7375 (tttm) cc_final: 0.6408 (tptp) REVERT: J 20 PHE cc_start: 0.7636 (t80) cc_final: 0.7322 (t80) REVERT: N 165 LEU cc_start: 0.8303 (mt) cc_final: 0.8063 (tp) REVERT: N 250 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7675 (tppt) REVERT: N 288 LYS cc_start: 0.7039 (tttt) cc_final: 0.6705 (tttt) REVERT: E 54 LYS cc_start: 0.7374 (tttm) cc_final: 0.7109 (mmpt) REVERT: R 13 LEU cc_start: 0.7900 (tp) cc_final: 0.7687 (tp) REVERT: R 33 LYS cc_start: 0.8061 (tttt) cc_final: 0.7827 (tttt) REVERT: Q 144 ARG cc_start: 0.7236 (mtm-85) cc_final: 0.6838 (mtt90) REVERT: L 29 LYS cc_start: 0.7089 (tttm) cc_final: 0.6573 (mttp) REVERT: L 32 THR cc_start: 0.8222 (m) cc_final: 0.7655 (p) REVERT: L 36 LYS cc_start: 0.6586 (mmtt) cc_final: 0.6297 (mmtm) REVERT: L 50 GLN cc_start: 0.6914 (mm-40) cc_final: 0.6411 (mm-40) REVERT: L 94 LEU cc_start: 0.6874 (mp) cc_final: 0.6670 (mp) REVERT: L 125 LYS cc_start: 0.7067 (mttp) cc_final: 0.6822 (mtmm) REVERT: L 128 GLU cc_start: 0.7062 (tm-30) cc_final: 0.6843 (tm-30) REVERT: L 149 GLU cc_start: 0.6349 (tm-30) cc_final: 0.6110 (tm-30) REVERT: L 153 ARG cc_start: 0.6493 (ttp-110) cc_final: 0.6278 (ttt90) REVERT: L 231 LYS cc_start: 0.7295 (tttt) cc_final: 0.7031 (tttp) REVERT: L 292 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7274 (pm20) REVERT: L 390 LYS cc_start: 0.7207 (tptt) cc_final: 0.6952 (ttmt) REVERT: L 422 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6589 (mt-10) REVERT: L 436 ARG cc_start: 0.8405 (mtp85) cc_final: 0.8115 (mtm-85) REVERT: L 471 MET cc_start: 0.8430 (mtt) cc_final: 0.8058 (mtm) REVERT: M 28 GLN cc_start: 0.7623 (tt0) cc_final: 0.7173 (tt0) REVERT: M 139 LYS cc_start: 0.7618 (tttt) cc_final: 0.7264 (ttpt) REVERT: M 180 GLU cc_start: 0.7030 (tp30) cc_final: 0.6733 (pp20) REVERT: M 353 GLU cc_start: 0.6015 (pp20) cc_final: 0.5790 (pp20) REVERT: M 364 MET cc_start: 0.7678 (tpp) cc_final: 0.7248 (tpt) REVERT: M 379 GLN cc_start: 0.6745 (tt0) cc_final: 0.6450 (tt0) REVERT: O 96 GLU cc_start: 0.7584 (mt-10) cc_final: 0.7200 (mp0) REVERT: O 154 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7113 (pt0) REVERT: O 164 GLU cc_start: 0.6946 (mm-30) cc_final: 0.6539 (mp0) REVERT: O 230 VAL cc_start: 0.7069 (t) cc_final: 0.6650 (m) REVERT: O 256 VAL cc_start: 0.8117 (m) cc_final: 0.7862 (p) REVERT: S 35 ARG cc_start: 0.7964 (mtm-85) cc_final: 0.7699 (mtm110) REVERT: S 78 GLU cc_start: 0.7680 (tt0) cc_final: 0.7230 (mt-10) REVERT: U 10 LYS cc_start: 0.7376 (tttm) cc_final: 0.6430 (tptp) REVERT: U 20 PHE cc_start: 0.7645 (t80) cc_final: 0.7330 (t80) outliers start: 30 outliers final: 11 residues processed: 490 average time/residue: 1.7286 time to fit residues: 983.1163 Evaluate side-chains 444 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 431 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 9.9990 chunk 259 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 232 optimal weight: 1.9990 chunk 346 optimal weight: 9.9990 chunk 367 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 328 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 197 ASN B 205 GLN B 319 HIS D 93 HIS D 269 GLN J 58 GLN N 11 ASN N 343 HIS M 205 GLN M 319 HIS M 354 ASN O 93 HIS O 269 GLN U 58 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 32392 Z= 0.368 Angle : 0.780 8.853 44030 Z= 0.399 Chirality : 0.049 0.221 4820 Planarity : 0.006 0.069 5526 Dihedral : 14.313 178.003 5140 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.43 % Allowed : 8.16 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 1.51 (0.13), residues: 3836 helix: 1.33 (0.11), residues: 2140 sheet: 0.85 (0.25), residues: 336 loop : 0.74 (0.18), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.004 TRP L 474 HIS 0.017 0.003 HIS C 96 PHE 0.034 0.004 PHE L 334 TYR 0.025 0.004 TYR N 224 ARG 0.008 0.001 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 453 time to evaluate : 4.067 Fit side-chains REVERT: C 159 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7099 (mp0) REVERT: C 288 LYS cc_start: 0.7102 (tttt) cc_final: 0.6726 (ttpp) REVERT: G 13 LEU cc_start: 0.7951 (tp) cc_final: 0.7709 (tp) REVERT: G 23 ILE cc_start: 0.7730 (mt) cc_final: 0.7428 (mm) REVERT: F 138 THR cc_start: 0.8095 (m) cc_final: 0.7879 (p) REVERT: A 32 THR cc_start: 0.8299 (m) cc_final: 0.7731 (p) REVERT: A 34 ASN cc_start: 0.7895 (m110) cc_final: 0.7629 (m-40) REVERT: A 36 LYS cc_start: 0.6705 (mmtt) cc_final: 0.6477 (ttmm) REVERT: A 48 LEU cc_start: 0.5671 (OUTLIER) cc_final: 0.5391 (tp) REVERT: A 68 TYR cc_start: 0.6738 (m-80) cc_final: 0.6370 (m-80) REVERT: A 153 ARG cc_start: 0.6449 (ttp-110) cc_final: 0.6163 (ttt180) REVERT: A 231 LYS cc_start: 0.7341 (tttt) cc_final: 0.7058 (tttp) REVERT: A 390 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6946 (ttmt) REVERT: A 422 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6791 (mt-10) REVERT: A 436 ARG cc_start: 0.8461 (mtp85) cc_final: 0.8150 (mtm-85) REVERT: B 19 GLU cc_start: 0.7435 (tp30) cc_final: 0.7197 (mm-30) REVERT: B 83 LYS cc_start: 0.8205 (mmtm) cc_final: 0.7799 (mmmm) REVERT: B 183 ARG cc_start: 0.7171 (mtm110) cc_final: 0.6476 (ttp80) REVERT: B 251 GLU cc_start: 0.6073 (mt-10) cc_final: 0.5839 (pm20) REVERT: B 307 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.8094 (pttp) REVERT: B 379 GLN cc_start: 0.6674 (tt0) cc_final: 0.6438 (tt0) REVERT: D 154 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7289 (pt0) REVERT: D 164 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6613 (mp0) REVERT: D 256 VAL cc_start: 0.8117 (m) cc_final: 0.7846 (p) REVERT: H 78 GLU cc_start: 0.7695 (tt0) cc_final: 0.7242 (mt-10) REVERT: N 250 LYS cc_start: 0.7899 (ttmt) cc_final: 0.7697 (tppt) REVERT: E 54 LYS cc_start: 0.7574 (tttm) cc_final: 0.7354 (ttmt) REVERT: R 13 LEU cc_start: 0.7917 (tp) cc_final: 0.7670 (tp) REVERT: R 23 ILE cc_start: 0.7813 (mt) cc_final: 0.7469 (mm) REVERT: Q 138 THR cc_start: 0.8043 (m) cc_final: 0.7783 (p) REVERT: Q 144 ARG cc_start: 0.7216 (mtm-85) cc_final: 0.6986 (mtt180) REVERT: L 32 THR cc_start: 0.8301 (m) cc_final: 0.7730 (p) REVERT: L 48 LEU cc_start: 0.5488 (OUTLIER) cc_final: 0.5279 (tp) REVERT: L 68 TYR cc_start: 0.6770 (m-80) cc_final: 0.6346 (m-80) REVERT: L 153 ARG cc_start: 0.6436 (ttp-110) cc_final: 0.6158 (ttt180) REVERT: L 231 LYS cc_start: 0.7384 (tttt) cc_final: 0.7089 (tttp) REVERT: L 390 LYS cc_start: 0.7208 (OUTLIER) cc_final: 0.6951 (ttmt) REVERT: L 422 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6794 (mt-10) REVERT: L 436 ARG cc_start: 0.8475 (mtp85) cc_final: 0.8164 (mtm-85) REVERT: M 180 GLU cc_start: 0.7196 (tp30) cc_final: 0.6840 (tm-30) REVERT: M 354 ASN cc_start: 0.5734 (t0) cc_final: 0.5426 (t0) REVERT: O 96 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7274 (mp0) REVERT: O 154 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7287 (pt0) REVERT: O 164 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6617 (mp0) REVERT: O 256 VAL cc_start: 0.8118 (m) cc_final: 0.7847 (p) REVERT: S 78 GLU cc_start: 0.7699 (tt0) cc_final: 0.7244 (mt-10) outliers start: 46 outliers final: 17 residues processed: 483 average time/residue: 1.6326 time to fit residues: 921.0898 Evaluate side-chains 459 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 437 time to evaluate : 3.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 119 ILE Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 307 LYS Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 20.0000 chunk 208 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 273 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 313 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 187 optimal weight: 0.1980 chunk 329 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 89 GLN B 205 GLN B 319 HIS J 58 GLN N 202 HIS ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN M 319 HIS U 58 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 32392 Z= 0.232 Angle : 0.630 10.526 44030 Z= 0.322 Chirality : 0.043 0.158 4820 Planarity : 0.005 0.042 5526 Dihedral : 13.887 170.333 5140 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.36 % Allowed : 8.56 % Favored : 90.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 1.70 (0.13), residues: 3836 helix: 1.51 (0.11), residues: 2138 sheet: 0.79 (0.25), residues: 340 loop : 0.80 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 474 HIS 0.011 0.002 HIS N 197 PHE 0.027 0.002 PHE L 334 TYR 0.022 0.002 TYR O 237 ARG 0.004 0.001 ARG S 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 447 time to evaluate : 3.885 Fit side-chains revert: symmetry clash REVERT: C 159 GLU cc_start: 0.7293 (mm-30) cc_final: 0.7062 (mp0) REVERT: C 288 LYS cc_start: 0.7086 (tttt) cc_final: 0.6729 (ttpp) REVERT: G 13 LEU cc_start: 0.7955 (tp) cc_final: 0.7746 (tp) REVERT: G 23 ILE cc_start: 0.7750 (mt) cc_final: 0.7447 (mm) REVERT: F 138 THR cc_start: 0.8165 (m) cc_final: 0.7942 (p) REVERT: A 32 THR cc_start: 0.8290 (m) cc_final: 0.7694 (p) REVERT: A 34 ASN cc_start: 0.7877 (m110) cc_final: 0.7638 (m-40) REVERT: A 36 LYS cc_start: 0.6784 (mmtt) cc_final: 0.6543 (ttmm) REVERT: A 48 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5445 (tp) REVERT: A 68 TYR cc_start: 0.6730 (m-80) cc_final: 0.6332 (m-80) REVERT: A 153 ARG cc_start: 0.6392 (ttp-110) cc_final: 0.6083 (ttt180) REVERT: A 160 LYS cc_start: 0.5171 (tptp) cc_final: 0.4882 (tppp) REVERT: A 231 LYS cc_start: 0.7301 (tttt) cc_final: 0.7026 (tttp) REVERT: A 390 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6933 (ttmt) REVERT: A 422 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6754 (mt-10) REVERT: A 436 ARG cc_start: 0.8456 (mtp85) cc_final: 0.8141 (mtm-85) REVERT: B 19 GLU cc_start: 0.7365 (tp30) cc_final: 0.7141 (OUTLIER) REVERT: B 83 LYS cc_start: 0.8257 (mmtm) cc_final: 0.7881 (mmmm) REVERT: B 183 ARG cc_start: 0.7003 (mtm110) cc_final: 0.6555 (ttp80) REVERT: B 251 GLU cc_start: 0.6084 (mt-10) cc_final: 0.5854 (pm20) REVERT: B 379 GLN cc_start: 0.6684 (tt0) cc_final: 0.6426 (tt0) REVERT: D 154 GLU cc_start: 0.7500 (mt-10) cc_final: 0.7241 (pt0) REVERT: D 164 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6589 (mp0) REVERT: D 256 VAL cc_start: 0.8134 (m) cc_final: 0.7868 (p) REVERT: H 78 GLU cc_start: 0.7691 (tt0) cc_final: 0.7238 (mt-10) REVERT: N 250 LYS cc_start: 0.7915 (ttmt) cc_final: 0.7708 (tppt) REVERT: N 288 LYS cc_start: 0.7041 (ttmm) cc_final: 0.6671 (tttt) REVERT: E 54 LYS cc_start: 0.7601 (tttm) cc_final: 0.7212 (mmpt) REVERT: R 23 ILE cc_start: 0.7784 (mt) cc_final: 0.7447 (mm) REVERT: Q 96 HIS cc_start: 0.7159 (t-90) cc_final: 0.6715 (t-90) REVERT: Q 138 THR cc_start: 0.8086 (m) cc_final: 0.7865 (p) REVERT: Q 144 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6974 (mtt180) REVERT: L 32 THR cc_start: 0.8290 (m) cc_final: 0.7693 (p) REVERT: L 48 LEU cc_start: 0.5487 (OUTLIER) cc_final: 0.5270 (tp) REVERT: L 68 TYR cc_start: 0.6735 (m-80) cc_final: 0.6342 (m-80) REVERT: L 153 ARG cc_start: 0.6347 (ttp-110) cc_final: 0.6138 (ttm110) REVERT: L 160 LYS cc_start: 0.5183 (tptp) cc_final: 0.4902 (tppp) REVERT: L 231 LYS cc_start: 0.7350 (tttt) cc_final: 0.7064 (tttp) REVERT: L 390 LYS cc_start: 0.7265 (tptt) cc_final: 0.6943 (ttmt) REVERT: L 422 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6757 (mt-10) REVERT: L 436 ARG cc_start: 0.8463 (mtp85) cc_final: 0.8149 (mtm-85) REVERT: M 19 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7329 (OUTLIER) REVERT: M 139 LYS cc_start: 0.7555 (tttt) cc_final: 0.7169 (ttpt) REVERT: M 180 GLU cc_start: 0.7189 (tp30) cc_final: 0.6845 (tt0) REVERT: M 354 ASN cc_start: 0.5738 (t0) cc_final: 0.5472 (t0) REVERT: M 379 GLN cc_start: 0.6751 (tt0) cc_final: 0.6461 (tt0) REVERT: O 154 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7240 (pt0) REVERT: O 164 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6584 (mp0) REVERT: O 256 VAL cc_start: 0.8131 (m) cc_final: 0.7866 (p) REVERT: S 78 GLU cc_start: 0.7691 (tt0) cc_final: 0.7238 (mt-10) REVERT: U 74 GLU cc_start: 0.4526 (OUTLIER) cc_final: 0.4236 (tt0) outliers start: 44 outliers final: 18 residues processed: 476 average time/residue: 1.6705 time to fit residues: 925.6996 Evaluate side-chains 452 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 431 time to evaluate : 3.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 74 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 6.9990 chunk 330 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 90 optimal weight: 0.6980 chunk 367 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 170 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 319 HIS B 392 GLN J 58 GLN N 202 HIS N 343 HIS M 319 HIS U 58 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 32392 Z= 0.237 Angle : 0.647 10.835 44030 Z= 0.329 Chirality : 0.044 0.154 4820 Planarity : 0.005 0.044 5526 Dihedral : 13.954 177.468 5139 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.49 % Allowed : 8.50 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 1.70 (0.13), residues: 3836 helix: 1.50 (0.11), residues: 2138 sheet: 0.78 (0.25), residues: 340 loop : 0.83 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 474 HIS 0.011 0.002 HIS N 197 PHE 0.027 0.003 PHE L 334 TYR 0.023 0.003 TYR D 237 ARG 0.004 0.001 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 438 time to evaluate : 3.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 159 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7092 (mp0) REVERT: C 288 LYS cc_start: 0.7103 (tttt) cc_final: 0.6816 (tttt) REVERT: G 13 LEU cc_start: 0.7977 (tp) cc_final: 0.7759 (tp) REVERT: G 23 ILE cc_start: 0.7784 (mt) cc_final: 0.7475 (mm) REVERT: F 138 THR cc_start: 0.8156 (m) cc_final: 0.7944 (p) REVERT: A 32 THR cc_start: 0.8285 (m) cc_final: 0.7689 (p) REVERT: A 34 ASN cc_start: 0.7908 (m110) cc_final: 0.7689 (m-40) REVERT: A 36 LYS cc_start: 0.6811 (mmtt) cc_final: 0.6486 (mppt) REVERT: A 48 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5481 (tp) REVERT: A 68 TYR cc_start: 0.6726 (m-80) cc_final: 0.6312 (m-80) REVERT: A 153 ARG cc_start: 0.6320 (ttp-110) cc_final: 0.6063 (ttm110) REVERT: A 160 LYS cc_start: 0.5162 (tptp) cc_final: 0.4900 (tppp) REVERT: A 390 LYS cc_start: 0.7241 (tptt) cc_final: 0.6951 (ttmt) REVERT: A 422 GLU cc_start: 0.6976 (mt-10) cc_final: 0.6700 (mt-10) REVERT: A 436 ARG cc_start: 0.8455 (mtp85) cc_final: 0.8142 (mtm-85) REVERT: B 19 GLU cc_start: 0.7412 (tp30) cc_final: 0.7179 (OUTLIER) REVERT: B 83 LYS cc_start: 0.8239 (mmtm) cc_final: 0.7854 (mmmm) REVERT: B 183 ARG cc_start: 0.7036 (mtm110) cc_final: 0.6573 (ttp80) REVERT: B 251 GLU cc_start: 0.6059 (mt-10) cc_final: 0.5844 (pm20) REVERT: B 339 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7214 (ttm110) REVERT: B 379 GLN cc_start: 0.6686 (tt0) cc_final: 0.6429 (tt0) REVERT: D 154 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7243 (pt0) REVERT: D 164 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6588 (mp0) REVERT: D 256 VAL cc_start: 0.8130 (m) cc_final: 0.7868 (p) REVERT: H 78 GLU cc_start: 0.7696 (tt0) cc_final: 0.7244 (mt-10) REVERT: N 250 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7708 (tppt) REVERT: N 288 LYS cc_start: 0.7072 (ttmm) cc_final: 0.6712 (tttt) REVERT: E 54 LYS cc_start: 0.7576 (tttm) cc_final: 0.7178 (mmpt) REVERT: R 13 LEU cc_start: 0.7964 (tp) cc_final: 0.7746 (tp) REVERT: R 23 ILE cc_start: 0.7820 (mt) cc_final: 0.7495 (mm) REVERT: Q 96 HIS cc_start: 0.7108 (t-90) cc_final: 0.6642 (t-90) REVERT: Q 138 THR cc_start: 0.8068 (m) cc_final: 0.7867 (p) REVERT: Q 144 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.6984 (mtt180) REVERT: L 32 THR cc_start: 0.8291 (m) cc_final: 0.7696 (p) REVERT: L 48 LEU cc_start: 0.5544 (OUTLIER) cc_final: 0.5313 (tp) REVERT: L 68 TYR cc_start: 0.6736 (m-80) cc_final: 0.6315 (m-80) REVERT: L 153 ARG cc_start: 0.6247 (ttp-110) cc_final: 0.6029 (ttm110) REVERT: L 160 LYS cc_start: 0.5198 (tptp) cc_final: 0.4903 (tppp) REVERT: L 390 LYS cc_start: 0.7327 (tptt) cc_final: 0.7056 (ttmt) REVERT: L 422 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6691 (mt-10) REVERT: L 436 ARG cc_start: 0.8460 (mtp85) cc_final: 0.8149 (mtm-85) REVERT: M 19 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7323 (mm-30) REVERT: M 180 GLU cc_start: 0.7194 (tp30) cc_final: 0.6826 (tt0) REVERT: M 183 ARG cc_start: 0.6998 (mtm110) cc_final: 0.6499 (ttp80) REVERT: M 253 LYS cc_start: 0.7392 (mtpt) cc_final: 0.7181 (mtmp) REVERT: M 354 ASN cc_start: 0.5729 (t0) cc_final: 0.5500 (t0) REVERT: M 364 MET cc_start: 0.7612 (tpp) cc_final: 0.7320 (tpt) REVERT: M 379 GLN cc_start: 0.6779 (tt0) cc_final: 0.6482 (tt0) REVERT: O 154 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7239 (pt0) REVERT: O 164 GLU cc_start: 0.6896 (mm-30) cc_final: 0.6594 (mp0) REVERT: O 256 VAL cc_start: 0.8132 (m) cc_final: 0.7870 (p) REVERT: S 78 GLU cc_start: 0.7699 (tt0) cc_final: 0.7245 (mt-10) REVERT: U 74 GLU cc_start: 0.4482 (OUTLIER) cc_final: 0.4210 (tt0) outliers start: 48 outliers final: 20 residues processed: 473 average time/residue: 1.6455 time to fit residues: 914.4029 Evaluate side-chains 454 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 431 time to evaluate : 3.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 74 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 209 optimal weight: 9.9990 chunk 268 optimal weight: 3.9990 chunk 208 optimal weight: 5.9990 chunk 309 optimal weight: 9.9990 chunk 205 optimal weight: 0.0970 chunk 366 optimal weight: 2.9990 chunk 229 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 HIS B 205 GLN B 319 HIS B 392 GLN N 202 HIS N 343 HIS L 379 ASN M 92 HIS M 205 GLN M 316 GLN M 319 HIS U 58 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 32392 Z= 0.222 Angle : 0.620 11.151 44030 Z= 0.315 Chirality : 0.043 0.157 4820 Planarity : 0.005 0.040 5526 Dihedral : 13.884 179.415 5139 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.36 % Allowed : 8.84 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 1.78 (0.14), residues: 3836 helix: 1.56 (0.11), residues: 2138 sheet: 0.81 (0.26), residues: 340 loop : 0.87 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 474 HIS 0.010 0.001 HIS N 197 PHE 0.026 0.002 PHE L 334 TYR 0.022 0.002 TYR D 237 ARG 0.004 0.001 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 436 time to evaluate : 4.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 159 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7086 (mp0) REVERT: G 13 LEU cc_start: 0.7989 (tp) cc_final: 0.7772 (tp) REVERT: G 20 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7091 (mm) REVERT: G 23 ILE cc_start: 0.7784 (mt) cc_final: 0.7470 (mm) REVERT: F 138 THR cc_start: 0.8177 (m) cc_final: 0.7961 (p) REVERT: A 32 THR cc_start: 0.8293 (m) cc_final: 0.7693 (p) REVERT: A 34 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7713 (m-40) REVERT: A 36 LYS cc_start: 0.6809 (mmtt) cc_final: 0.6485 (mppt) REVERT: A 48 LEU cc_start: 0.5749 (OUTLIER) cc_final: 0.5440 (tp) REVERT: A 68 TYR cc_start: 0.6745 (m-80) cc_final: 0.6327 (m-80) REVERT: A 153 ARG cc_start: 0.6255 (ttp-110) cc_final: 0.6031 (ttm110) REVERT: A 160 LYS cc_start: 0.5135 (tptp) cc_final: 0.4870 (tppp) REVERT: A 390 LYS cc_start: 0.7243 (OUTLIER) cc_final: 0.6950 (ttmt) REVERT: A 422 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6690 (mt-10) REVERT: A 436 ARG cc_start: 0.8452 (mtp85) cc_final: 0.8138 (mtm-85) REVERT: B 19 GLU cc_start: 0.7407 (tp30) cc_final: 0.7171 (OUTLIER) REVERT: B 83 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7874 (mmmm) REVERT: B 183 ARG cc_start: 0.7027 (mtm110) cc_final: 0.6585 (ttp80) REVERT: B 331 GLU cc_start: 0.5126 (OUTLIER) cc_final: 0.4756 (tm-30) REVERT: B 339 ARG cc_start: 0.7594 (ttp80) cc_final: 0.7257 (ttm110) REVERT: B 364 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.7392 (tpp) REVERT: B 379 GLN cc_start: 0.6671 (tt0) cc_final: 0.6407 (tt0) REVERT: D 154 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7236 (pt0) REVERT: D 164 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6537 (mp0) REVERT: D 256 VAL cc_start: 0.8134 (m) cc_final: 0.7876 (p) REVERT: H 78 GLU cc_start: 0.7695 (tt0) cc_final: 0.7240 (mt-10) REVERT: N 250 LYS cc_start: 0.7927 (ttmt) cc_final: 0.7711 (tppt) REVERT: N 288 LYS cc_start: 0.7076 (ttmm) cc_final: 0.6712 (tttt) REVERT: E 54 LYS cc_start: 0.7600 (tttm) cc_final: 0.7211 (mmpt) REVERT: R 20 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.7131 (mm) REVERT: R 23 ILE cc_start: 0.7834 (mt) cc_final: 0.7514 (mm) REVERT: Q 96 HIS cc_start: 0.7085 (t-90) cc_final: 0.6603 (t-90) REVERT: Q 138 THR cc_start: 0.8061 (m) cc_final: 0.7847 (p) REVERT: Q 144 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.7006 (mtt180) REVERT: L 32 THR cc_start: 0.8290 (m) cc_final: 0.7687 (p) REVERT: L 48 LEU cc_start: 0.5582 (OUTLIER) cc_final: 0.5338 (tp) REVERT: L 68 TYR cc_start: 0.6756 (m-80) cc_final: 0.6333 (m-80) REVERT: L 153 ARG cc_start: 0.6253 (ttp-110) cc_final: 0.6030 (ttt180) REVERT: L 160 LYS cc_start: 0.5148 (tptp) cc_final: 0.4843 (tppp) REVERT: L 390 LYS cc_start: 0.7265 (tptt) cc_final: 0.6987 (ttmt) REVERT: L 422 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6689 (mt-10) REVERT: L 436 ARG cc_start: 0.8445 (mtp85) cc_final: 0.8128 (mtm-85) REVERT: M 19 GLU cc_start: 0.7544 (OUTLIER) cc_final: 0.7333 (mm-30) REVERT: M 180 GLU cc_start: 0.7189 (tp30) cc_final: 0.6838 (tm-30) REVERT: M 183 ARG cc_start: 0.6991 (mtm110) cc_final: 0.6493 (ttp80) REVERT: M 339 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7313 (ttm110) REVERT: M 354 ASN cc_start: 0.5730 (t0) cc_final: 0.5512 (t0) REVERT: M 379 GLN cc_start: 0.6780 (tt0) cc_final: 0.6488 (tt0) REVERT: O 154 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7234 (pt0) REVERT: O 164 GLU cc_start: 0.6841 (mm-30) cc_final: 0.6544 (mp0) REVERT: O 256 VAL cc_start: 0.8132 (m) cc_final: 0.7874 (p) REVERT: S 78 GLU cc_start: 0.7698 (tt0) cc_final: 0.7242 (mt-10) REVERT: U 74 GLU cc_start: 0.4559 (OUTLIER) cc_final: 0.4151 (tt0) outliers start: 44 outliers final: 22 residues processed: 465 average time/residue: 1.6691 time to fit residues: 904.5998 Evaluate side-chains 462 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 429 time to evaluate : 3.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 83 LYS Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain J residue 55 ARG Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain N residue 119 ILE Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 74 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 0.4980 chunk 146 optimal weight: 0.0170 chunk 218 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 232 optimal weight: 3.9990 chunk 249 optimal weight: 10.0000 chunk 181 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 287 optimal weight: 2.9990 overall best weight: 1.9024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN C 202 HIS ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 205 GLN B 319 HIS B 392 GLN N 11 ASN N 202 HIS N 343 HIS L 379 ASN M 319 HIS U 58 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 32392 Z= 0.180 Angle : 0.572 11.748 44030 Z= 0.290 Chirality : 0.041 0.154 4820 Planarity : 0.004 0.038 5526 Dihedral : 13.479 179.648 5139 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.18 % Allowed : 9.24 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 1.90 (0.14), residues: 3836 helix: 1.68 (0.11), residues: 2140 sheet: 0.88 (0.26), residues: 340 loop : 0.87 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 474 HIS 0.009 0.001 HIS C 197 PHE 0.023 0.002 PHE L 334 TYR 0.021 0.002 TYR D 237 ARG 0.004 0.000 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 441 time to evaluate : 2.916 Fit side-chains revert: symmetry clash REVERT: C 288 LYS cc_start: 0.7156 (tttp) cc_final: 0.6791 (tttt) REVERT: G 13 LEU cc_start: 0.7953 (tp) cc_final: 0.7727 (tp) REVERT: G 20 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7053 (mm) REVERT: G 23 ILE cc_start: 0.7764 (mt) cc_final: 0.7466 (mm) REVERT: F 138 THR cc_start: 0.8134 (m) cc_final: 0.7910 (p) REVERT: A 32 THR cc_start: 0.8259 (m) cc_final: 0.7699 (p) REVERT: A 34 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7707 (m-40) REVERT: A 36 LYS cc_start: 0.6808 (mmtt) cc_final: 0.6508 (mppt) REVERT: A 48 LEU cc_start: 0.5821 (OUTLIER) cc_final: 0.5524 (tp) REVERT: A 68 TYR cc_start: 0.6751 (m-80) cc_final: 0.6325 (m-80) REVERT: A 153 ARG cc_start: 0.6238 (ttp-110) cc_final: 0.6016 (ttm110) REVERT: A 160 LYS cc_start: 0.5055 (tptp) cc_final: 0.4811 (tppp) REVERT: A 390 LYS cc_start: 0.7244 (OUTLIER) cc_final: 0.6930 (ttmt) REVERT: A 422 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6706 (mt-10) REVERT: A 436 ARG cc_start: 0.8441 (mtp85) cc_final: 0.8134 (mtm-85) REVERT: B 19 GLU cc_start: 0.7331 (tp30) cc_final: 0.7098 (OUTLIER) REVERT: B 183 ARG cc_start: 0.7043 (mtm110) cc_final: 0.6583 (ttp80) REVERT: B 339 ARG cc_start: 0.7578 (ttp80) cc_final: 0.7264 (ttm110) REVERT: B 364 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7378 (tpp) REVERT: B 379 GLN cc_start: 0.6705 (tt0) cc_final: 0.6416 (tt0) REVERT: D 154 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7256 (pt0) REVERT: D 256 VAL cc_start: 0.8102 (m) cc_final: 0.7859 (p) REVERT: H 78 GLU cc_start: 0.7704 (tt0) cc_final: 0.7247 (mt-10) REVERT: N 160 ASP cc_start: 0.7800 (m-30) cc_final: 0.7573 (m-30) REVERT: N 186 MET cc_start: 0.8466 (tpp) cc_final: 0.8213 (mmp) REVERT: N 250 LYS cc_start: 0.7918 (ttmt) cc_final: 0.7696 (tppt) REVERT: N 288 LYS cc_start: 0.7073 (ttmm) cc_final: 0.6724 (tttt) REVERT: E 54 LYS cc_start: 0.7692 (tttm) cc_final: 0.7310 (mmpt) REVERT: R 13 LEU cc_start: 0.7949 (tp) cc_final: 0.7737 (tp) REVERT: R 20 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.7100 (mm) REVERT: R 23 ILE cc_start: 0.7743 (mt) cc_final: 0.7427 (mm) REVERT: Q 96 HIS cc_start: 0.7065 (t-90) cc_final: 0.6618 (t-90) REVERT: Q 138 THR cc_start: 0.8012 (m) cc_final: 0.7802 (p) REVERT: Q 144 ARG cc_start: 0.7231 (mtm-85) cc_final: 0.7023 (mtt180) REVERT: L 32 THR cc_start: 0.8252 (m) cc_final: 0.7696 (p) REVERT: L 48 LEU cc_start: 0.5598 (OUTLIER) cc_final: 0.5356 (tp) REVERT: L 68 TYR cc_start: 0.6756 (m-80) cc_final: 0.6329 (m-80) REVERT: L 153 ARG cc_start: 0.6215 (ttp-110) cc_final: 0.6000 (ttm110) REVERT: L 160 LYS cc_start: 0.5118 (tptp) cc_final: 0.4810 (tppp) REVERT: L 390 LYS cc_start: 0.7271 (tptt) cc_final: 0.6947 (ttmt) REVERT: L 422 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6705 (mt-10) REVERT: L 436 ARG cc_start: 0.8435 (mtp85) cc_final: 0.8127 (mtm-85) REVERT: M 180 GLU cc_start: 0.7178 (tp30) cc_final: 0.6842 (tt0) REVERT: M 183 ARG cc_start: 0.6968 (mtm110) cc_final: 0.6493 (ttp80) REVERT: M 339 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7317 (ttm110) REVERT: M 354 ASN cc_start: 0.5911 (t0) cc_final: 0.5686 (t0) REVERT: M 379 GLN cc_start: 0.6743 (tt0) cc_final: 0.6440 (tt0) REVERT: O 154 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7255 (pt0) REVERT: O 256 VAL cc_start: 0.8101 (m) cc_final: 0.7862 (p) REVERT: S 78 GLU cc_start: 0.7707 (tt0) cc_final: 0.7248 (mt-10) REVERT: U 74 GLU cc_start: 0.4496 (OUTLIER) cc_final: 0.4105 (tt0) outliers start: 38 outliers final: 21 residues processed: 466 average time/residue: 1.6965 time to fit residues: 923.7922 Evaluate side-chains 462 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 433 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain R residue 20 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 74 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 1.9990 chunk 350 optimal weight: 10.0000 chunk 320 optimal weight: 1.9990 chunk 341 optimal weight: 9.9990 chunk 205 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 268 optimal weight: 0.5980 chunk 104 optimal weight: 10.0000 chunk 308 optimal weight: 5.9990 chunk 322 optimal weight: 20.0000 chunk 340 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN B 319 HIS N 202 HIS N 343 HIS L 379 ASN M 319 HIS U 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 32392 Z= 0.228 Angle : 0.628 11.075 44030 Z= 0.319 Chirality : 0.043 0.155 4820 Planarity : 0.005 0.042 5526 Dihedral : 13.649 179.116 5139 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.09 % Allowed : 9.68 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 1.84 (0.14), residues: 3836 helix: 1.63 (0.11), residues: 2126 sheet: 0.85 (0.26), residues: 340 loop : 0.89 (0.18), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 474 HIS 0.011 0.002 HIS N 197 PHE 0.027 0.002 PHE A 334 TYR 0.022 0.002 TYR O 237 ARG 0.005 0.001 ARG C 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 439 time to evaluate : 3.948 Fit side-chains revert: symmetry clash REVERT: C 288 LYS cc_start: 0.7127 (tttp) cc_final: 0.6760 (tttt) REVERT: G 13 LEU cc_start: 0.7986 (tp) cc_final: 0.7766 (tp) REVERT: G 20 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.7131 (mm) REVERT: G 23 ILE cc_start: 0.7700 (mt) cc_final: 0.7400 (mm) REVERT: F 138 THR cc_start: 0.8147 (m) cc_final: 0.7930 (p) REVERT: A 32 THR cc_start: 0.8291 (m) cc_final: 0.7690 (p) REVERT: A 34 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7692 (m-40) REVERT: A 36 LYS cc_start: 0.6875 (mmtt) cc_final: 0.6641 (mtmt) REVERT: A 48 LEU cc_start: 0.5856 (OUTLIER) cc_final: 0.5546 (tp) REVERT: A 68 TYR cc_start: 0.6752 (m-80) cc_final: 0.6318 (m-80) REVERT: A 153 ARG cc_start: 0.6185 (ttp-110) cc_final: 0.5974 (ttm110) REVERT: A 160 LYS cc_start: 0.5052 (tptp) cc_final: 0.4808 (tppp) REVERT: A 390 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.6939 (ttmt) REVERT: A 422 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6702 (mt-10) REVERT: A 436 ARG cc_start: 0.8451 (mtp85) cc_final: 0.8140 (mtm-85) REVERT: B 19 GLU cc_start: 0.7390 (tp30) cc_final: 0.7155 (OUTLIER) REVERT: B 183 ARG cc_start: 0.7058 (mtm110) cc_final: 0.6586 (ttp80) REVERT: B 251 GLU cc_start: 0.6205 (tt0) cc_final: 0.5677 (pm20) REVERT: B 339 ARG cc_start: 0.7584 (ttp80) cc_final: 0.7275 (ttm110) REVERT: B 364 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7363 (tpp) REVERT: B 379 GLN cc_start: 0.6677 (tt0) cc_final: 0.6395 (tt0) REVERT: D 154 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7267 (pt0) REVERT: D 164 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6537 (mp0) REVERT: D 256 VAL cc_start: 0.8099 (m) cc_final: 0.7858 (p) REVERT: H 78 GLU cc_start: 0.7704 (tt0) cc_final: 0.7261 (mt-10) REVERT: N 250 LYS cc_start: 0.7923 (ttmt) cc_final: 0.7705 (tppt) REVERT: N 288 LYS cc_start: 0.7064 (ttmm) cc_final: 0.6713 (tttt) REVERT: E 54 LYS cc_start: 0.7599 (tttm) cc_final: 0.7209 (mmpt) REVERT: R 13 LEU cc_start: 0.7972 (tp) cc_final: 0.7753 (tp) REVERT: R 23 ILE cc_start: 0.7797 (mt) cc_final: 0.7483 (mm) REVERT: Q 96 HIS cc_start: 0.7088 (t-90) cc_final: 0.6629 (t-90) REVERT: Q 138 THR cc_start: 0.8030 (m) cc_final: 0.7823 (p) REVERT: L 32 THR cc_start: 0.8290 (m) cc_final: 0.7693 (p) REVERT: L 48 LEU cc_start: 0.5609 (OUTLIER) cc_final: 0.5361 (tp) REVERT: L 68 TYR cc_start: 0.6756 (m-80) cc_final: 0.6321 (m-80) REVERT: L 160 LYS cc_start: 0.5123 (tptp) cc_final: 0.4869 (tppp) REVERT: L 390 LYS cc_start: 0.7284 (OUTLIER) cc_final: 0.7008 (ttmt) REVERT: L 422 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6703 (mt-10) REVERT: L 436 ARG cc_start: 0.8454 (mtp85) cc_final: 0.8143 (mtm-85) REVERT: M 180 GLU cc_start: 0.7177 (tp30) cc_final: 0.6862 (tm-30) REVERT: M 183 ARG cc_start: 0.6994 (mtm110) cc_final: 0.6499 (ttp80) REVERT: M 354 ASN cc_start: 0.5830 (t0) cc_final: 0.5627 (t0) REVERT: M 379 GLN cc_start: 0.6775 (tt0) cc_final: 0.6479 (tt0) REVERT: O 154 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7265 (pt0) REVERT: O 164 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6559 (mp0) REVERT: O 256 VAL cc_start: 0.8101 (m) cc_final: 0.7858 (p) REVERT: S 78 GLU cc_start: 0.7709 (tt0) cc_final: 0.7262 (mt-10) REVERT: U 74 GLU cc_start: 0.4525 (OUTLIER) cc_final: 0.4118 (tt0) outliers start: 35 outliers final: 21 residues processed: 460 average time/residue: 1.6228 time to fit residues: 873.8052 Evaluate side-chains 460 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 432 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 138 LYS Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 390 LYS Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain L residue 138 LYS Chi-restraints excluded: chain L residue 152 THR Chi-restraints excluded: chain L residue 188 ARG Chi-restraints excluded: chain L residue 390 LYS Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 371 SER Chi-restraints excluded: chain U residue 55 ARG Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 74 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 0.0980 chunk 360 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 250 optimal weight: 0.5980 chunk 378 optimal weight: 6.9990 chunk 348 optimal weight: 0.6980 chunk 301 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 184 optimal weight: 0.0770 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 205 GLN B 319 HIS B 406 GLN N 202 HIS N 343 HIS L 379 ASN M 205 GLN M 319 HIS U 58 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32392 Z= 0.136 Angle : 0.507 12.293 44030 Z= 0.251 Chirality : 0.039 0.153 4820 Planarity : 0.004 0.039 5526 Dihedral : 12.708 178.747 5139 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.62 % Allowed : 10.17 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 2.18 (0.14), residues: 3836 helix: 1.93 (0.11), residues: 2114 sheet: 1.08 (0.27), residues: 340 loop : 0.96 (0.18), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 156 HIS 0.007 0.001 HIS C 197 PHE 0.018 0.001 PHE A 334 TYR 0.017 0.001 TYR O 237 ARG 0.003 0.000 ARG L 153 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7672 Ramachandran restraints generated. 3836 Oldfield, 0 Emsley, 3836 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 459 time to evaluate : 3.686 Fit side-chains REVERT: C 186 MET cc_start: 0.8390 (tpp) cc_final: 0.8169 (mmp) REVERT: C 288 LYS cc_start: 0.7109 (tttp) cc_final: 0.6751 (tttt) REVERT: G 13 LEU cc_start: 0.7939 (tp) cc_final: 0.7716 (tp) REVERT: G 20 LEU cc_start: 0.7259 (OUTLIER) cc_final: 0.6979 (mm) REVERT: G 23 ILE cc_start: 0.7666 (mt) cc_final: 0.7408 (mm) REVERT: F 138 THR cc_start: 0.8000 (m) cc_final: 0.7776 (p) REVERT: A 32 THR cc_start: 0.8241 (m) cc_final: 0.7660 (p) REVERT: A 36 LYS cc_start: 0.6759 (mmtt) cc_final: 0.6476 (mppt) REVERT: A 48 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5583 (tp) REVERT: A 68 TYR cc_start: 0.6772 (m-80) cc_final: 0.6390 (m-80) REVERT: A 90 HIS cc_start: 0.6566 (t70) cc_final: 0.6307 (t70) REVERT: A 153 ARG cc_start: 0.6217 (ttp-110) cc_final: 0.5964 (ttt180) REVERT: A 390 LYS cc_start: 0.7189 (tptt) cc_final: 0.6929 (mtmt) REVERT: A 422 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6614 (mt-10) REVERT: A 436 ARG cc_start: 0.8411 (mtp85) cc_final: 0.8108 (mtm-85) REVERT: B 19 GLU cc_start: 0.7230 (tp30) cc_final: 0.7018 (mm-30) REVERT: B 183 ARG cc_start: 0.7108 (mtm110) cc_final: 0.6647 (ttp80) REVERT: B 213 ASP cc_start: 0.7007 (m-30) cc_final: 0.6687 (m-30) REVERT: B 236 ARG cc_start: 0.6687 (ttp-170) cc_final: 0.5828 (ttm-80) REVERT: B 251 GLU cc_start: 0.6086 (tt0) cc_final: 0.5635 (pm20) REVERT: B 253 LYS cc_start: 0.7427 (mtpt) cc_final: 0.7186 (mtmp) REVERT: B 339 ARG cc_start: 0.7546 (ttp80) cc_final: 0.7262 (ttm110) REVERT: B 364 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7399 (tpp) REVERT: B 379 GLN cc_start: 0.6697 (tt0) cc_final: 0.6347 (tt0) REVERT: D 256 VAL cc_start: 0.8080 (m) cc_final: 0.7865 (p) REVERT: H 78 GLU cc_start: 0.7719 (tt0) cc_final: 0.7281 (mt-10) REVERT: J 10 LYS cc_start: 0.7102 (tttp) cc_final: 0.6882 (tppt) REVERT: N 250 LYS cc_start: 0.7939 (ttmt) cc_final: 0.7717 (tppt) REVERT: N 288 LYS cc_start: 0.7025 (ttmm) cc_final: 0.6673 (tttt) REVERT: E 54 LYS cc_start: 0.7695 (tttm) cc_final: 0.7473 (ttmt) REVERT: R 13 LEU cc_start: 0.7936 (tp) cc_final: 0.7713 (tp) REVERT: R 23 ILE cc_start: 0.7672 (mt) cc_final: 0.7395 (mm) REVERT: Q 84 GLU cc_start: 0.6812 (tp30) cc_final: 0.6482 (mm-30) REVERT: Q 138 THR cc_start: 0.7919 (m) cc_final: 0.7711 (p) REVERT: L 32 THR cc_start: 0.8240 (m) cc_final: 0.7661 (p) REVERT: L 48 LEU cc_start: 0.5523 (OUTLIER) cc_final: 0.5289 (tp) REVERT: L 68 TYR cc_start: 0.6771 (m-80) cc_final: 0.6390 (m-80) REVERT: L 160 LYS cc_start: 0.5115 (tptp) cc_final: 0.4798 (tppp) REVERT: L 390 LYS cc_start: 0.7167 (tptt) cc_final: 0.6929 (mtmt) REVERT: L 422 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6605 (mt-10) REVERT: L 436 ARG cc_start: 0.8411 (mtp85) cc_final: 0.8110 (mtm-85) REVERT: M 139 LYS cc_start: 0.7609 (tttt) cc_final: 0.7265 (ttpt) REVERT: M 183 ARG cc_start: 0.6975 (mtm110) cc_final: 0.6522 (ttp80) REVERT: M 339 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7308 (ttm110) REVERT: M 354 ASN cc_start: 0.5866 (t0) cc_final: 0.5662 (t0) REVERT: M 379 GLN cc_start: 0.6736 (tt0) cc_final: 0.6370 (tt0) REVERT: O 256 VAL cc_start: 0.8082 (m) cc_final: 0.7860 (p) REVERT: S 78 GLU cc_start: 0.7721 (tt0) cc_final: 0.7281 (mt-10) REVERT: U 10 LYS cc_start: 0.7118 (tttp) cc_final: 0.6870 (tppt) REVERT: U 74 GLU cc_start: 0.4522 (OUTLIER) cc_final: 0.4106 (tt0) outliers start: 20 outliers final: 11 residues processed: 470 average time/residue: 1.6812 time to fit residues: 922.3089 Evaluate side-chains 462 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 445 time to evaluate : 3.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain L residue 48 LEU Chi-restraints excluded: chain L residue 99 MET Chi-restraints excluded: chain M residue 17 THR Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 339 ARG Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 74 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 0.7980 chunk 321 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 277 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 83 optimal weight: 8.9990 chunk 301 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 310 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 HIS B 205 GLN B 319 HIS J 58 GLN N 343 HIS L 90 HIS M 319 HIS U 58 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.141218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.121862 restraints weight = 29993.994| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 0.60 r_work: 0.3089 rms_B_bonded: 1.27 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 2.03 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 32392 Z= 0.168 Angle : 0.562 11.603 44030 Z= 0.281 Chirality : 0.041 0.151 4820 Planarity : 0.004 0.039 5526 Dihedral : 12.910 179.034 5137 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.81 % Allowed : 10.33 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % 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: 2.05 (0.14), residues: 3836 helix: 1.80 (0.11), residues: 2140 sheet: 1.00 (0.26), residues: 340 loop : 0.94 (0.18), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 474 HIS 0.015 0.001 HIS C 197 PHE 0.024 0.002 PHE L 334 TYR 0.020 0.002 TYR O 237 ARG 0.004 0.000 ARG R 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14152.75 seconds wall clock time: 250 minutes 31.41 seconds (15031.41 seconds total)