Starting phenix.real_space_refine on Tue Nov 21 07:42:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/11_2023/8ab6_15312_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/11_2023/8ab6_15312.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/11_2023/8ab6_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_15312/11_2023/8ab6_15312_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/11_2023/8ab6_15312_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/11_2023/8ab6_15312.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/11_2023/8ab6_15312.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/11_2023/8ab6_15312_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ab6_15312/11_2023/8ab6_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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 119 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: 119 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: 19.20, per 1000 atoms: 0.58 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: 12.80 Conformation dependent library (CDL) restraints added in 6.6 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: 5.76 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: 11.12 Time building geometry restraints manager: 13.73 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 - 28.54: 17870 28.54 - 57.09: 912 57.09 - 85.63: 143 85.63 - 114.17: 11 114.17 - 142.72: 2 Dihedral angle restraints: 18938 sinusoidal: 7652 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 18935 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.420 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 87.390 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.320 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:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.560 ------------------------------------------------------------------------------- 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 : 16.941 142.718 11654 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 *********************** 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 : 4.082 Fit side-chains outliers start: 60 outliers final: 8 residues processed: 633 average time/residue: 1.8052 time to fit residues: 1323.3953 Evaluate side-chains 429 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 421 time to evaluate : 3.755 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 4.9402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 159 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 153 optimal weight: 0.7980 chunk 297 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 181 optimal weight: 0.7980 chunk 221 optimal weight: 1.9990 chunk 345 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 11 ASN 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 192 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 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: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32392 Z= 0.198 Angle : 0.620 10.126 44030 Z= 0.317 Chirality : 0.042 0.168 4820 Planarity : 0.004 0.032 5526 Dihedral : 12.260 93.259 4686 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.40 % Allowed : 7.69 % Favored : 90.91 % 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: 1.19 (0.13), residues: 3836 helix: 1.14 (0.11), residues: 2138 sheet: 0.82 (0.26), residues: 336 loop : 0.43 (0.17), residues: 1362 *********************** 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 519 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 475 time to evaluate : 3.886 Fit side-chains outliers start: 44 outliers final: 15 residues processed: 500 average time/residue: 1.6922 time to fit residues: 989.2526 Evaluate side-chains 445 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 430 time to evaluate : 3.624 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 0.9795 time to fit residues: 9.7946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 287 optimal weight: 4.9990 chunk 234 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 345 optimal weight: 3.9990 chunk 373 optimal weight: 0.0870 chunk 307 optimal weight: 4.9990 chunk 342 optimal weight: 0.0570 chunk 117 optimal weight: 0.8980 chunk 277 optimal weight: 5.9990 overall best weight: 1.1278 ------------------------------------------------------------------------------- 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 50 GLN A 89 GLN B 319 HIS D 93 HIS J 58 GLN ** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 32392 Z= 0.155 Angle : 0.540 12.102 44030 Z= 0.273 Chirality : 0.040 0.151 4820 Planarity : 0.004 0.036 5526 Dihedral : 11.668 89.639 4686 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.21 % Allowed : 8.87 % Favored : 89.92 % 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: 1.77 (0.14), residues: 3836 helix: 1.61 (0.11), residues: 2130 sheet: 0.97 (0.26), residues: 340 loop : 0.72 (0.18), residues: 1366 *********************** 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 473 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 435 time to evaluate : 3.360 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 460 average time/residue: 1.7414 time to fit residues: 934.4586 Evaluate side-chains 425 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 409 time to evaluate : 3.760 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 1.3875 time to fit residues: 11.6554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 3.9990 chunk 259 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 346 optimal weight: 5.9990 chunk 367 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 328 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 50 GLN A 371 ASN B 205 GLN B 316 GLN B 319 HIS B 408 HIS D 93 HIS D 269 GLN J 58 GLN ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN L 89 GLN M 205 GLN M 316 GLN M 319 HIS M 354 ASN O 269 GLN U 58 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 32392 Z= 0.252 Angle : 0.659 10.544 44030 Z= 0.336 Chirality : 0.044 0.156 4820 Planarity : 0.005 0.043 5526 Dihedral : 12.140 92.644 4686 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.24 % Allowed : 8.62 % Favored : 90.14 % 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: 1.68 (0.13), residues: 3836 helix: 1.51 (0.11), residues: 2132 sheet: 0.81 (0.26), residues: 340 loop : 0.77 (0.18), residues: 1364 *********************** 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 469 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 429 time to evaluate : 3.537 Fit side-chains outliers start: 40 outliers final: 14 residues processed: 459 average time/residue: 1.7060 time to fit residues: 914.5408 Evaluate side-chains 435 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 421 time to evaluate : 3.717 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 1.0837 time to fit residues: 7.5247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 5 optimal weight: 8.9990 chunk 273 optimal weight: 2.9990 chunk 151 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 chunk 253 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 0.8980 chunk 329 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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 50 GLN A 89 GLN B 319 HIS J 58 GLN N 202 HIS ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN M 319 HIS U 58 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32392 Z= 0.202 Angle : 0.595 11.430 44030 Z= 0.302 Chirality : 0.042 0.156 4820 Planarity : 0.004 0.037 5526 Dihedral : 11.747 89.287 4686 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.24 % Allowed : 8.72 % Favored : 90.04 % 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: 1.59 (0.11), residues: 2140 sheet: 0.81 (0.26), residues: 340 loop : 0.81 (0.18), residues: 1356 *********************** 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 472 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 432 time to evaluate : 3.704 Fit side-chains outliers start: 40 outliers final: 16 residues processed: 459 average time/residue: 1.7017 time to fit residues: 916.6673 Evaluate side-chains 435 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 419 time to evaluate : 3.387 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.3459 time to fit residues: 5.7031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 0.5980 chunk 330 optimal weight: 0.3980 chunk 72 optimal weight: 9.9990 chunk 215 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 367 optimal weight: 8.9990 chunk 305 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 193 optimal weight: 0.7980 overall best weight: 1.3182 ------------------------------------------------------------------------------- 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 50 GLN B 205 GLN B 319 HIS B 392 GLN N 202 HIS ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN L 89 GLN 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: 0.8406 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 32392 Z= 0.158 Angle : 0.546 12.147 44030 Z= 0.275 Chirality : 0.040 0.150 4820 Planarity : 0.004 0.040 5526 Dihedral : 11.352 87.646 4686 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.05 % Allowed : 9.37 % 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: 1.93 (0.14), residues: 3836 helix: 1.72 (0.11), residues: 2134 sheet: 0.88 (0.26), residues: 340 loop : 0.86 (0.18), residues: 1362 *********************** 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 467 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 433 time to evaluate : 3.868 Fit side-chains outliers start: 34 outliers final: 14 residues processed: 461 average time/residue: 1.7718 time to fit residues: 952.7211 Evaluate side-chains 431 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 417 time to evaluate : 3.693 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 4.9414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 209 optimal weight: 10.0000 chunk 268 optimal weight: 0.0050 chunk 208 optimal weight: 0.9990 chunk 309 optimal weight: 10.0000 chunk 205 optimal weight: 0.8980 chunk 366 optimal weight: 4.9990 chunk 229 optimal weight: 7.9990 chunk 223 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 overall best weight: 2.3800 ------------------------------------------------------------------------------- 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 50 GLN A 89 GLN A 192 GLN B 319 HIS B 392 GLN N 202 HIS ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 379 ASN M 319 HIS U 58 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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 0.067 32392 Z= 0.203 Angle : 0.606 11.683 44030 Z= 0.306 Chirality : 0.042 0.153 4820 Planarity : 0.004 0.040 5526 Dihedral : 11.641 89.268 4686 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.93 % Allowed : 9.65 % Favored : 89.42 % 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: 1.82 (0.14), residues: 3836 helix: 1.62 (0.11), residues: 2140 sheet: 0.82 (0.26), residues: 340 loop : 0.85 (0.18), residues: 1356 *********************** 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 460 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 430 time to evaluate : 3.701 Fit side-chains outliers start: 30 outliers final: 16 residues processed: 451 average time/residue: 1.7640 time to fit residues: 929.1320 Evaluate side-chains 435 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 419 time to evaluate : 3.949 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 2.2601 time to fit residues: 10.1005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 71 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 181 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 287 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 50 GLN A 192 GLN B 197 ASN B 319 HIS N 202 HIS ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 50 GLN L 379 ASN M 319 HIS U 58 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 32392 Z= 0.211 Angle : 0.614 11.198 44030 Z= 0.311 Chirality : 0.043 0.152 4820 Planarity : 0.005 0.041 5526 Dihedral : 11.701 89.183 4686 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.90 % Allowed : 9.71 % Favored : 89.39 % 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: 1.80 (0.14), residues: 3836 helix: 1.60 (0.11), residues: 2140 sheet: 0.79 (0.26), residues: 340 loop : 0.85 (0.18), residues: 1356 *********************** 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 454 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 425 time to evaluate : 3.740 Fit side-chains outliers start: 29 outliers final: 16 residues processed: 445 average time/residue: 1.7504 time to fit residues: 912.5977 Evaluate side-chains 433 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 417 time to evaluate : 3.690 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 15 residues processed: 2 average time/residue: 0.4127 time to fit residues: 6.2881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 3.9990 chunk 350 optimal weight: 9.9990 chunk 320 optimal weight: 3.9990 chunk 341 optimal weight: 9.9990 chunk 205 optimal weight: 0.0370 chunk 148 optimal weight: 0.9980 chunk 268 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 308 optimal weight: 0.5980 chunk 322 optimal weight: 0.7980 chunk 340 optimal weight: 1.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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** A 50 GLN A 192 GLN A 371 ASN B 205 GLN B 319 HIS N 202 HIS ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 379 ASN M 92 HIS M 319 HIS U 58 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2537 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= 0.139 Angle : 0.516 12.411 44030 Z= 0.258 Chirality : 0.040 0.151 4820 Planarity : 0.004 0.041 5526 Dihedral : 10.921 87.359 4686 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.68 % Allowed : 10.30 % Favored : 89.02 % 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: 2.06 (0.14), residues: 3836 helix: 1.85 (0.11), residues: 2132 sheet: 1.00 (0.27), residues: 340 loop : 0.88 (0.18), residues: 1364 *********************** 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 460 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 438 time to evaluate : 4.053 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 456 average time/residue: 1.7271 time to fit residues: 922.9064 Evaluate side-chains 435 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 421 time to evaluate : 4.402 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 5.3070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 0.5980 chunk 360 optimal weight: 20.0000 chunk 220 optimal weight: 4.9990 chunk 171 optimal weight: 0.8980 chunk 250 optimal weight: 0.6980 chunk 378 optimal weight: 9.9990 chunk 348 optimal weight: 1.9990 chunk 301 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 232 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 A 50 GLN A 192 GLN B 205 GLN B 319 HIS J 58 GLN N 202 HIS ** N 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 HIS M 205 GLN M 319 HIS U 58 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 32392 Z= 0.137 Angle : 0.514 12.357 44030 Z= 0.256 Chirality : 0.039 0.147 4820 Planarity : 0.004 0.042 5526 Dihedral : 10.571 86.849 4686 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.50 % Allowed : 10.55 % Favored : 88.96 % 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: 2.15 (0.14), residues: 3836 helix: 1.90 (0.11), residues: 2118 sheet: 1.04 (0.27), residues: 340 loop : 0.96 (0.18), residues: 1378 ********************** 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 442 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 426 time to evaluate : 4.051 Fit side-chains outliers start: 16 outliers final: 14 residues processed: 441 average time/residue: 1.7466 time to fit residues: 903.1245 Evaluate side-chains 428 residues out of total 3220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 414 time to evaluate : 3.815 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 14 residues processed: 0 time to fit residues: 4.8432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 1.9990 chunk 321 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 277 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 301 optimal weight: 0.4980 chunk 126 optimal weight: 3.9990 chunk 310 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN A 90 HIS B 92 HIS B 205 GLN B 319 HIS J 58 GLN N 343 HIS L 90 HIS M 205 GLN U 58 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.141485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.122403 restraints weight = 30102.099| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 0.60 r_work: 0.3098 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 1.80 restraints_weight: 0.2500 r_work: 0.2757 rms_B_bonded: 4.85 restraints_weight: 0.1250 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2740 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2740 r_free = 0.2740 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2740 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32392 Z= 0.166 Angle : 0.559 11.819 44030 Z= 0.280 Chirality : 0.041 0.151 4820 Planarity : 0.004 0.041 5526 Dihedral : 10.810 88.378 4686 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.65 % Allowed : 10.55 % Favored : 88.80 % 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: 2.05 (0.14), residues: 3836 helix: 1.82 (0.11), residues: 2132 sheet: 0.93 (0.26), residues: 340 loop : 0.93 (0.18), residues: 1364 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14653.65 seconds wall clock time: 262 minutes 9.19 seconds (15729.19 seconds total)