Starting phenix.real_space_refine on Fri Mar 22 00:17:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abl_15325/03_2024/8abl_15325_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abl_15325/03_2024/8abl_15325.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abl_15325/03_2024/8abl_15325_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abl_15325/03_2024/8abl_15325_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abl_15325/03_2024/8abl_15325_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abl_15325/03_2024/8abl_15325.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abl_15325/03_2024/8abl_15325.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abl_15325/03_2024/8abl_15325_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8abl_15325/03_2024/8abl_15325_updated.pdb" } resolution = 2.1 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= 0.005 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 20480 2.51 5 N 5132 2.21 5 O 5916 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 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 GLU 97": "OE1" <-> "OE2" Residue "A TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 117": "OE1" <-> "OE2" 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 "N ARG 4": "NH1" <-> "NH2" Residue "N ARG 70": "NH1" <-> "NH2" Residue "N ARG 79": "NH1" <-> "NH2" 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 44": "OE1" <-> "OE2" Residue "L GLU 97": "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 ARG 140": "NH1" <-> "NH2" Residue "M GLU 150": "OE1" <-> "OE2" Residue "M ARG 234": "NH1" <-> "NH2" Residue "M GLU 313": "OE1" <-> "OE2" Residue "M GLU 350": "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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31660 Number of models: 1 Model: "" Number of chains: 33 Chain: "C" 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: "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: 478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 478 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} 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: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 287 Unusual residues: {'AWB': 1, 'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "P" 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: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'HEC': 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: "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: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 287 Unusual residues: {'AWB': 1, 'CDL': 1, 'HEM': 2, 'LMT': 1, 'PC1': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 77 Chain: "L" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'CDL': 2, 'XP4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 89 Unusual residues: {'CDL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 111 Unresolved non-hydrogen dihedrals: 111 Chain: "T" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "U" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.43, per 1000 atoms: 0.52 Number of scatterers: 31660 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 5916 8.00 N 5132 7.00 C 20480 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=2.06 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 123 " distance=2.07 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=2.06 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: 12.95 Conformation dependent library (CDL) restraints added in 5.3 seconds 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7268 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 182 helices and 12 sheets defined 55.8% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.66 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: 4.012A pdb=" N PHE C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY C 33 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR C 46 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 3.755A 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: 3.750A pdb=" N SER C 87 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 135 removed outlier: 3.545A pdb=" N LEU C 134 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL C 135 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 153 removed outlier: 3.534A pdb=" N LEU C 150 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL C 151 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER C 152 " --> pdb=" O CYS C 148 " (cutoff:3.500A) removed outlier: 4.310A 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: 4.006A pdb=" N THR C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 246 removed outlier: 6.874A pdb=" N SER C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE C 231 " --> pdb=" O PHE C 227 " (cutoff:3.500A) removed outlier: 3.805A 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: 3.834A pdb=" N ILE C 299 " --> pdb=" O MET C 295 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.952A 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: 4.088A pdb=" N PHE C 363 " --> pdb=" O TYR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 382 Processing helix chain 'P' and resid 59 through 91 removed outlier: 3.627A pdb=" N SER P 65 " --> pdb=" O ASN P 61 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN P 90 " --> pdb=" O ASP P 86 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N MET P 91 " --> pdb=" O PHE P 87 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 100 removed outlier: 3.663A 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: 3.647A 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 136 Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.581A 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: 4.152A 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: 3.814A pdb=" N VAL A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Proline residue: A 124 - end of helix removed outlier: 3.784A pdb=" N VAL A 127 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA A 131 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 134 " --> pdb=" O ALA A 131 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 135 " --> pdb=" O ASP A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 155 removed outlier: 3.973A pdb=" N GLU A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 3.808A 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 removed outlier: 3.502A pdb=" N THR A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) 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: 3.537A pdb=" N ILE A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 4.012A pdb=" N ARG A 315 " --> pdb=" O GLY A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 328 Processing helix chain 'A' and resid 359 through 375 removed outlier: 3.561A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 3.951A 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: 3.708A pdb=" N ALA A 391 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 4.184A 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: 3.647A pdb=" N ASP A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.969A 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: 3.659A pdb=" N LYS B 116 " --> pdb=" O ASN B 113 " (cutoff:3.500A) removed outlier: 4.144A 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 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' 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: 3.639A 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 '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: 3.604A 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 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 40 through 80 removed outlier: 4.398A pdb=" N THR H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU H 57 " --> pdb=" O LYS H 53 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N PHE H 58 " --> pdb=" O ASN H 54 " (cutoff:3.500A) removed outlier: 3.728A 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: 5.173A pdb=" N HIS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LYS I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 removed outlier: 3.509A pdb=" N LYS J 30 " --> pdb=" O PRO J 26 " (cutoff:3.500A) removed outlier: 3.539A 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: 4.011A pdb=" N PHE N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY N 33 " --> pdb=" O TRP N 30 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR N 46 " --> pdb=" O GLN N 43 " (cutoff:3.500A) removed outlier: 3.756A 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: 3.751A pdb=" N SER N 87 " --> pdb=" O ALA N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 135 removed outlier: 3.545A pdb=" N LEU N 134 " --> pdb=" O MET N 130 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL N 135 " --> pdb=" O GLY N 131 " (cutoff:3.500A) Processing helix chain 'N' and resid 138 through 153 removed outlier: 3.531A pdb=" N LEU N 150 " --> pdb=" O VAL N 146 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL N 151 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER N 152 " --> pdb=" O CYS N 148 " (cutoff:3.500A) removed outlier: 4.304A 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: 4.005A pdb=" N THR N 203 " --> pdb=" O ILE N 199 " (cutoff:3.500A) Processing helix chain 'N' and resid 221 through 246 removed outlier: 6.873A pdb=" N SER N 226 " --> pdb=" O HIS N 222 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE N 231 " --> pdb=" O PHE N 227 " (cutoff:3.500A) removed outlier: 3.806A 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: 3.833A pdb=" N ILE N 299 " --> pdb=" O MET N 295 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU N 302 " --> pdb=" O ALA N 298 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU N 303 " --> pdb=" O ILE N 299 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.951A 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: 4.087A 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: 3.617A pdb=" N SER E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASN E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N MET E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 100 removed outlier: 3.665A 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 60 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: 3.649A 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 136 Processing helix chain 'Q' and resid 139 through 145 removed outlier: 3.582A 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 81 removed outlier: 4.087A pdb=" N PHE L 81 " --> pdb=" O GLU L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 99 Processing helix chain 'L' and resid 120 through 135 removed outlier: 3.752A pdb=" N VAL L 123 " --> pdb=" O LYS L 120 " (cutoff:3.500A) Proline residue: L 124 - end of helix removed outlier: 3.714A pdb=" N LEU L 134 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN L 135 " --> pdb=" O ASP L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 156 removed outlier: 3.746A pdb=" N GLU L 149 " --> pdb=" O ASP L 145 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL L 150 " --> pdb=" O ARG L 146 " (cutoff:3.500A) removed outlier: 3.564A 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 193 removed outlier: 3.513A pdb=" N THR L 193 " --> pdb=" O GLU L 189 " (cutoff:3.500A) 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: 3.536A pdb=" N ILE L 304 " --> pdb=" O ALA L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 312 through 316 removed outlier: 4.013A pdb=" N ARG L 315 " --> pdb=" O GLY L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 320 through 328 Processing helix chain 'L' and resid 359 through 375 removed outlier: 3.523A pdb=" N LEU L 373 " --> pdb=" O GLU L 369 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER L 374 " --> pdb=" O TRP L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 379 through 395 removed outlier: 3.796A pdb=" N ALA L 391 " --> pdb=" O SER L 387 " (cutoff:3.500A) removed outlier: 4.133A 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: 3.641A pdb=" N ASP L 468 " --> pdb=" O ARG L 464 " (cutoff:3.500A) removed outlier: 3.969A 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: 3.570A pdb=" N VAL M 108 " --> pdb=" O PRO M 105 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS M 116 " --> pdb=" O ASN M 113 " (cutoff:3.500A) removed outlier: 4.143A 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: 3.506A 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 366 removed outlier: 3.909A 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 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: 3.603A 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 31 through 33 No H-bonds generated for 'chain 'S' and resid 31 through 33' Processing helix chain 'S' and resid 40 through 80 removed outlier: 4.398A 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: 6.016A pdb=" N PHE S 58 " --> pdb=" O ASN S 54 " (cutoff:3.500A) removed outlier: 3.728A 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: 5.173A pdb=" N HIS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LYS T 56 " --> pdb=" O ASP T 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 49 removed outlier: 3.534A pdb=" N LYS U 30 " --> pdb=" O PRO U 26 " (cutoff:3.500A) removed outlier: 3.540A 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: 4.157A pdb=" N LYS B 24 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 399 through 404 removed outlier: 3.628A 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: 4.151A 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: 3.665A pdb=" N GLY M 231 " --> pdb=" O PRO M 399 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'O' and resid 156 through 158 1555 hydrogen bonds defined for protein. 4248 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: 9.85 Time building geometry restraints manager: 13.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.30: 5046 1.30 - 1.51: 14789 1.51 - 1.71: 12435 1.71 - 1.91: 174 1.91 - 2.12: 20 Bond restraints: 32464 Sorted by residual: bond pdb=" C2C HEC O 401 " pdb=" C3C HEC O 401 " ideal model delta sigma weight residual 1.334 1.464 -0.130 2.00e-02 2.50e+03 4.23e+01 bond pdb=" C2C HEC D 401 " pdb=" C3C HEC D 401 " ideal model delta sigma weight residual 1.334 1.464 -0.130 2.00e-02 2.50e+03 4.22e+01 bond pdb=" C23 AWB N 507 " pdb=" O7 AWB N 507 " ideal model delta sigma weight residual 1.354 1.477 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" C21 AWB N 507 " pdb=" O5 AWB N 507 " ideal model delta sigma weight residual 1.220 1.099 0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" C2A HEC D 401 " pdb=" C3A HEC D 401 " ideal model delta sigma weight residual 1.334 1.452 -0.118 2.00e-02 2.50e+03 3.48e+01 ... (remaining 32459 not shown) Histogram of bond angle deviations from ideal: 86.41 - 104.90: 896 104.90 - 123.38: 40517 123.38 - 141.87: 2699 141.87 - 160.35: 0 160.35 - 178.83: 12 Bond angle restraints: 44124 Sorted by residual: angle pdb=" C GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta sigma weight residual 111.27 95.71 15.56 1.47e+00 4.63e-01 1.12e+02 angle pdb=" C GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta sigma weight residual 111.27 95.94 15.33 1.47e+00 4.63e-01 1.09e+02 angle pdb=" CG ARG B 90 " pdb=" CD ARG B 90 " pdb=" NE ARG B 90 " ideal model delta sigma weight residual 112.00 91.48 20.52 2.20e+00 2.07e-01 8.70e+01 angle pdb=" CG ARG O 289 " pdb=" CD ARG O 289 " pdb=" NE ARG O 289 " ideal model delta sigma weight residual 112.00 91.85 20.15 2.20e+00 2.07e-01 8.39e+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 91.86 20.14 2.20e+00 2.07e-01 8.38e+01 ... (remaining 44119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.67: 18292 31.67 - 63.34: 1052 63.34 - 95.01: 118 95.01 - 126.68: 3 126.68 - 158.36: 3 Dihedral angle restraints: 19468 sinusoidal: 8190 harmonic: 11278 Sorted by residual: dihedral pdb=" C GLU O 283 " pdb=" N GLU O 283 " pdb=" CA GLU O 283 " pdb=" CB GLU O 283 " ideal model delta harmonic sigma weight residual -122.60 -104.77 -17.83 0 2.50e+00 1.60e-01 5.09e+01 dihedral pdb=" C GLU D 283 " pdb=" N GLU D 283 " pdb=" CA GLU D 283 " pdb=" CB GLU D 283 " ideal model delta harmonic sigma weight residual -122.60 -105.09 -17.51 0 2.50e+00 1.60e-01 4.91e+01 dihedral pdb=" C2B HEC D 401 " pdb=" C3B HEC D 401 " pdb=" CAB HEC D 401 " pdb=" CBB HEC D 401 " ideal model delta sinusoidal sigma weight residual 60.00 -0.83 60.83 2 1.00e+01 1.00e-02 3.66e+01 ... (remaining 19465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.152: 4143 0.152 - 0.303: 629 0.303 - 0.455: 49 0.455 - 0.606: 3 0.606 - 0.758: 4 Chirality restraints: 4828 Sorted by residual: chirality pdb=" CB4 CDL N 505 " pdb=" CB3 CDL N 505 " pdb=" CB6 CDL N 505 " pdb=" OB6 CDL N 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.82 -0.76 2.00e-01 2.50e+01 1.44e+01 chirality pdb=" CB4 CDL C 505 " pdb=" CB3 CDL C 505 " pdb=" CB6 CDL C 505 " pdb=" OB6 CDL C 505 " both_signs ideal model delta sigma weight residual False -2.57 -1.82 -0.75 2.00e-01 2.50e+01 1.42e+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 1.26e+01 ... (remaining 4825 not shown) Planarity restraints: 5536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 AWB C 507 " 0.049 2.00e-02 2.50e+03 5.64e-02 3.18e+01 pdb=" C21 AWB C 507 " -0.063 2.00e-02 2.50e+03 pdb=" N1 AWB C 507 " -0.048 2.00e-02 2.50e+03 pdb=" O5 AWB C 507 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 76 " -0.129 9.50e-02 1.11e+02 7.20e-02 2.49e+01 pdb=" NE ARG G 76 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG G 76 " -0.081 2.00e-02 2.50e+03 pdb=" NH1 ARG G 76 " 0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG G 76 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG R 76 " 0.130 9.50e-02 1.11e+02 7.22e-02 2.45e+01 pdb=" NE ARG R 76 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG R 76 " 0.080 2.00e-02 2.50e+03 pdb=" NH1 ARG R 76 " -0.029 2.00e-02 2.50e+03 pdb=" NH2 ARG R 76 " -0.021 2.00e-02 2.50e+03 ... (remaining 5533 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 268 2.63 - 3.20: 28039 3.20 - 3.76: 52763 3.76 - 4.33: 77675 4.33 - 4.90: 118842 Nonbonded interactions: 277587 Sorted by model distance: nonbonded pdb=" NE2 HIS N 183 " pdb="FE HEM N 501 " model vdw 2.060 3.080 nonbonded pdb=" OE2 GLU A 156 " pdb=" NH2 ARG A 188 " model vdw 2.062 2.520 nonbonded pdb=" NE2 HIS C 82 " pdb="FE HEM C 501 " model vdw 2.072 3.080 nonbonded pdb=" NE2 HIS N 197 " pdb="FE HEM N 502 " model vdw 2.162 3.080 nonbonded pdb=" NE2 HIS C 96 " pdb="FE HEM C 502 " model vdw 2.202 3.080 ... (remaining 277582 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' selection = chain 'N' } ncs_group { reference = (chain 'D' and (resid 85 through 328 or resid 401)) selection = chain 'O' } ncs_group { reference = chain 'E' selection = (chain 'P' and resid 39 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' 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 11.400 Check model and map are aligned: 0.470 Set scattering table: 0.260 Process input model: 81.310 Find NCS groups from input model: 1.840 Set up NCS constraints: 0.280 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:13.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8842 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 0.199 32464 Z= 0.660 Angle : 1.687 20.515 44124 Z= 1.039 Chirality : 0.109 0.758 4828 Planarity : 0.008 0.072 5536 Dihedral : 18.714 158.356 12188 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.22 % Favored : 97.76 % Rotamer: Outliers : 4.41 % Allowed : 7.57 % Favored : 88.02 % Cbeta Deviations : 0.94 % 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: -0.94 (0.12), residues: 3834 helix: -0.60 (0.10), residues: 2142 sheet: -0.19 (0.26), residues: 338 loop : -0.47 (0.16), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP L 438 HIS 0.021 0.005 HIS L 171 PHE 0.051 0.007 PHE B 107 TYR 0.053 0.008 TYR O 237 ARG 0.083 0.003 ARG G 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 652 time to evaluate : 4.101 Fit side-chains revert: symmetry clash REVERT: C 6 LYS cc_start: 0.8624 (tttt) cc_final: 0.8417 (ttpt) REVERT: C 139 MET cc_start: 0.9132 (mmm) cc_final: 0.8915 (mmm) REVERT: C 165 LEU cc_start: 0.8446 (mt) cc_final: 0.8194 (tp) REVERT: C 186 MET cc_start: 0.8897 (tpp) cc_final: 0.8662 (tpp) REVERT: C 288 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7713 (ttpp) REVERT: C 295 MET cc_start: 0.8840 (ttp) cc_final: 0.8398 (ttp) REVERT: F 107 LYS cc_start: 0.7304 (tttt) cc_final: 0.6985 (ttmt) REVERT: F 126 GLU cc_start: 0.8605 (mp0) cc_final: 0.8388 (mp0) REVERT: F 138 THR cc_start: 0.8571 (m) cc_final: 0.8212 (p) REVERT: A 68 TYR cc_start: 0.7696 (m-80) cc_final: 0.7472 (m-80) REVERT: A 97 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7469 (mm-30) REVERT: A 99 MET cc_start: 0.7265 (ttp) cc_final: 0.7034 (tmm) REVERT: A 128 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7927 (tm-30) REVERT: A 149 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7119 (pp20) REVERT: A 153 ARG cc_start: 0.7163 (ttp-110) cc_final: 0.6568 (ttt-90) REVERT: A 160 LYS cc_start: 0.6283 (tptp) cc_final: 0.5956 (mmtp) REVERT: A 188 ARG cc_start: 0.7765 (ttm-80) cc_final: 0.7449 (ttm-80) REVERT: A 196 ASN cc_start: 0.8155 (p0) cc_final: 0.7745 (p0) REVERT: A 212 MET cc_start: 0.9114 (mtp) cc_final: 0.8613 (mtp) REVERT: A 275 MET cc_start: 0.9114 (mtp) cc_final: 0.8903 (mtp) REVERT: A 320 ARG cc_start: 0.8729 (tpt170) cc_final: 0.8358 (tpt170) REVERT: A 390 LYS cc_start: 0.8245 (tptt) cc_final: 0.7850 (mtmm) REVERT: A 433 HIS cc_start: 0.8006 (t70) cc_final: 0.7714 (m90) REVERT: B 31 GLN cc_start: 0.7433 (mt0) cc_final: 0.7060 (mm-40) REVERT: B 139 LYS cc_start: 0.8218 (tttt) cc_final: 0.7906 (ttpt) REVERT: B 215 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8201 (pt0) REVERT: B 239 THR cc_start: 0.6283 (OUTLIER) cc_final: 0.5992 (t) REVERT: B 251 GLU cc_start: 0.7179 (mp0) cc_final: 0.6819 (pm20) REVERT: B 289 VAL cc_start: 0.8892 (t) cc_final: 0.8624 (p) REVERT: B 309 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7027 (m-30) REVERT: B 313 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 364 MET cc_start: 0.8099 (tpp) cc_final: 0.7852 (tpt) REVERT: B 373 ILE cc_start: 0.7600 (mm) cc_final: 0.7384 (mp) REVERT: B 376 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7100 (pt0) REVERT: D 86 THR cc_start: 0.8377 (m) cc_final: 0.8074 (p) REVERT: D 160 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7290 (mm-30) REVERT: D 164 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7280 (mp0) REVERT: D 166 ASN cc_start: 0.8206 (m110) cc_final: 0.7977 (m-40) REVERT: D 185 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7795 (tt0) REVERT: H 41 VAL cc_start: 0.8419 (t) cc_final: 0.8182 (t) REVERT: H 51 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8710 (mtp180) REVERT: H 78 GLU cc_start: 0.8341 (tt0) cc_final: 0.8128 (tt0) REVERT: H 88 GLU cc_start: 0.7478 (mp0) cc_final: 0.7265 (mm-30) REVERT: I 30 ASP cc_start: 0.8336 (t70) cc_final: 0.8080 (t0) REVERT: I 43 ARG cc_start: 0.8001 (mtm110) cc_final: 0.7407 (ttm170) REVERT: J 10 LYS cc_start: 0.7810 (tttm) cc_final: 0.7551 (tmtp) REVERT: J 11 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6978 (mttm) REVERT: J 30 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8329 (mmtm) REVERT: N 6 LYS cc_start: 0.8626 (tttt) cc_final: 0.8417 (ttpt) REVERT: N 139 MET cc_start: 0.9137 (mmm) cc_final: 0.8847 (mmm) REVERT: N 165 LEU cc_start: 0.8433 (mt) cc_final: 0.8169 (tp) REVERT: N 178 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8968 (ptp-170) REVERT: N 186 MET cc_start: 0.8891 (tpp) cc_final: 0.8660 (tpp) REVERT: N 288 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7714 (ttpp) REVERT: N 295 MET cc_start: 0.8837 (ttp) cc_final: 0.8395 (ttp) REVERT: E 54 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7982 (mmpt) REVERT: E 55 ASP cc_start: 0.7058 (OUTLIER) cc_final: 0.6851 (p0) REVERT: E 91 MET cc_start: 0.8770 (mtp) cc_final: 0.8569 (mtm) REVERT: Q 126 GLU cc_start: 0.8597 (mp0) cc_final: 0.8306 (mp0) REVERT: Q 138 THR cc_start: 0.8572 (m) cc_final: 0.8210 (p) REVERT: L 44 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8024 (tm-30) REVERT: L 94 LEU cc_start: 0.7935 (mt) cc_final: 0.7679 (mm) REVERT: L 122 ASP cc_start: 0.7540 (m-30) cc_final: 0.7277 (m-30) REVERT: L 146 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7239 (mtp85) REVERT: L 160 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.5523 (mmtp) REVERT: L 198 GLU cc_start: 0.7418 (mt-10) cc_final: 0.7092 (tp30) REVERT: L 212 MET cc_start: 0.9037 (mtp) cc_final: 0.8688 (mtp) REVERT: L 231 LYS cc_start: 0.8105 (tttt) cc_final: 0.7779 (tptm) REVERT: L 275 MET cc_start: 0.9112 (mtp) cc_final: 0.8902 (mtp) REVERT: L 320 ARG cc_start: 0.8711 (tpt170) cc_final: 0.8315 (tpt170) REVERT: L 390 LYS cc_start: 0.8127 (tptt) cc_final: 0.7911 (mtmm) REVERT: L 426 LYS cc_start: 0.8489 (mmtp) cc_final: 0.8255 (mttt) REVERT: M 31 GLN cc_start: 0.7589 (mt0) cc_final: 0.7006 (mt0) REVERT: M 139 LYS cc_start: 0.8229 (tttt) cc_final: 0.7909 (ttpt) REVERT: M 170 TYR cc_start: 0.7613 (p90) cc_final: 0.7194 (p90) REVERT: M 215 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8181 (pt0) REVERT: M 236 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7073 (ttm-80) REVERT: M 238 SER cc_start: 0.7529 (m) cc_final: 0.7096 (p) REVERT: M 251 GLU cc_start: 0.7464 (mt-10) cc_final: 0.7182 (pm20) REVERT: M 269 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8608 (ptt) REVERT: M 288 SER cc_start: 0.8645 (OUTLIER) cc_final: 0.8438 (p) REVERT: M 309 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6718 (m-30) REVERT: M 379 GLN cc_start: 0.7476 (tt0) cc_final: 0.7237 (tt0) REVERT: O 160 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7282 (mm-30) REVERT: O 164 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7292 (mp0) REVERT: O 166 ASN cc_start: 0.8110 (m110) cc_final: 0.7871 (m-40) REVERT: O 185 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7794 (tt0) REVERT: O 288 GLU cc_start: 0.8499 (tp30) cc_final: 0.7829 (mp0) REVERT: S 41 VAL cc_start: 0.8416 (t) cc_final: 0.8177 (t) REVERT: S 78 GLU cc_start: 0.8347 (tt0) cc_final: 0.8135 (tt0) REVERT: S 88 GLU cc_start: 0.7483 (mp0) cc_final: 0.7276 (mm-30) REVERT: T 30 ASP cc_start: 0.8342 (t70) cc_final: 0.8057 (t0) REVERT: T 43 ARG cc_start: 0.7943 (mtm110) cc_final: 0.7356 (ttm170) REVERT: U 11 LYS cc_start: 0.7251 (tttt) cc_final: 0.6879 (mttm) REVERT: U 15 LYS cc_start: 0.8723 (pttt) cc_final: 0.8521 (pttt) REVERT: U 21 LEU cc_start: 0.8388 (mt) cc_final: 0.8187 (mt) outliers start: 142 outliers final: 13 residues processed: 722 average time/residue: 1.5667 time to fit residues: 1307.7509 Evaluate side-chains 472 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 439 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 288 LYS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain P residue 62 ARG Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain B residue 215 GLN Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain H residue 51 ARG Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 178 ARG Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 288 LYS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain E residue 54 LYS Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 146 ARG Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 16 SER Chi-restraints excluded: chain M residue 215 GLN Chi-restraints excluded: chain M residue 236 ARG Chi-restraints excluded: chain M residue 269 MET Chi-restraints excluded: chain M residue 288 SER Chi-restraints excluded: chain M residue 309 ASP Chi-restraints excluded: chain M residue 333 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 4.9990 chunk 288 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 297 optimal weight: 8.9990 chunk 115 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 221 optimal weight: 2.9990 chunk 345 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 173 ASN C 332 ASN C 343 HIS P 90 ASN G 54 ASN G 84 HIS A 74 HIS A 222 HIS A 332 ASN B 87 HIS ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 215 GLN B 241 ASN B 257 HIS B 354 ASN B 392 GLN D 186 GLN D 269 GLN I 39 ASN J 58 GLN N 14 ASN N 202 HIS N 332 ASN E 90 ASN R 84 HIS L 46 ASN L 98 ASN L 332 ASN L 433 HIS M 87 HIS M 205 GLN M 215 GLN M 241 ASN M 316 GLN M 354 ASN O 186 GLN O 269 GLN T 39 ASN U 58 GLN U 70 HIS Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32464 Z= 0.216 Angle : 0.629 13.953 44124 Z= 0.314 Chirality : 0.043 0.164 4828 Planarity : 0.005 0.040 5536 Dihedral : 14.878 158.076 5311 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.86 % Allowed : 10.21 % Favored : 87.93 % 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: 1.15 (0.13), residues: 3834 helix: 1.16 (0.11), residues: 2120 sheet: 0.45 (0.27), residues: 342 loop : 0.42 (0.17), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 156 HIS 0.009 0.001 HIS N 96 PHE 0.024 0.002 PHE M 107 TYR 0.023 0.002 TYR O 237 ARG 0.007 0.001 ARG U 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 458 time to evaluate : 3.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 139 MET cc_start: 0.9108 (mmm) cc_final: 0.8873 (mmm) REVERT: C 288 LYS cc_start: 0.7892 (tttp) cc_final: 0.7570 (ttpp) REVERT: C 295 MET cc_start: 0.8806 (ttp) cc_final: 0.8464 (ttp) REVERT: F 77 ASP cc_start: 0.8093 (t0) cc_final: 0.7555 (t70) REVERT: F 107 LYS cc_start: 0.7354 (tttt) cc_final: 0.7108 (ttmt) REVERT: F 138 THR cc_start: 0.8542 (m) cc_final: 0.8291 (p) REVERT: A 97 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7483 (mm-30) REVERT: A 121 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7322 (m-30) REVERT: A 149 GLU cc_start: 0.7237 (mt-10) cc_final: 0.7037 (tm-30) REVERT: A 153 ARG cc_start: 0.7279 (ttp-110) cc_final: 0.6800 (ttt-90) REVERT: A 160 LYS cc_start: 0.6261 (tptp) cc_final: 0.5968 (mmtp) REVERT: A 196 ASN cc_start: 0.8005 (p0) cc_final: 0.7780 (p0) REVERT: A 212 MET cc_start: 0.8868 (mtp) cc_final: 0.8463 (mtp) REVERT: A 236 LEU cc_start: 0.7930 (mt) cc_final: 0.7688 (mt) REVERT: A 320 ARG cc_start: 0.8619 (tpt170) cc_final: 0.8263 (tpt170) REVERT: A 390 LYS cc_start: 0.8115 (tptt) cc_final: 0.7838 (mtmm) REVERT: A 433 HIS cc_start: 0.8034 (t70) cc_final: 0.7791 (m90) REVERT: A 471 MET cc_start: 0.8840 (mtt) cc_final: 0.8626 (mtm) REVERT: B 31 GLN cc_start: 0.7599 (mt0) cc_final: 0.6839 (mp-120) REVERT: B 139 LYS cc_start: 0.8268 (tttt) cc_final: 0.7949 (ttpt) REVERT: B 239 THR cc_start: 0.6395 (OUTLIER) cc_final: 0.6085 (t) REVERT: B 251 GLU cc_start: 0.7257 (mp0) cc_final: 0.6905 (pm20) REVERT: B 289 VAL cc_start: 0.8906 (t) cc_final: 0.8649 (p) REVERT: B 313 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7694 (mt-10) REVERT: B 379 GLN cc_start: 0.7745 (tt0) cc_final: 0.7501 (tt0) REVERT: D 160 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7347 (mm-30) REVERT: D 164 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7229 (mt-10) REVERT: D 166 ASN cc_start: 0.8145 (m110) cc_final: 0.7933 (m-40) REVERT: D 254 ASP cc_start: 0.8452 (m-30) cc_final: 0.8235 (m-30) REVERT: H 78 GLU cc_start: 0.8329 (tt0) cc_final: 0.8098 (tt0) REVERT: H 88 GLU cc_start: 0.7623 (mp0) cc_final: 0.7373 (mm-30) REVERT: J 10 LYS cc_start: 0.7849 (tttm) cc_final: 0.7498 (tptm) REVERT: J 11 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6768 (mttm) REVERT: J 74 GLU cc_start: 0.5809 (pm20) cc_final: 0.5518 (mm-30) REVERT: N 288 LYS cc_start: 0.7902 (tttp) cc_final: 0.7579 (ttpp) REVERT: N 295 MET cc_start: 0.8806 (ttp) cc_final: 0.8467 (ttp) REVERT: E 86 ASP cc_start: 0.8993 (m-30) cc_final: 0.8767 (m-30) REVERT: E 91 MET cc_start: 0.8707 (mtp) cc_final: 0.8496 (mtm) REVERT: Q 77 ASP cc_start: 0.8080 (t0) cc_final: 0.7540 (t70) REVERT: Q 107 LYS cc_start: 0.7254 (tttt) cc_final: 0.6983 (ttmt) REVERT: Q 138 THR cc_start: 0.8532 (m) cc_final: 0.8291 (p) REVERT: L 44 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8170 (tp30) REVERT: L 99 MET cc_start: 0.7245 (tmm) cc_final: 0.6710 (tmm) REVERT: L 160 LYS cc_start: 0.5864 (tptp) cc_final: 0.5554 (mmtp) REVERT: L 198 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7144 (tp30) REVERT: L 212 MET cc_start: 0.8884 (mtp) cc_final: 0.8494 (mtp) REVERT: L 320 ARG cc_start: 0.8618 (tpt170) cc_final: 0.8244 (tpt170) REVERT: L 390 LYS cc_start: 0.8114 (tptt) cc_final: 0.7908 (mttm) REVERT: L 436 ARG cc_start: 0.8424 (mtp85) cc_final: 0.8126 (mtm-85) REVERT: M 31 GLN cc_start: 0.7651 (mt0) cc_final: 0.6884 (mp-120) REVERT: M 139 LYS cc_start: 0.8246 (tttt) cc_final: 0.7909 (ttpt) REVERT: M 236 ARG cc_start: 0.7441 (mtt90) cc_final: 0.7060 (ttm-80) REVERT: M 238 SER cc_start: 0.7500 (m) cc_final: 0.6928 (p) REVERT: M 273 VAL cc_start: 0.7667 (OUTLIER) cc_final: 0.7345 (t) REVERT: M 309 ASP cc_start: 0.7201 (OUTLIER) cc_final: 0.6843 (m-30) REVERT: M 379 GLN cc_start: 0.7507 (tt0) cc_final: 0.7285 (tt0) REVERT: O 121 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8655 (ttpt) REVERT: O 160 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7322 (mm-30) REVERT: O 164 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7234 (mp0) REVERT: O 166 ASN cc_start: 0.8219 (m110) cc_final: 0.8014 (m-40) REVERT: O 254 ASP cc_start: 0.8444 (m-30) cc_final: 0.8227 (m-30) REVERT: S 78 GLU cc_start: 0.8331 (tt0) cc_final: 0.8099 (tt0) REVERT: S 88 GLU cc_start: 0.7620 (mp0) cc_final: 0.7368 (mm-30) REVERT: U 11 LYS cc_start: 0.7127 (OUTLIER) cc_final: 0.6863 (mttm) REVERT: U 74 GLU cc_start: 0.5850 (pm20) cc_final: 0.5548 (mm-30) outliers start: 60 outliers final: 14 residues processed: 498 average time/residue: 1.6351 time to fit residues: 942.9823 Evaluate side-chains 434 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 411 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain A residue 87 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 58 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 273 VAL Chi-restraints excluded: chain M residue 309 ASP Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain U residue 11 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 191 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 287 optimal weight: 0.1980 chunk 234 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 345 optimal weight: 5.9990 chunk 373 optimal weight: 10.0000 chunk 307 optimal weight: 0.6980 chunk 342 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 277 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 85 GLN A 371 ASN B 354 ASN I 39 ASN E 85 GLN M 197 ASN M 316 GLN M 354 ASN O 90 HIS T 39 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 32464 Z= 0.162 Angle : 0.542 14.188 44124 Z= 0.266 Chirality : 0.040 0.155 4828 Planarity : 0.004 0.043 5536 Dihedral : 13.506 152.764 5248 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.46 % Allowed : 11.05 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.14), residues: 3834 helix: 1.57 (0.11), residues: 2112 sheet: 0.71 (0.27), residues: 342 loop : 0.74 (0.18), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 156 HIS 0.007 0.001 HIS N 96 PHE 0.022 0.002 PHE A 334 TYR 0.017 0.002 TYR N 16 ARG 0.009 0.000 ARG J 55 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 420 time to evaluate : 3.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 139 MET cc_start: 0.9100 (mmm) cc_final: 0.8868 (mmm) REVERT: C 288 LYS cc_start: 0.7770 (tttp) cc_final: 0.7443 (ttpp) REVERT: C 295 MET cc_start: 0.8782 (ttp) cc_final: 0.8487 (ttp) REVERT: F 107 LYS cc_start: 0.7395 (tttt) cc_final: 0.7139 (ttmt) REVERT: F 138 THR cc_start: 0.8510 (m) cc_final: 0.8251 (p) REVERT: A 90 HIS cc_start: 0.7741 (t70) cc_final: 0.7026 (t-170) REVERT: A 97 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: A 128 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7816 (tm-30) REVERT: A 149 GLU cc_start: 0.7257 (mt-10) cc_final: 0.7035 (tm-30) REVERT: A 153 ARG cc_start: 0.7285 (ttp-110) cc_final: 0.6782 (ttt-90) REVERT: A 160 LYS cc_start: 0.6173 (tptp) cc_final: 0.5855 (mmtp) REVERT: A 188 ARG cc_start: 0.7392 (ttm-80) cc_final: 0.7160 (ttm-80) REVERT: A 212 MET cc_start: 0.8849 (mtp) cc_final: 0.8489 (mtp) REVERT: A 230 GLU cc_start: 0.8072 (tp30) cc_final: 0.7771 (mt-10) REVERT: A 236 LEU cc_start: 0.7880 (mt) cc_final: 0.7646 (mt) REVERT: A 390 LYS cc_start: 0.8144 (tptt) cc_final: 0.7911 (mtmm) REVERT: A 424 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: A 433 HIS cc_start: 0.8050 (t70) cc_final: 0.7795 (m90) REVERT: A 471 MET cc_start: 0.8803 (mtt) cc_final: 0.8601 (mtm) REVERT: B 31 GLN cc_start: 0.7647 (mt0) cc_final: 0.6876 (mp-120) REVERT: B 139 LYS cc_start: 0.8321 (tttt) cc_final: 0.7993 (ttpt) REVERT: B 236 ARG cc_start: 0.7733 (ttm170) cc_final: 0.7067 (ttm-80) REVERT: B 251 GLU cc_start: 0.7254 (mp0) cc_final: 0.6982 (pm20) REVERT: B 289 VAL cc_start: 0.8877 (t) cc_final: 0.8587 (p) REVERT: B 313 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7712 (mt-10) REVERT: D 121 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8642 (ttpt) REVERT: D 160 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7358 (mm-30) REVERT: D 164 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7166 (mt-10) REVERT: D 166 ASN cc_start: 0.8097 (m110) cc_final: 0.7888 (m-40) REVERT: H 78 GLU cc_start: 0.8375 (tt0) cc_final: 0.8159 (tt0) REVERT: H 88 GLU cc_start: 0.7734 (mp0) cc_final: 0.7472 (mm-30) REVERT: J 10 LYS cc_start: 0.7836 (tttm) cc_final: 0.7603 (tptt) REVERT: J 11 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6748 (mttm) REVERT: J 74 GLU cc_start: 0.5757 (pm20) cc_final: 0.5478 (mm-30) REVERT: N 288 LYS cc_start: 0.7776 (tttp) cc_final: 0.7449 (ttpp) REVERT: N 295 MET cc_start: 0.8785 (ttp) cc_final: 0.8487 (ttp) REVERT: Q 96 HIS cc_start: 0.7399 (t-90) cc_final: 0.7008 (t70) REVERT: Q 107 LYS cc_start: 0.7318 (tttt) cc_final: 0.7096 (ttmt) REVERT: Q 138 THR cc_start: 0.8502 (m) cc_final: 0.8250 (p) REVERT: L 87 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.6952 (ptp90) REVERT: L 90 HIS cc_start: 0.7574 (t70) cc_final: 0.7176 (t-170) REVERT: L 99 MET cc_start: 0.7311 (tmm) cc_final: 0.6923 (tmm) REVERT: L 146 ARG cc_start: 0.7502 (ttm110) cc_final: 0.7157 (mtm-85) REVERT: L 160 LYS cc_start: 0.5851 (tptp) cc_final: 0.5573 (mmtp) REVERT: L 198 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7214 (tp30) REVERT: L 212 MET cc_start: 0.8843 (mtp) cc_final: 0.8490 (mtp) REVERT: L 424 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: M 31 GLN cc_start: 0.7710 (mt0) cc_final: 0.6918 (mp-120) REVERT: M 139 LYS cc_start: 0.8286 (tttt) cc_final: 0.7960 (ttpt) REVERT: M 236 ARG cc_start: 0.7498 (mtt90) cc_final: 0.7090 (ttm-80) REVERT: M 309 ASP cc_start: 0.7310 (OUTLIER) cc_final: 0.6935 (m-30) REVERT: O 160 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7336 (mm-30) REVERT: O 164 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7179 (mt-10) REVERT: O 166 ASN cc_start: 0.8165 (m110) cc_final: 0.7952 (m-40) REVERT: O 254 ASP cc_start: 0.8427 (m-30) cc_final: 0.8185 (m-30) REVERT: S 78 GLU cc_start: 0.8373 (tt0) cc_final: 0.8153 (tt0) REVERT: S 88 GLU cc_start: 0.7738 (mp0) cc_final: 0.7465 (mm-30) REVERT: U 11 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6883 (mttm) REVERT: U 74 GLU cc_start: 0.5862 (pm20) cc_final: 0.5430 (mm-30) outliers start: 47 outliers final: 19 residues processed: 458 average time/residue: 1.6557 time to fit residues: 876.7870 Evaluate side-chains 434 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 407 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 157 LEU Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 424 GLU Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 309 ASP Chi-restraints excluded: chain U residue 11 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 341 optimal weight: 9.9990 chunk 259 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 38 optimal weight: 0.2980 chunk 164 optimal weight: 8.9990 chunk 232 optimal weight: 9.9990 chunk 346 optimal weight: 6.9990 chunk 367 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 328 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS A 332 ASN A 371 ASN B 205 GLN B 280 GLN B 354 ASN L 90 HIS L 332 ASN M 316 GLN M 379 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 32464 Z= 0.373 Angle : 0.721 14.585 44124 Z= 0.359 Chirality : 0.048 0.298 4828 Planarity : 0.006 0.053 5536 Dihedral : 13.922 145.485 5240 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.42 % Allowed : 10.21 % Favored : 87.37 % 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: 1.46 (0.14), residues: 3834 helix: 1.26 (0.11), residues: 2138 sheet: 0.71 (0.27), residues: 340 loop : 0.80 (0.19), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 474 HIS 0.012 0.002 HIS C 197 PHE 0.029 0.003 PHE N 240 TYR 0.025 0.003 TYR C 16 ARG 0.009 0.001 ARG G 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 414 time to evaluate : 3.528 Fit side-chains REVERT: C 1 MET cc_start: 0.8216 (ttm) cc_final: 0.8004 (ttm) REVERT: C 186 MET cc_start: 0.8806 (tpp) cc_final: 0.8600 (tpp) REVERT: C 202 HIS cc_start: 0.8951 (OUTLIER) cc_final: 0.8481 (t-90) REVERT: C 288 LYS cc_start: 0.8008 (tttp) cc_final: 0.7642 (ttpp) REVERT: G 116 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8586 (ttmm) REVERT: F 107 LYS cc_start: 0.7313 (tttt) cc_final: 0.7090 (ttmt) REVERT: F 138 THR cc_start: 0.8528 (m) cc_final: 0.8321 (p) REVERT: A 36 LYS cc_start: 0.8314 (OUTLIER) cc_final: 0.8089 (mptm) REVERT: A 97 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7481 (mm-30) REVERT: A 144 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8074 (mm) REVERT: A 149 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7135 (pp20) REVERT: A 153 ARG cc_start: 0.7324 (ttp-110) cc_final: 0.6792 (ttt-90) REVERT: A 160 LYS cc_start: 0.6231 (tptp) cc_final: 0.5945 (mmtp) REVERT: A 194 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7136 (tp) REVERT: A 205 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7299 (mp0) REVERT: A 212 MET cc_start: 0.8879 (mtp) cc_final: 0.8482 (mtp) REVERT: A 320 ARG cc_start: 0.8602 (tpt170) cc_final: 0.8324 (tpt170) REVERT: A 390 LYS cc_start: 0.8183 (tptt) cc_final: 0.7927 (mtmm) REVERT: A 433 HIS cc_start: 0.8167 (t70) cc_final: 0.7828 (m90) REVERT: B 31 GLN cc_start: 0.7686 (mt0) cc_final: 0.6948 (mp-120) REVERT: B 139 LYS cc_start: 0.8312 (tttt) cc_final: 0.8007 (ttpt) REVERT: B 239 THR cc_start: 0.6483 (OUTLIER) cc_final: 0.6281 (t) REVERT: B 289 VAL cc_start: 0.8906 (t) cc_final: 0.8647 (p) REVERT: B 313 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7729 (mt-10) REVERT: D 85 MET cc_start: 0.7606 (mtp) cc_final: 0.7295 (mtp) REVERT: D 121 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8644 (ttpt) REVERT: D 160 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7300 (mm-30) REVERT: D 164 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7292 (mp0) REVERT: H 78 GLU cc_start: 0.8377 (tt0) cc_final: 0.8099 (tt0) REVERT: H 88 GLU cc_start: 0.7686 (mp0) cc_final: 0.7363 (mm-30) REVERT: J 10 LYS cc_start: 0.7844 (tttm) cc_final: 0.7605 (tptm) REVERT: J 11 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6739 (mtmm) REVERT: J 74 GLU cc_start: 0.5746 (pm20) cc_final: 0.5500 (mm-30) REVERT: N 1 MET cc_start: 0.8200 (ttm) cc_final: 0.7987 (ttm) REVERT: N 288 LYS cc_start: 0.7994 (tttp) cc_final: 0.7626 (ttpp) REVERT: R 116 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8585 (ttmm) REVERT: Q 107 LYS cc_start: 0.7381 (tttt) cc_final: 0.7131 (ttmt) REVERT: Q 138 THR cc_start: 0.8532 (m) cc_final: 0.8329 (p) REVERT: L 44 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7503 (tp30) REVERT: L 87 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.6806 (ptp90) REVERT: L 160 LYS cc_start: 0.5935 (OUTLIER) cc_final: 0.5658 (mmtp) REVERT: L 198 GLU cc_start: 0.7554 (mt-10) cc_final: 0.7321 (tp30) REVERT: L 212 MET cc_start: 0.8870 (mtp) cc_final: 0.8469 (mtp) REVERT: M 31 GLN cc_start: 0.7604 (mt0) cc_final: 0.6721 (mp-120) REVERT: M 139 LYS cc_start: 0.8319 (tttt) cc_final: 0.7996 (ttpt) REVERT: M 236 ARG cc_start: 0.7520 (mtt90) cc_final: 0.7106 (mtp85) REVERT: M 309 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: M 356 ASP cc_start: 0.6902 (m-30) cc_final: 0.6684 (m-30) REVERT: O 121 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8652 (ttpt) REVERT: O 160 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7313 (mm-30) REVERT: O 164 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7156 (mm-30) REVERT: O 166 ASN cc_start: 0.8195 (m110) cc_final: 0.7984 (m-40) REVERT: S 78 GLU cc_start: 0.8377 (tt0) cc_final: 0.8097 (tt0) REVERT: S 88 GLU cc_start: 0.7700 (mp0) cc_final: 0.7376 (mm-30) REVERT: U 11 LYS cc_start: 0.7194 (OUTLIER) cc_final: 0.6754 (mttm) REVERT: U 74 GLU cc_start: 0.5769 (pm20) cc_final: 0.5504 (mm-30) outliers start: 78 outliers final: 32 residues processed: 472 average time/residue: 1.6711 time to fit residues: 917.6226 Evaluate side-chains 454 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 405 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 202 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 36 LYS Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain R residue 116 LYS Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 44 GLU Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 137 SER Chi-restraints excluded: chain L residue 160 LYS Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 234 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 400 THR Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 289 VAL Chi-restraints excluded: chain M residue 309 ASP Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain U residue 11 LYS Chi-restraints excluded: chain U residue 67 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 305 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 273 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 313 optimal weight: 7.9990 chunk 253 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 4.9990 chunk 329 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 202 HIS A 235 HIS B 354 ASN I 39 ASN N 202 HIS L 235 HIS L 410 GLN M 316 GLN M 354 ASN T 39 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32464 Z= 0.202 Angle : 0.579 14.786 44124 Z= 0.286 Chirality : 0.042 0.172 4828 Planarity : 0.004 0.052 5536 Dihedral : 13.456 146.689 5240 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.89 % Allowed : 10.68 % Favored : 87.43 % 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 (0.14), residues: 3834 helix: 1.47 (0.11), residues: 2130 sheet: 0.77 (0.27), residues: 340 loop : 0.85 (0.18), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 156 HIS 0.013 0.001 HIS C 202 PHE 0.023 0.002 PHE A 334 TYR 0.019 0.002 TYR N 16 ARG 0.009 0.001 ARG U 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 425 time to evaluate : 3.891 Fit side-chains REVERT: C 186 MET cc_start: 0.8787 (tpp) cc_final: 0.8525 (mmp) REVERT: C 288 LYS cc_start: 0.7866 (tttp) cc_final: 0.7549 (ttpp) REVERT: F 107 LYS cc_start: 0.7314 (tttt) cc_final: 0.7112 (ttmt) REVERT: F 138 THR cc_start: 0.8476 (m) cc_final: 0.8262 (p) REVERT: A 90 HIS cc_start: 0.7678 (t70) cc_final: 0.7217 (t-170) REVERT: A 97 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: A 144 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8065 (mm) REVERT: A 153 ARG cc_start: 0.7240 (ttp-110) cc_final: 0.6744 (ttt-90) REVERT: A 160 LYS cc_start: 0.6207 (tptp) cc_final: 0.5932 (mmtp) REVERT: A 188 ARG cc_start: 0.7479 (ttm-80) cc_final: 0.7252 (ttm-80) REVERT: A 205 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7207 (mp0) REVERT: A 212 MET cc_start: 0.8842 (mtp) cc_final: 0.8454 (mtp) REVERT: A 230 GLU cc_start: 0.8066 (tp30) cc_final: 0.7763 (mt-10) REVERT: A 320 ARG cc_start: 0.8561 (tpt170) cc_final: 0.8283 (tpt170) REVERT: A 390 LYS cc_start: 0.8139 (tptt) cc_final: 0.7927 (mtmm) REVERT: A 433 HIS cc_start: 0.8161 (t70) cc_final: 0.7813 (m90) REVERT: B 31 GLN cc_start: 0.7729 (mt0) cc_final: 0.6915 (mp-120) REVERT: B 139 LYS cc_start: 0.8341 (tttt) cc_final: 0.8005 (ttpt) REVERT: B 289 VAL cc_start: 0.8849 (t) cc_final: 0.8617 (p) REVERT: B 313 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7705 (mt-10) REVERT: D 85 MET cc_start: 0.7454 (mtp) cc_final: 0.6976 (mtp) REVERT: D 121 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8656 (ttpt) REVERT: D 160 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7249 (mm-30) REVERT: D 164 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7242 (mt-10) REVERT: H 78 GLU cc_start: 0.8387 (tt0) cc_final: 0.8126 (tt0) REVERT: H 88 GLU cc_start: 0.7677 (mp0) cc_final: 0.7396 (mm-30) REVERT: J 10 LYS cc_start: 0.7877 (tttm) cc_final: 0.7654 (tptm) REVERT: J 11 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6784 (mtmm) REVERT: J 74 GLU cc_start: 0.5785 (pm20) cc_final: 0.5472 (mm-30) REVERT: N 288 LYS cc_start: 0.7866 (tttp) cc_final: 0.7550 (ttpp) REVERT: R 66 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8067 (mm-30) REVERT: Q 107 LYS cc_start: 0.7454 (tttt) cc_final: 0.7240 (ttmt) REVERT: Q 138 THR cc_start: 0.8485 (m) cc_final: 0.8272 (p) REVERT: L 36 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7773 (mppt) REVERT: L 87 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.6831 (ptp90) REVERT: L 146 ARG cc_start: 0.7467 (ttm110) cc_final: 0.7132 (mtm-85) REVERT: L 160 LYS cc_start: 0.5858 (tptp) cc_final: 0.5628 (mmtp) REVERT: L 198 GLU cc_start: 0.7495 (mt-10) cc_final: 0.7264 (tp30) REVERT: L 212 MET cc_start: 0.8846 (mtp) cc_final: 0.8471 (mtp) REVERT: M 19 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7906 (tp30) REVERT: M 31 GLN cc_start: 0.7662 (mt0) cc_final: 0.6778 (mp-120) REVERT: M 139 LYS cc_start: 0.8322 (tttt) cc_final: 0.7979 (ttpt) REVERT: M 236 ARG cc_start: 0.7461 (mtt90) cc_final: 0.7073 (mtp85) REVERT: M 309 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7225 (m-30) REVERT: M 356 ASP cc_start: 0.6765 (m-30) cc_final: 0.6558 (m-30) REVERT: O 121 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8665 (ttpt) REVERT: O 160 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7266 (mm-30) REVERT: O 164 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7222 (mp0) REVERT: S 78 GLU cc_start: 0.8383 (tt0) cc_final: 0.8109 (tt0) REVERT: S 88 GLU cc_start: 0.7669 (mp0) cc_final: 0.7414 (mm-30) REVERT: U 10 LYS cc_start: 0.7922 (tttm) cc_final: 0.7691 (tptt) REVERT: U 11 LYS cc_start: 0.7182 (tttt) cc_final: 0.6753 (mttm) REVERT: U 74 GLU cc_start: 0.5808 (pm20) cc_final: 0.5399 (mm-30) outliers start: 61 outliers final: 33 residues processed: 465 average time/residue: 1.6658 time to fit residues: 894.7943 Evaluate side-chains 455 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 411 time to evaluate : 3.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain R residue 23 ILE Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 201 LYS Chi-restraints excluded: chain L residue 220 VAL Chi-restraints excluded: chain L residue 234 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 309 ASP Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain S residue 86 ARG Chi-restraints excluded: chain U residue 67 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 123 optimal weight: 9.9990 chunk 330 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 215 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 367 optimal weight: 9.9990 chunk 305 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 chunk 193 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN I 39 ASN L 235 HIS M 316 GLN M 354 ASN T 39 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32464 Z= 0.246 Angle : 0.612 14.858 44124 Z= 0.303 Chirality : 0.043 0.208 4828 Planarity : 0.005 0.051 5536 Dihedral : 13.403 146.437 5239 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.89 % Allowed : 10.68 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.14), residues: 3834 helix: 1.46 (0.11), residues: 2138 sheet: 0.78 (0.27), residues: 340 loop : 0.91 (0.19), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 280 HIS 0.011 0.001 HIS C 197 PHE 0.024 0.002 PHE L 334 TYR 0.024 0.002 TYR C 16 ARG 0.010 0.001 ARG U 55 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 413 time to evaluate : 3.360 Fit side-chains REVERT: C 288 LYS cc_start: 0.7912 (tttp) cc_final: 0.7590 (ttpp) REVERT: F 138 THR cc_start: 0.8485 (m) cc_final: 0.8281 (p) REVERT: A 90 HIS cc_start: 0.7699 (t70) cc_final: 0.7250 (t-170) REVERT: A 97 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7467 (mm-30) REVERT: A 144 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8051 (mm) REVERT: A 153 ARG cc_start: 0.7252 (ttp-110) cc_final: 0.6732 (ttt-90) REVERT: A 160 LYS cc_start: 0.6262 (tptp) cc_final: 0.5965 (mmtp) REVERT: A 188 ARG cc_start: 0.7437 (ttm-80) cc_final: 0.7214 (ttm-80) REVERT: A 194 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.7030 (tp) REVERT: A 205 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: A 212 MET cc_start: 0.8853 (mtp) cc_final: 0.8460 (mtp) REVERT: A 230 GLU cc_start: 0.8052 (tp30) cc_final: 0.7765 (mt-10) REVERT: A 320 ARG cc_start: 0.8575 (tpt170) cc_final: 0.8300 (tpt170) REVERT: A 390 LYS cc_start: 0.8188 (tptt) cc_final: 0.7932 (mtmm) REVERT: A 424 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: A 433 HIS cc_start: 0.8146 (t70) cc_final: 0.7792 (m90) REVERT: A 471 MET cc_start: 0.8867 (mtt) cc_final: 0.8625 (mtm) REVERT: B 31 GLN cc_start: 0.7752 (mt0) cc_final: 0.6866 (mp-120) REVERT: B 139 LYS cc_start: 0.8274 (tttt) cc_final: 0.7984 (ttpt) REVERT: B 239 THR cc_start: 0.6469 (OUTLIER) cc_final: 0.6236 (t) REVERT: B 289 VAL cc_start: 0.8853 (t) cc_final: 0.8625 (p) REVERT: B 313 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7714 (mt-10) REVERT: D 85 MET cc_start: 0.7448 (mtp) cc_final: 0.6976 (mtp) REVERT: D 121 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8670 (ttpt) REVERT: D 160 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7269 (mm-30) REVERT: D 164 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7209 (mt-10) REVERT: H 78 GLU cc_start: 0.8388 (tt0) cc_final: 0.8108 (tt0) REVERT: H 88 GLU cc_start: 0.7652 (mp0) cc_final: 0.7355 (mm-30) REVERT: J 11 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6735 (mtmm) REVERT: J 74 GLU cc_start: 0.5829 (pm20) cc_final: 0.5418 (mm-30) REVERT: N 1 MET cc_start: 0.8204 (ttm) cc_final: 0.7996 (ttm) REVERT: N 288 LYS cc_start: 0.7915 (tttp) cc_final: 0.7592 (ttpp) REVERT: R 66 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8076 (mm-30) REVERT: Q 107 LYS cc_start: 0.7471 (tttt) cc_final: 0.7264 (ttmt) REVERT: Q 138 THR cc_start: 0.8488 (m) cc_final: 0.8285 (p) REVERT: L 36 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7764 (mppt) REVERT: L 87 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.6737 (ptp90) REVERT: L 146 ARG cc_start: 0.7479 (ttm110) cc_final: 0.7137 (mtm-85) REVERT: L 160 LYS cc_start: 0.5937 (tptp) cc_final: 0.5691 (mmtp) REVERT: L 198 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7295 (tp30) REVERT: L 205 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7184 (mp0) REVERT: L 212 MET cc_start: 0.8859 (mtp) cc_final: 0.8479 (mtp) REVERT: M 19 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8027 (tp30) REVERT: M 31 GLN cc_start: 0.7673 (mt0) cc_final: 0.6777 (mp10) REVERT: M 139 LYS cc_start: 0.8276 (tttt) cc_final: 0.7975 (ttpt) REVERT: M 180 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7544 (tm-30) REVERT: M 236 ARG cc_start: 0.7423 (mtt90) cc_final: 0.7061 (mtp85) REVERT: M 289 VAL cc_start: 0.8896 (t) cc_final: 0.8596 (p) REVERT: M 309 ASP cc_start: 0.7628 (p0) cc_final: 0.7192 (m-30) REVERT: O 121 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8672 (ttpt) REVERT: O 160 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7273 (mm-30) REVERT: O 164 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7171 (mp0) REVERT: S 78 GLU cc_start: 0.8385 (tt0) cc_final: 0.8108 (tt0) REVERT: S 88 GLU cc_start: 0.7658 (mp0) cc_final: 0.7365 (mm-30) REVERT: U 10 LYS cc_start: 0.7892 (tttm) cc_final: 0.7675 (tptt) REVERT: U 11 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6740 (mttm) REVERT: U 74 GLU cc_start: 0.5818 (pm20) cc_final: 0.5404 (mm-30) outliers start: 61 outliers final: 30 residues processed: 458 average time/residue: 1.6508 time to fit residues: 874.8166 Evaluate side-chains 454 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 408 time to evaluate : 3.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 201 LYS Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 234 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 400 THR Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 180 GLU Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain S residue 86 ARG Chi-restraints excluded: chain U residue 11 LYS Chi-restraints excluded: chain U residue 67 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 354 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 209 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 309 optimal weight: 3.9990 chunk 205 optimal weight: 4.9990 chunk 366 optimal weight: 10.0000 chunk 229 optimal weight: 8.9990 chunk 223 optimal weight: 0.9980 chunk 169 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN I 39 ASN M 354 ASN T 39 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32464 Z= 0.212 Angle : 0.581 14.785 44124 Z= 0.286 Chirality : 0.042 0.174 4828 Planarity : 0.004 0.050 5536 Dihedral : 13.236 146.898 5237 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.77 % Allowed : 11.02 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.14), residues: 3834 helix: 1.55 (0.11), residues: 2126 sheet: 0.78 (0.27), residues: 340 loop : 0.99 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 280 HIS 0.009 0.001 HIS C 197 PHE 0.023 0.002 PHE L 334 TYR 0.020 0.002 TYR C 16 ARG 0.007 0.000 ARG J 55 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 415 time to evaluate : 3.325 Fit side-chains REVERT: C 1 MET cc_start: 0.8207 (ttm) cc_final: 0.7992 (ttm) REVERT: C 288 LYS cc_start: 0.7880 (tttp) cc_final: 0.7562 (ttpp) REVERT: G 66 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8049 (mm-30) REVERT: F 138 THR cc_start: 0.8467 (m) cc_final: 0.8258 (p) REVERT: A 90 HIS cc_start: 0.7668 (t70) cc_final: 0.7191 (t-170) REVERT: A 97 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7470 (mm-30) REVERT: A 144 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.8041 (mm) REVERT: A 146 ARG cc_start: 0.7652 (ttm110) cc_final: 0.7366 (mtm-85) REVERT: A 153 ARG cc_start: 0.7261 (ttp-110) cc_final: 0.6737 (ttt-90) REVERT: A 160 LYS cc_start: 0.6219 (tptp) cc_final: 0.5942 (mmtp) REVERT: A 188 ARG cc_start: 0.7467 (ttm-80) cc_final: 0.7248 (ttm-80) REVERT: A 194 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7020 (tp) REVERT: A 205 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7209 (mp0) REVERT: A 212 MET cc_start: 0.8844 (mtp) cc_final: 0.8450 (mtp) REVERT: A 230 GLU cc_start: 0.8060 (tp30) cc_final: 0.7761 (mt-10) REVERT: A 292 GLU cc_start: 0.8048 (mp0) cc_final: 0.7792 (mp0) REVERT: A 320 ARG cc_start: 0.8561 (tpt170) cc_final: 0.8289 (tpt170) REVERT: A 390 LYS cc_start: 0.8154 (tptt) cc_final: 0.7940 (mtmm) REVERT: A 433 HIS cc_start: 0.8136 (t70) cc_final: 0.7788 (m90) REVERT: A 471 MET cc_start: 0.8854 (mtt) cc_final: 0.8609 (mtm) REVERT: B 31 GLN cc_start: 0.7722 (mt0) cc_final: 0.6835 (mp-120) REVERT: B 139 LYS cc_start: 0.8308 (tttt) cc_final: 0.8017 (ttpt) REVERT: B 239 THR cc_start: 0.6493 (OUTLIER) cc_final: 0.6233 (t) REVERT: B 289 VAL cc_start: 0.8833 (t) cc_final: 0.8614 (p) REVERT: B 313 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7699 (mt-10) REVERT: D 85 MET cc_start: 0.7421 (mtp) cc_final: 0.6928 (mtp) REVERT: D 121 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8657 (ttpt) REVERT: D 160 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7284 (mm-30) REVERT: D 164 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7216 (mt-10) REVERT: H 78 GLU cc_start: 0.8382 (tt0) cc_final: 0.8104 (tt0) REVERT: H 88 GLU cc_start: 0.7604 (mp0) cc_final: 0.7317 (mm-30) REVERT: J 11 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6697 (mtmm) REVERT: J 74 GLU cc_start: 0.5785 (pm20) cc_final: 0.5388 (mm-30) REVERT: N 1 MET cc_start: 0.8203 (ttm) cc_final: 0.7990 (ttm) REVERT: N 288 LYS cc_start: 0.7872 (tttp) cc_final: 0.7553 (ttpp) REVERT: R 66 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.8068 (mm-30) REVERT: Q 96 HIS cc_start: 0.7335 (t-90) cc_final: 0.6978 (t70) REVERT: Q 107 LYS cc_start: 0.7492 (tttt) cc_final: 0.7282 (ttmt) REVERT: Q 138 THR cc_start: 0.8472 (m) cc_final: 0.8264 (p) REVERT: L 36 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7776 (mppt) REVERT: L 87 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.6652 (ptp90) REVERT: L 146 ARG cc_start: 0.7458 (ttm110) cc_final: 0.7128 (mtm-85) REVERT: L 160 LYS cc_start: 0.5917 (tptp) cc_final: 0.5687 (mmtp) REVERT: L 198 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7293 (tp30) REVERT: L 205 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7149 (mp0) REVERT: L 212 MET cc_start: 0.8848 (mtp) cc_final: 0.8466 (mtp) REVERT: L 292 GLU cc_start: 0.8047 (mp0) cc_final: 0.7791 (mp0) REVERT: M 19 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8020 (tp30) REVERT: M 31 GLN cc_start: 0.7644 (mt0) cc_final: 0.6706 (mp10) REVERT: M 139 LYS cc_start: 0.8319 (tttt) cc_final: 0.8013 (ttpt) REVERT: M 236 ARG cc_start: 0.7419 (mtt90) cc_final: 0.7062 (mtp85) REVERT: M 289 VAL cc_start: 0.8899 (t) cc_final: 0.8591 (p) REVERT: O 121 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8643 (ttpt) REVERT: O 160 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7295 (mm-30) REVERT: O 164 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7179 (mt-10) REVERT: S 78 GLU cc_start: 0.8380 (tt0) cc_final: 0.8102 (tt0) REVERT: S 88 GLU cc_start: 0.7622 (mp0) cc_final: 0.7332 (mm-30) REVERT: U 11 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6723 (mttm) REVERT: U 74 GLU cc_start: 0.5770 (pm20) cc_final: 0.5374 (mm-30) outliers start: 57 outliers final: 35 residues processed: 453 average time/residue: 1.6679 time to fit residues: 871.8635 Evaluate side-chains 457 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 407 time to evaluate : 3.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 144 ILE Chi-restraints excluded: chain A residue 149 GLU Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 201 LYS Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 234 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 400 THR Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain S residue 86 ARG Chi-restraints excluded: chain U residue 11 LYS Chi-restraints excluded: chain U residue 67 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 226 optimal weight: 0.8980 chunk 146 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 chunk 249 optimal weight: 0.0870 chunk 181 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 287 optimal weight: 8.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN B 354 ASN I 39 ASN L 196 ASN M 379 GLN T 39 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 32464 Z= 0.223 Angle : 0.592 14.833 44124 Z= 0.292 Chirality : 0.042 0.187 4828 Planarity : 0.004 0.049 5536 Dihedral : 13.189 146.689 5237 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.96 % Allowed : 10.80 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.14), residues: 3834 helix: 1.55 (0.11), residues: 2120 sheet: 0.80 (0.27), residues: 340 loop : 1.01 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 280 HIS 0.009 0.001 HIS N 197 PHE 0.023 0.002 PHE A 334 TYR 0.021 0.002 TYR C 16 ARG 0.008 0.001 ARG J 55 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 408 time to evaluate : 3.572 Fit side-chains REVERT: C 1 MET cc_start: 0.8206 (ttm) cc_final: 0.7988 (ttm) REVERT: C 288 LYS cc_start: 0.7896 (tttp) cc_final: 0.7577 (ttpp) REVERT: G 66 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8059 (mm-30) REVERT: G 116 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8565 (ttmm) REVERT: F 138 THR cc_start: 0.8469 (m) cc_final: 0.8259 (p) REVERT: A 90 HIS cc_start: 0.7662 (t70) cc_final: 0.6888 (t-170) REVERT: A 97 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: A 153 ARG cc_start: 0.7268 (ttp-110) cc_final: 0.6751 (ttt-90) REVERT: A 160 LYS cc_start: 0.6223 (tptp) cc_final: 0.5941 (mmtp) REVERT: A 188 ARG cc_start: 0.7455 (ttm-80) cc_final: 0.7243 (ttm-80) REVERT: A 194 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7009 (tp) REVERT: A 205 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7255 (mp0) REVERT: A 212 MET cc_start: 0.8847 (mtp) cc_final: 0.8449 (mtp) REVERT: A 230 GLU cc_start: 0.8061 (tp30) cc_final: 0.7763 (mt-10) REVERT: A 320 ARG cc_start: 0.8564 (tpt170) cc_final: 0.8291 (tpt170) REVERT: A 390 LYS cc_start: 0.8206 (tptt) cc_final: 0.7921 (mtmm) REVERT: A 424 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: A 433 HIS cc_start: 0.8132 (t70) cc_final: 0.7780 (m90) REVERT: A 471 MET cc_start: 0.8869 (mtt) cc_final: 0.8625 (mtm) REVERT: B 31 GLN cc_start: 0.7713 (mt0) cc_final: 0.6831 (mp-120) REVERT: B 139 LYS cc_start: 0.8303 (tttt) cc_final: 0.8017 (ttpt) REVERT: B 289 VAL cc_start: 0.8830 (t) cc_final: 0.8615 (p) REVERT: B 313 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7702 (mt-10) REVERT: D 85 MET cc_start: 0.7402 (mtp) cc_final: 0.6891 (mtp) REVERT: D 121 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8661 (ttpt) REVERT: D 160 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7278 (mm-30) REVERT: D 164 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7186 (mt-10) REVERT: H 78 GLU cc_start: 0.8382 (tt0) cc_final: 0.8103 (tt0) REVERT: H 88 GLU cc_start: 0.7597 (mp0) cc_final: 0.7332 (mm-30) REVERT: J 11 LYS cc_start: 0.7172 (OUTLIER) cc_final: 0.6651 (mttm) REVERT: J 74 GLU cc_start: 0.5776 (pm20) cc_final: 0.5382 (mm-30) REVERT: N 288 LYS cc_start: 0.7900 (tttp) cc_final: 0.7583 (ttpp) REVERT: R 66 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8070 (mm-30) REVERT: Q 96 HIS cc_start: 0.7325 (t-90) cc_final: 0.7023 (t70) REVERT: Q 107 LYS cc_start: 0.7484 (tttt) cc_final: 0.7280 (ttmt) REVERT: Q 138 THR cc_start: 0.8480 (m) cc_final: 0.8271 (p) REVERT: L 36 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7783 (mppt) REVERT: L 87 ARG cc_start: 0.8252 (OUTLIER) cc_final: 0.6671 (ptp90) REVERT: L 198 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7273 (tp30) REVERT: L 205 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: L 212 MET cc_start: 0.8852 (mtp) cc_final: 0.8468 (mtp) REVERT: M 19 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7961 (tp30) REVERT: M 31 GLN cc_start: 0.7651 (mt0) cc_final: 0.6723 (mp-120) REVERT: M 139 LYS cc_start: 0.8303 (tttt) cc_final: 0.8007 (ttpt) REVERT: M 180 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: M 236 ARG cc_start: 0.7408 (mtt90) cc_final: 0.7065 (mtp85) REVERT: M 289 VAL cc_start: 0.8859 (t) cc_final: 0.8582 (p) REVERT: O 121 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8624 (ttpt) REVERT: O 160 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7288 (mm-30) REVERT: O 164 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7175 (mt-10) REVERT: S 78 GLU cc_start: 0.8364 (tt0) cc_final: 0.8087 (tt0) REVERT: S 88 GLU cc_start: 0.7626 (mp0) cc_final: 0.7331 (mm-30) REVERT: U 11 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6714 (mttm) REVERT: U 74 GLU cc_start: 0.5775 (pm20) cc_final: 0.5379 (mm-30) outliers start: 63 outliers final: 36 residues processed: 452 average time/residue: 1.7192 time to fit residues: 899.8871 Evaluate side-chains 454 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 402 time to evaluate : 3.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 121 LYS Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain R residue 66 GLU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 201 LYS Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 234 SER Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 400 THR Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 180 GLU Chi-restraints excluded: chain O residue 121 LYS Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain S residue 86 ARG Chi-restraints excluded: chain U residue 11 LYS Chi-restraints excluded: chain U residue 67 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 333 optimal weight: 1.9990 chunk 350 optimal weight: 0.3980 chunk 320 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 205 optimal weight: 0.1980 chunk 148 optimal weight: 9.9990 chunk 268 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 322 optimal weight: 3.9990 chunk 340 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN B 354 ASN I 39 ASN M 354 ASN T 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32464 Z= 0.168 Angle : 0.541 14.427 44124 Z= 0.265 Chirality : 0.041 0.173 4828 Planarity : 0.004 0.049 5536 Dihedral : 12.813 148.173 5237 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.46 % Allowed : 11.30 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.97 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.14), residues: 3834 helix: 1.73 (0.11), residues: 2114 sheet: 0.87 (0.27), residues: 340 loop : 1.02 (0.18), residues: 1380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 280 HIS 0.008 0.001 HIS C 197 PHE 0.021 0.002 PHE L 334 TYR 0.017 0.002 TYR C 16 ARG 0.009 0.000 ARG J 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 413 time to evaluate : 3.553 Fit side-chains REVERT: C 1 MET cc_start: 0.8204 (ttm) cc_final: 0.7984 (ttm) REVERT: C 288 LYS cc_start: 0.7789 (tttp) cc_final: 0.7472 (ttpp) REVERT: G 66 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8009 (mm-30) REVERT: F 138 THR cc_start: 0.8480 (m) cc_final: 0.8267 (p) REVERT: A 90 HIS cc_start: 0.7672 (t70) cc_final: 0.6894 (t-170) REVERT: A 97 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7456 (mm-30) REVERT: A 128 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7861 (tm-30) REVERT: A 146 ARG cc_start: 0.7604 (ttm110) cc_final: 0.7323 (mtm-85) REVERT: A 153 ARG cc_start: 0.7275 (ttp-110) cc_final: 0.6766 (ttt-90) REVERT: A 154 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7303 (mt-10) REVERT: A 160 LYS cc_start: 0.6242 (tptp) cc_final: 0.5954 (mmtp) REVERT: A 205 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: A 212 MET cc_start: 0.8838 (mtp) cc_final: 0.8451 (mtp) REVERT: A 230 GLU cc_start: 0.8069 (tp30) cc_final: 0.7773 (mt-10) REVERT: A 320 ARG cc_start: 0.8531 (tpt170) cc_final: 0.8327 (tpt170) REVERT: A 390 LYS cc_start: 0.8170 (tptt) cc_final: 0.7917 (mtmm) REVERT: A 424 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: A 433 HIS cc_start: 0.8128 (t70) cc_final: 0.7779 (m90) REVERT: A 471 MET cc_start: 0.8830 (mtt) cc_final: 0.8609 (mtm) REVERT: B 31 GLN cc_start: 0.7701 (mt0) cc_final: 0.6814 (mp-120) REVERT: B 139 LYS cc_start: 0.8314 (tttt) cc_final: 0.8021 (ttpt) REVERT: B 289 VAL cc_start: 0.8798 (t) cc_final: 0.8580 (p) REVERT: B 313 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7676 (mt-10) REVERT: B 373 ILE cc_start: 0.7684 (mp) cc_final: 0.7483 (mm) REVERT: D 85 MET cc_start: 0.7337 (mtp) cc_final: 0.6781 (mtp) REVERT: D 160 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7305 (mm-30) REVERT: D 164 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7184 (mt-10) REVERT: H 78 GLU cc_start: 0.8417 (tt0) cc_final: 0.8133 (tt0) REVERT: H 88 GLU cc_start: 0.7600 (mp0) cc_final: 0.7330 (mm-30) REVERT: J 11 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6552 (mttm) REVERT: J 74 GLU cc_start: 0.5801 (pm20) cc_final: 0.5331 (mm-30) REVERT: N 1 MET cc_start: 0.8200 (ttm) cc_final: 0.7981 (ttm) REVERT: N 288 LYS cc_start: 0.7804 (tttp) cc_final: 0.7500 (ttpp) REVERT: Q 96 HIS cc_start: 0.7318 (t-90) cc_final: 0.6991 (t-90) REVERT: Q 107 LYS cc_start: 0.7481 (tttt) cc_final: 0.7050 (mttp) REVERT: Q 138 THR cc_start: 0.8440 (m) cc_final: 0.8226 (p) REVERT: L 36 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7783 (mppt) REVERT: L 87 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.6654 (ptp90) REVERT: L 146 ARG cc_start: 0.7474 (ttm110) cc_final: 0.7070 (mtm110) REVERT: L 198 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7306 (tp30) REVERT: L 205 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7162 (mp0) REVERT: L 212 MET cc_start: 0.8843 (mtp) cc_final: 0.8467 (mtp) REVERT: M 19 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7954 (tp30) REVERT: M 31 GLN cc_start: 0.7641 (mt0) cc_final: 0.6708 (mp10) REVERT: M 83 LYS cc_start: 0.8871 (mmpt) cc_final: 0.8624 (mtmt) REVERT: M 139 LYS cc_start: 0.8311 (tttt) cc_final: 0.8011 (ttpt) REVERT: M 180 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: M 236 ARG cc_start: 0.7438 (mtt90) cc_final: 0.7079 (mtp85) REVERT: M 289 VAL cc_start: 0.8833 (t) cc_final: 0.8552 (p) REVERT: O 160 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7281 (mm-30) REVERT: O 164 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7188 (mt-10) REVERT: S 78 GLU cc_start: 0.8414 (tt0) cc_final: 0.8128 (tt0) REVERT: S 88 GLU cc_start: 0.7645 (mp0) cc_final: 0.7369 (mm-30) REVERT: U 11 LYS cc_start: 0.7128 (OUTLIER) cc_final: 0.6718 (mttm) REVERT: U 74 GLU cc_start: 0.5773 (pm20) cc_final: 0.5292 (mm-30) outliers start: 47 outliers final: 33 residues processed: 446 average time/residue: 1.7381 time to fit residues: 899.4162 Evaluate side-chains 449 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 405 time to evaluate : 3.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 400 THR Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 180 GLU Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain S residue 86 ARG Chi-restraints excluded: chain U residue 11 LYS Chi-restraints excluded: chain U residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 224 optimal weight: 10.0000 chunk 360 optimal weight: 7.9990 chunk 220 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 250 optimal weight: 20.0000 chunk 378 optimal weight: 0.6980 chunk 348 optimal weight: 8.9990 chunk 301 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 184 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN I 39 ASN M 316 GLN M 379 GLN T 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 32464 Z= 0.208 Angle : 0.576 14.778 44124 Z= 0.283 Chirality : 0.042 0.170 4828 Planarity : 0.004 0.048 5536 Dihedral : 12.885 147.796 5237 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.77 % Allowed : 11.30 % Favored : 86.93 % 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: 1.95 (0.14), residues: 3834 helix: 1.67 (0.11), residues: 2108 sheet: 0.87 (0.27), residues: 340 loop : 1.03 (0.18), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 271 HIS 0.009 0.001 HIS C 197 PHE 0.023 0.002 PHE L 334 TYR 0.020 0.002 TYR C 16 ARG 0.010 0.001 ARG U 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7668 Ramachandran restraints generated. 3834 Oldfield, 0 Emsley, 3834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 404 time to evaluate : 3.436 Fit side-chains REVERT: C 1 MET cc_start: 0.8205 (ttm) cc_final: 0.7984 (ttm) REVERT: C 288 LYS cc_start: 0.7870 (tttp) cc_final: 0.7550 (ttpp) REVERT: G 66 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8037 (mm-30) REVERT: G 116 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8533 (ttmm) REVERT: F 138 THR cc_start: 0.8448 (m) cc_final: 0.8237 (p) REVERT: A 90 HIS cc_start: 0.7679 (t70) cc_final: 0.6886 (t-170) REVERT: A 97 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7463 (mm-30) REVERT: A 146 ARG cc_start: 0.7599 (ttm110) cc_final: 0.7304 (mtm-85) REVERT: A 153 ARG cc_start: 0.7219 (ttp-110) cc_final: 0.6746 (ttt-90) REVERT: A 160 LYS cc_start: 0.6220 (tptp) cc_final: 0.5936 (mmtp) REVERT: A 205 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7193 (mp0) REVERT: A 212 MET cc_start: 0.8849 (mtp) cc_final: 0.8458 (mtp) REVERT: A 230 GLU cc_start: 0.8058 (tp30) cc_final: 0.7761 (mt-10) REVERT: A 320 ARG cc_start: 0.8548 (tpt170) cc_final: 0.8276 (tpt170) REVERT: A 390 LYS cc_start: 0.8170 (tptt) cc_final: 0.7920 (mtmm) REVERT: A 424 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: A 433 HIS cc_start: 0.8126 (t70) cc_final: 0.7775 (m90) REVERT: A 471 MET cc_start: 0.8866 (mtt) cc_final: 0.8622 (mtm) REVERT: B 19 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: B 31 GLN cc_start: 0.7701 (mt0) cc_final: 0.6816 (mp-120) REVERT: B 139 LYS cc_start: 0.8303 (tttt) cc_final: 0.8015 (ttpt) REVERT: B 289 VAL cc_start: 0.8820 (t) cc_final: 0.8597 (p) REVERT: B 313 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7689 (mt-10) REVERT: B 373 ILE cc_start: 0.7684 (mp) cc_final: 0.7479 (mm) REVERT: D 85 MET cc_start: 0.7343 (mtp) cc_final: 0.6791 (mtp) REVERT: D 160 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7301 (mm-30) REVERT: D 164 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7176 (mt-10) REVERT: H 78 GLU cc_start: 0.8410 (tt0) cc_final: 0.8126 (tt0) REVERT: H 88 GLU cc_start: 0.7608 (mp0) cc_final: 0.7336 (mm-30) REVERT: J 11 LYS cc_start: 0.6988 (OUTLIER) cc_final: 0.6504 (mttm) REVERT: J 74 GLU cc_start: 0.5790 (pm20) cc_final: 0.5323 (mm-30) REVERT: N 1 MET cc_start: 0.8202 (ttm) cc_final: 0.7979 (ttm) REVERT: N 288 LYS cc_start: 0.7871 (tttp) cc_final: 0.7558 (ttpp) REVERT: Q 96 HIS cc_start: 0.7316 (t-90) cc_final: 0.7034 (t70) REVERT: Q 107 LYS cc_start: 0.7480 (tttt) cc_final: 0.7275 (ttmt) REVERT: Q 138 THR cc_start: 0.8454 (m) cc_final: 0.8243 (p) REVERT: L 36 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7782 (mppt) REVERT: L 87 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.6667 (ptp90) REVERT: L 198 GLU cc_start: 0.7521 (mt-10) cc_final: 0.7262 (tp30) REVERT: L 205 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: L 212 MET cc_start: 0.8855 (mtp) cc_final: 0.8474 (mtp) REVERT: M 19 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7977 (tp30) REVERT: M 31 GLN cc_start: 0.7647 (mt0) cc_final: 0.6717 (mp-120) REVERT: M 83 LYS cc_start: 0.8877 (mmpt) cc_final: 0.8628 (mtmt) REVERT: M 139 LYS cc_start: 0.8311 (tttt) cc_final: 0.8012 (ttpt) REVERT: M 180 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: M 236 ARG cc_start: 0.7448 (mtt90) cc_final: 0.7086 (mtp85) REVERT: M 289 VAL cc_start: 0.8835 (t) cc_final: 0.8557 (p) REVERT: O 160 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7308 (mm-30) REVERT: O 164 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7190 (mt-10) REVERT: O 283 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8335 (mt-10) REVERT: S 78 GLU cc_start: 0.8408 (tt0) cc_final: 0.8129 (tt0) REVERT: S 88 GLU cc_start: 0.7628 (mp0) cc_final: 0.7334 (mm-30) REVERT: U 11 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.6721 (mttm) REVERT: U 69 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: U 74 GLU cc_start: 0.5774 (pm20) cc_final: 0.5292 (mm-30) outliers start: 57 outliers final: 36 residues processed: 444 average time/residue: 1.6630 time to fit residues: 851.5290 Evaluate side-chains 455 residues out of total 3222 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 404 time to evaluate : 3.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 6 LYS Chi-restraints excluded: chain C residue 197 HIS Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 116 LYS Chi-restraints excluded: chain F residue 107 LYS Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 188 ARG Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 205 GLU Chi-restraints excluded: chain A residue 351 LEU Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 424 GLU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 60 PHE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain D residue 258 GLU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain N residue 6 LYS Chi-restraints excluded: chain N residue 197 HIS Chi-restraints excluded: chain N residue 324 LEU Chi-restraints excluded: chain L residue 33 SER Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 197 THR Chi-restraints excluded: chain L residue 205 GLU Chi-restraints excluded: chain L residue 351 LEU Chi-restraints excluded: chain L residue 377 VAL Chi-restraints excluded: chain L residue 400 THR Chi-restraints excluded: chain M residue 19 GLU Chi-restraints excluded: chain M residue 50 VAL Chi-restraints excluded: chain M residue 60 PHE Chi-restraints excluded: chain M residue 180 GLU Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain O residue 258 GLU Chi-restraints excluded: chain O residue 283 GLU Chi-restraints excluded: chain S residue 86 ARG Chi-restraints excluded: chain U residue 11 LYS Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 69 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 239 optimal weight: 0.8980 chunk 321 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 301 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 310 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 55 optimal weight: 0.3980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 ASN I 39 ASN M 354 ASN M 379 GLN T 39 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.121456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.099253 restraints weight = 31071.786| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 0.82 r_work: 0.2963 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 32464 Z= 0.142 Angle : 0.514 14.038 44124 Z= 0.250 Chirality : 0.040 0.178 4828 Planarity : 0.004 0.048 5536 Dihedral : 12.417 149.350 5237 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.37 % Allowed : 11.70 % Favored : 86.93 % 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: 2.13 (0.14), residues: 3834 helix: 1.81 (0.11), residues: 2114 sheet: 1.00 (0.27), residues: 342 loop : 1.09 (0.18), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 271 HIS 0.007 0.001 HIS N 96 PHE 0.020 0.001 PHE A 334 TYR 0.015 0.001 TYR M 170 ARG 0.010 0.000 ARG J 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13804.49 seconds wall clock time: 244 minutes 22.13 seconds (14662.13 seconds total)