Starting phenix.real_space_refine on Sat Aug 10 10:09:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqk_41506/08_2024/8tqk_41506.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqk_41506/08_2024/8tqk_41506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqk_41506/08_2024/8tqk_41506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqk_41506/08_2024/8tqk_41506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqk_41506/08_2024/8tqk_41506.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqk_41506/08_2024/8tqk_41506.cif" } resolution = 3.2 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= 0.001 sd= 0.049 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: 5 Type Number sf(0) Gaussians S 76 5.16 5 C 9322 2.51 5 N 2473 2.21 5 O 2854 1.98 5 H 14504 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 105": "OE1" <-> "OE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 100": "OD1" <-> "OD2" Residue "L PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 105": "OE1" <-> "OE2" Residue "A ASP 76": "OD1" <-> "OD2" Residue "A ASP 84": "OD1" <-> "OD2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A GLU 193": "OE1" <-> "OE2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "A ASP 297": "OD1" <-> "OD2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "B ASP 21": "OD1" <-> "OD2" Residue "B ASP 59": "OD1" <-> "OD2" Residue "B ASP 143": "OD1" <-> "OD2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 249": "OD1" <-> "OD2" Residue "B ASP 297": "OD1" <-> "OD2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "C ASP 76": "OD1" <-> "OD2" Residue "C ASP 273": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29229 Number of models: 1 Model: "" Number of chains: 9 Chain: "D" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1757 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1528 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP%NH3:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "F" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1765 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 1527 Classifications: {'peptide': 105} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1740 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1514 Classifications: {'peptide': 104} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 6440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6440 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 14, 'TRANS': 402} Chain breaks: 5 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 6463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 6463 Classifications: {'peptide': 415} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 399} Chain breaks: 4 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 6495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 6495 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 14, 'TRANS': 403} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 12.10, per 1000 atoms: 0.41 Number of scatterers: 29229 At special positions: 0 Unit cell: (101.48, 103.2, 158.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 O 2854 8.00 N 2473 7.00 C 9322 6.00 H 14504 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.79 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.69 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.26 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.80 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 230 " distance=2.53 Simple disulfide: pdb=" SG CYS A 331 " - pdb=" SG CYS A 340 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 394 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 192 " distance=2.04 Simple disulfide: pdb=" SG CYS B 213 " - pdb=" SG CYS B 230 " distance=2.05 Simple disulfide: pdb=" SG CYS B 331 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 394 " - pdb=" SG CYS B 417 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 168 " distance=2.03 Simple disulfide: pdb=" SG CYS C 213 " - pdb=" SG CYS C 230 " distance=2.05 Simple disulfide: pdb=" SG CYS C 331 " - pdb=" SG CYS C 340 " distance=2.03 Simple disulfide: pdb=" SG CYS C 355 " - pdb=" SG CYS C 363 " distance=2.03 Simple disulfide: pdb=" SG CYS C 387 " - pdb=" SG CYS C 392 " distance=2.03 Simple disulfide: pdb=" SG CYS C 394 " - pdb=" SG CYS C 417 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 19.08 Conformation dependent library (CDL) restraints added in 3.3 seconds 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3548 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 32 sheets defined 25.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'D' and resid 28 through 32 removed outlier: 4.284A pdb=" N LYS D 31 " --> pdb=" O THR D 28 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 28 through 32' Processing helix chain 'F' and resid 28 through 32 removed outlier: 3.784A pdb=" N LYS F 31 " --> pdb=" O THR F 28 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR F 32 " --> pdb=" O PHE F 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 28 through 32' Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.116A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.150A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 28 removed outlier: 3.597A pdb=" N GLN A 26 " --> pdb=" O THR A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 89 removed outlier: 3.846A pdb=" N ARG A 77 " --> pdb=" O ARG A 73 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Proline residue: A 81 - end of helix removed outlier: 3.617A pdb=" N LYS A 87 " --> pdb=" O TYR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 139 removed outlier: 4.000A pdb=" N ALA A 130 " --> pdb=" O ALA A 126 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 133 " --> pdb=" O THR A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 151 removed outlier: 3.886A pdb=" N ILE A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 191 removed outlier: 4.784A pdb=" N VAL A 184 " --> pdb=" O ASN A 180 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 4.494A pdb=" N ALA A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 210 Processing helix chain 'A' and resid 227 through 234 removed outlier: 4.260A pdb=" N ILE A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 removed outlier: 3.618A pdb=" N ILE A 242 " --> pdb=" O ASN A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 removed outlier: 4.277A pdb=" N ASP A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 260 removed outlier: 3.774A pdb=" N LEU A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE A 258 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 358 through 363 removed outlier: 5.500A pdb=" N SER A 361 " --> pdb=" O GLY A 358 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN A 362 " --> pdb=" O ASN A 359 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N CYS A 363 " --> pdb=" O ILE A 360 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 358 through 363' Processing helix chain 'A' and resid 452 through 471 removed outlier: 3.540A pdb=" N LYS A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 26 removed outlier: 3.605A pdb=" N GLN B 26 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 88 removed outlier: 3.815A pdb=" N ARG B 77 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LEU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Proline residue: B 81 - end of helix Processing helix chain 'B' and resid 124 through 152 removed outlier: 3.751A pdb=" N THR B 129 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ALA B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER B 142 " --> pdb=" O LYS B 138 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ASP B 143 " --> pdb=" O GLN B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 210 removed outlier: 5.449A pdb=" N VAL B 184 " --> pdb=" O ASN B 180 " (cutoff:3.500A) Proline residue: B 185 - end of helix removed outlier: 4.338A pdb=" N ALA B 188 " --> pdb=" O VAL B 184 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N CYS B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N GLU B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 235 Processing helix chain 'B' and resid 238 through 243 removed outlier: 3.601A pdb=" N ILE B 242 " --> pdb=" O ASN B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 removed outlier: 4.083A pdb=" N ASP B 249 " --> pdb=" O SER B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 260 removed outlier: 3.502A pdb=" N LEU B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU B 257 " --> pdb=" O ILE B 253 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE B 258 " --> pdb=" O TYR B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 359 through 363 removed outlier: 3.605A pdb=" N GLN B 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 472 removed outlier: 3.951A pdb=" N GLU B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 removed outlier: 3.711A pdb=" N GLN C 26 " --> pdb=" O ILE C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 89 removed outlier: 3.829A pdb=" N ARG C 77 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 78 " --> pdb=" O LEU C 74 " (cutoff:3.500A) Proline residue: C 81 - end of helix removed outlier: 3.505A pdb=" N GLN C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 4.045A pdb=" N ALA C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 151 Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 191 through 210 Processing helix chain 'C' and resid 227 through 236 removed outlier: 3.602A pdb=" N ILE C 231 " --> pdb=" O LYS C 227 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG C 236 " --> pdb=" O ALA C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 251 removed outlier: 3.870A pdb=" N ASP C 249 " --> pdb=" O SER C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.623A pdb=" N LEU C 257 " --> pdb=" O ILE C 253 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 262 " --> pdb=" O PHE C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 357 Processing helix chain 'C' and resid 359 through 363 removed outlier: 3.583A pdb=" N GLN C 362 " --> pdb=" O ASN C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 472 Processing sheet with id=AA1, first strand: chain 'D' and resid 19 through 23 removed outlier: 3.632A pdb=" N THR D 77 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP D 79 " --> pdb=" O SER D 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 58 through 59 removed outlier: 4.048A pdb=" N SER D 50 " --> pdb=" O PHE D 58 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.662A pdb=" N THR E 22 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL E 19 " --> pdb=" O ILE E 75 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER E 67 " --> pdb=" O GLU E 70 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR E 72 " --> pdb=" O SER E 65 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER E 65 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 10 through 11 Processing sheet with id=AA5, first strand: chain 'E' and resid 45 through 48 removed outlier: 5.798A pdb=" N ILE E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLN E 37 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 3 through 4 Processing sheet with id=AA7, first strand: chain 'F' and resid 58 through 59 removed outlier: 5.108A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL F 33 " --> pdb=" O MET F 95 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 4 through 5 removed outlier: 3.682A pdb=" N VAL G 19 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYS G 23 " --> pdb=" O PHE G 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE G 71 " --> pdb=" O CYS G 23 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 45 through 48 removed outlier: 6.701A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.525A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.161A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL H 33 " --> pdb=" O MET H 95 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA H 35 " --> pdb=" O ALA H 93 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.521A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 34 through 38 removed outlier: 3.587A pdb=" N THR L 85 " --> pdb=" O HIS L 38 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N TYR L 86 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 30 through 32 removed outlier: 3.608A pdb=" N ILE A 316 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N HIS A 315 " --> pdb=" O ALA A 326 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 326 " --> pdb=" O HIS A 315 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY A 325 " --> pdb=" O PHE A 346 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 158 through 161 removed outlier: 8.767A pdb=" N VAL A 170 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR A 48 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE A 172 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 50 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N SER A 41 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N THR A 286 " --> pdb=" O SER A 41 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN A 43 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 268 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN A 279 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL A 266 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 158 through 161 removed outlier: 8.767A pdb=" N VAL A 170 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR A 48 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N ILE A 172 " --> pdb=" O TYR A 48 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 50 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A 41 " --> pdb=" O CYS A 340 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.856A pdb=" N VAL C 383 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 301 through 302 Processing sheet with id=AC1, first strand: chain 'A' and resid 378 through 380 removed outlier: 5.279A pdb=" N VAL A 379 " --> pdb=" O GLY B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 383 through 385 removed outlier: 3.645A pdb=" N VAL A 383 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA A 385 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 392 through 393 Processing sheet with id=AC4, first strand: chain 'B' and resid 31 through 32 removed outlier: 4.357A pdb=" N HIS B 315 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 326 " --> pdb=" O HIS B 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 285 through 287 removed outlier: 3.560A pdb=" N ILE B 40 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LYS B 39 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.646A pdb=" N ALA B 171 " --> pdb=" O GLN B 159 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 170 " --> pdb=" O TYR B 48 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP B 268 " --> pdb=" O THR B 277 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN B 279 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 266 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ARG B 281 " --> pdb=" O VAL B 264 " (cutoff:3.500A) removed outlier: 8.378A pdb=" N VAL B 264 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 301 through 302 Processing sheet with id=AC8, first strand: chain 'B' and resid 410 through 411 removed outlier: 4.285A pdb=" N ASN B 380 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLY C 121 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 420 through 421 Processing sheet with id=AD1, first strand: chain 'C' and resid 30 through 32 removed outlier: 3.648A pdb=" N ILE C 316 " --> pdb=" O TYR C 294 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N HIS C 315 " --> pdb=" O ALA C 326 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 326 " --> pdb=" O HIS C 315 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 325 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 285 through 287 removed outlier: 3.590A pdb=" N ILE C 40 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY C 37 " --> pdb=" O TYR C 338 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N CYS C 340 " --> pdb=" O GLY C 37 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LYS C 39 " --> pdb=" O CYS C 340 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 158 through 161 removed outlier: 7.021A pdb=" N SER C 275 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL C 269 " --> pdb=" O SER C 275 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR C 277 " --> pdb=" O ILE C 267 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG C 265 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 301 through 303 Processing sheet with id=AD5, first strand: chain 'C' and resid 419 through 421 519 hydrogen bonds defined for protein. 1383 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: 9.81 Time building geometry restraints manager: 20.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 14502 1.02 - 1.22: 19 1.22 - 1.43: 6105 1.43 - 1.63: 8746 1.63 - 1.83: 100 Bond restraints: 29472 Sorted by residual: bond pdb=" N PRO D 14 " pdb=" CD PRO D 14 " ideal model delta sigma weight residual 1.473 1.545 -0.072 1.40e-02 5.10e+03 2.68e+01 bond pdb=" CA ASN C 305 " pdb=" C ASN C 305 " ideal model delta sigma weight residual 1.524 1.590 -0.066 1.50e-02 4.44e+03 1.93e+01 bond pdb=" N LYS A 227 " pdb=" CA LYS A 227 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.29e-02 6.01e+03 1.44e+01 bond pdb=" CA GLN B 362 " pdb=" C GLN B 362 " ideal model delta sigma weight residual 1.523 1.574 -0.051 1.34e-02 5.57e+03 1.43e+01 bond pdb=" N THR B 429 " pdb=" CA THR B 429 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.29e-02 6.01e+03 1.30e+01 ... (remaining 29467 not shown) Histogram of bond angle deviations from ideal: 96.69 - 104.21: 181 104.21 - 111.73: 33649 111.73 - 119.26: 7529 119.26 - 126.78: 11659 126.78 - 134.30: 192 Bond angle restraints: 53210 Sorted by residual: angle pdb=" N GLY E 101 " pdb=" CA GLY E 101 " pdb=" C GLY E 101 " ideal model delta sigma weight residual 112.08 123.55 -11.47 1.01e+00 9.80e-01 1.29e+02 angle pdb=" C GLU B 432 " pdb=" N GLY B 433 " pdb=" CA GLY B 433 " ideal model delta sigma weight residual 120.10 127.58 -7.48 9.50e-01 1.11e+00 6.20e+01 angle pdb=" N CYS B 363 " pdb=" CA CYS B 363 " pdb=" C CYS B 363 " ideal model delta sigma weight residual 109.93 100.29 9.64 1.24e+00 6.50e-01 6.04e+01 angle pdb=" N ILE B 456 " pdb=" CA ILE B 456 " pdb=" C ILE B 456 " ideal model delta sigma weight residual 110.62 118.64 -8.02 1.14e+00 7.69e-01 4.95e+01 angle pdb=" CA THR A 237 " pdb=" C THR A 237 " pdb=" O THR A 237 " ideal model delta sigma weight residual 120.51 110.70 9.81 1.43e+00 4.89e-01 4.71e+01 ... (remaining 53205 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 12089 17.99 - 35.97: 1285 35.97 - 53.96: 437 53.96 - 71.95: 92 71.95 - 89.94: 25 Dihedral angle restraints: 13928 sinusoidal: 7640 harmonic: 6288 Sorted by residual: dihedral pdb=" CB CYS B 394 " pdb=" SG CYS B 394 " pdb=" SG CYS B 417 " pdb=" CB CYS B 417 " ideal model delta sinusoidal sigma weight residual 93.00 -178.93 -88.07 1 1.00e+01 1.00e-02 9.28e+01 dihedral pdb=" CB CYS C 394 " pdb=" SG CYS C 394 " pdb=" SG CYS C 417 " pdb=" CB CYS C 417 " ideal model delta sinusoidal sigma weight residual -86.00 -170.95 84.95 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual -86.00 -16.67 -69.33 1 1.00e+01 1.00e-02 6.21e+01 ... (remaining 13925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2075 0.082 - 0.164: 269 0.164 - 0.246: 31 0.246 - 0.328: 11 0.328 - 0.410: 2 Chirality restraints: 2388 Sorted by residual: chirality pdb=" CA ASN C 305 " pdb=" N ASN C 305 " pdb=" C ASN C 305 " pdb=" CB ASN C 305 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.21e+00 chirality pdb=" CA GLU A 182 " pdb=" N GLU A 182 " pdb=" C GLU A 182 " pdb=" CB GLU A 182 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA ASN A 180 " pdb=" N ASN A 180 " pdb=" C ASN A 180 " pdb=" CB ASN A 180 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 2385 not shown) Planarity restraints: 4384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 92 " -0.237 2.00e-02 2.50e+03 3.88e-01 2.26e+03 pdb=" CG ASN G 92 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN G 92 " 0.230 2.00e-02 2.50e+03 pdb=" ND2 ASN G 92 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN G 92 " -0.637 2.00e-02 2.50e+03 pdb="HD22 ASN G 92 " 0.624 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 176 " 0.196 2.00e-02 2.50e+03 2.19e-01 7.20e+02 pdb=" CD GLN C 176 " -0.014 2.00e-02 2.50e+03 pdb=" OE1 GLN C 176 " -0.188 2.00e-02 2.50e+03 pdb=" NE2 GLN C 176 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN C 176 " -0.324 2.00e-02 2.50e+03 pdb="HE22 GLN C 176 " 0.330 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 238 " -0.123 2.00e-02 2.50e+03 1.32e-01 2.61e+02 pdb=" CG ASN C 238 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN C 238 " 0.118 2.00e-02 2.50e+03 pdb=" ND2 ASN C 238 " 0.000 2.00e-02 2.50e+03 pdb="HD21 ASN C 238 " -0.196 2.00e-02 2.50e+03 pdb="HD22 ASN C 238 " 0.192 2.00e-02 2.50e+03 ... (remaining 4381 not shown) Histogram of nonbonded interaction distances: 0.98 - 1.70: 34 1.70 - 2.43: 14741 2.43 - 3.15: 84203 3.15 - 3.88: 104174 3.88 - 4.60: 166230 Warning: very small nonbonded interaction distances. Nonbonded interactions: 369382 Sorted by model distance: nonbonded pdb="HD22 ASN G 92 " pdb=" HA3 GLY C 191 " model vdw 0.981 2.270 nonbonded pdb=" NE2 GLN G 89 " pdb=" CZ PHE G 98 " model vdw 1.019 3.300 nonbonded pdb="HG22 ILE B 422 " pdb=" H ASN B 423 " model vdw 1.242 2.270 nonbonded pdb=" NE2 GLN G 89 " pdb=" CE2 PHE G 98 " model vdw 1.248 3.300 nonbonded pdb=" NE2 GLN G 89 " pdb=" CE1 PHE G 98 " model vdw 1.262 3.300 ... (remaining 369377 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 161 or (resid 169 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2 or name CD1 or name HA or name \ HB or name HG12 or name HG13 or name HG21 or name HG22 or name HG23 or name HD11 \ or name HD12 or name HD13)) or resid 170 through 472)) selection = (chain 'B' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA )) or resid 73 through 89 or (resid 90 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or na \ me HA )) or resid 91 through 94 or resid 114 through 212 or (resid 213 and (name \ N or name CA or name C or name O or name CB or name SG or name H or name HA or \ name HB2 or name HB3)) or resid 214 through 229 or (resid 230 and (name N or nam \ e CA or name C or name O or name CB or name SG or name H or name HA or name HB2 \ or name HB3)) or resid 231 through 336 or (resid 337 and (name N or name CA or n \ ame C or name O or name CB or name H or name HA )) or resid 338 through 413 or ( \ resid 415 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or na \ me HG3 or name HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 o \ r name HZ3)) or resid 416 through 430 or (resid 431 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 432 through 472)) selection = (chain 'C' and (resid 19 through 71 or (resid 72 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE or name NZ or name H or \ name HA )) or resid 73 through 89 or (resid 90 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name CE or name NZ or name H or na \ me HA )) or resid 91 through 94 or resid 114 through 161 or (resid 169 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1 \ or name HA or name HB or name HG12 or name HG13 or name HG21 or name HG22 or na \ me HG23 or name HD11 or name HD12 or name HD13)) or resid 170 through 336 or (re \ sid 337 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 338 through 430 or (resid 431 and (name N or name CA or name C or \ name O or name CB or name H or name HA )) or resid 432 through 472)) } ncs_group { reference = (chain 'D' and (resid 2 through 82C or (resid 83 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 84 through 109)) selection = (chain 'F' and (resid 2 through 5 or (resid 6 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 7 through 82C or (resid 83 \ and (name N or name CA or name C or name O or name CB or name H or name HA )) or \ resid 84 through 109)) selection = chain 'H' } ncs_group { reference = (chain 'E' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name \ HZ )) or resid 3 through 23 or (resid 24 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 25 through 89 or (resid 90 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name O \ E1 or name NE2 or name H or name HA )) or resid 91 through 105)) selection = (chain 'G' and ((resid 2 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name HA \ or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or name \ HZ )) or resid 3 through 23 or (resid 24 and (name N or name CA or name C or nam \ e O or name CB or name H or name HA )) or resid 25 through 105)) selection = (chain 'L' and (resid 2 through 82 or (resid 83 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 84 through 89 or (resid 9 \ 0 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name NE2 or name H or name HA )) or resid 91 through 105)) } 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: 1.540 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: 0.460 Extract box with map and model: 1.040 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 80.340 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.090 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: 0.000 Load rotamer database and sin/cos tables:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 87.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 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 : 0.005 0.072 14968 Z= 0.330 Angle : 0.995 12.638 20284 Z= 0.651 Chirality : 0.057 0.410 2388 Planarity : 0.005 0.060 2562 Dihedral : 17.677 89.937 5438 Min Nonbonded Distance : 1.019 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.31 % Favored : 94.53 % Rotamer: Outliers : 2.37 % Allowed : 33.50 % Favored : 64.13 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % 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: -1.26 (0.19), residues: 1866 helix: 0.88 (0.27), residues: 402 sheet: -0.44 (0.25), residues: 431 loop : -1.77 (0.17), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 103 HIS 0.005 0.001 HIS B 414 PHE 0.021 0.002 PHE L 91 TYR 0.015 0.001 TYR G 94 ARG 0.003 0.000 ARG D 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 247 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 208 time to evaluate : 2.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 75 ILE cc_start: 0.7988 (pt) cc_final: 0.7482 (tt) REVERT: L 105 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.5491 (tp30) outliers start: 39 outliers final: 10 residues processed: 246 average time/residue: 0.7324 time to fit residues: 244.6954 Evaluate side-chains 129 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 118 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 161 VAL Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 361 SER Chi-restraints excluded: chain C residue 401 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.8980 chunk 140 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 75 optimal weight: 0.0980 chunk 145 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN A 407 GLN ** C 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14968 Z= 0.191 Angle : 0.639 7.141 20284 Z= 0.345 Chirality : 0.044 0.186 2388 Planarity : 0.004 0.057 2562 Dihedral : 5.497 59.510 2057 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.47 % Favored : 94.37 % Rotamer: Outliers : 1.95 % Allowed : 32.64 % Favored : 65.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % 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: -0.87 (0.19), residues: 1866 helix: 1.10 (0.26), residues: 418 sheet: -0.04 (0.25), residues: 447 loop : -1.62 (0.18), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 308 HIS 0.003 0.001 HIS B 414 PHE 0.015 0.001 PHE C 258 TYR 0.017 0.001 TYR A 71 ARG 0.004 0.000 ARG F 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 152 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 75 ILE cc_start: 0.8078 (pt) cc_final: 0.7656 (tt) REVERT: E 103 ARG cc_start: 0.3186 (tmt170) cc_final: 0.2978 (tmt170) REVERT: L 105 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5224 (tp30) REVERT: B 435 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7660 (tp) outliers start: 32 outliers final: 15 residues processed: 151 average time/residue: 0.7987 time to fit residues: 166.8319 Evaluate side-chains 121 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 238 ASN Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 401 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 7.9990 chunk 52 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 6 GLN G 89 GLN C 205 GLN C 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14968 Z= 0.189 Angle : 0.584 10.178 20284 Z= 0.309 Chirality : 0.042 0.180 2388 Planarity : 0.003 0.042 2562 Dihedral : 5.117 58.405 2048 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.41 % Favored : 94.48 % Rotamer: Outliers : 1.88 % Allowed : 31.12 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % 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: -0.81 (0.19), residues: 1866 helix: 1.17 (0.26), residues: 424 sheet: -0.13 (0.25), residues: 460 loop : -1.55 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 35 HIS 0.003 0.000 HIS B 414 PHE 0.010 0.001 PHE A 378 TYR 0.011 0.001 TYR E 86 ARG 0.006 0.000 ARG F 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 106 time to evaluate : 2.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 105 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.5026 (tp30) outliers start: 31 outliers final: 20 residues processed: 135 average time/residue: 0.7833 time to fit residues: 145.6213 Evaluate side-chains 122 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 356 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 302 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 113 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14968 Z= 0.211 Angle : 0.551 6.663 20284 Z= 0.294 Chirality : 0.041 0.179 2388 Planarity : 0.003 0.038 2562 Dihedral : 4.838 58.756 2043 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.73 % Favored : 94.16 % Rotamer: Outliers : 2.01 % Allowed : 29.73 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % 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: -0.71 (0.19), residues: 1866 helix: 1.31 (0.26), residues: 419 sheet: 0.01 (0.25), residues: 441 loop : -1.52 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 32 HIS 0.003 0.001 HIS B 414 PHE 0.011 0.001 PHE G 98 TYR 0.011 0.001 TYR C 235 ARG 0.002 0.000 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 103 time to evaluate : 2.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 105 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.5116 (tp30) outliers start: 33 outliers final: 25 residues processed: 134 average time/residue: 0.7910 time to fit residues: 148.2356 Evaluate side-chains 123 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 97 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain G residue 89 GLN Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 91 optimal weight: 0.0970 chunk 161 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14968 Z= 0.229 Angle : 0.548 5.815 20284 Z= 0.294 Chirality : 0.041 0.179 2388 Planarity : 0.003 0.037 2562 Dihedral : 4.803 58.617 2043 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.84 % Favored : 94.05 % Rotamer: Outliers : 2.43 % Allowed : 28.51 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % 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: -0.68 (0.19), residues: 1866 helix: 1.33 (0.26), residues: 423 sheet: -0.02 (0.25), residues: 441 loop : -1.50 (0.18), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 32 HIS 0.003 0.001 HIS B 414 PHE 0.011 0.001 PHE A 378 TYR 0.019 0.001 TYR C 178 ARG 0.003 0.000 ARG F 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 97 time to evaluate : 2.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 100 GLN cc_start: 0.7047 (pm20) cc_final: 0.6839 (pm20) REVERT: L 105 GLU cc_start: 0.6611 (OUTLIER) cc_final: 0.5027 (tp30) REVERT: B 435 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7655 (tp) outliers start: 40 outliers final: 32 residues processed: 133 average time/residue: 0.7216 time to fit residues: 132.6437 Evaluate side-chains 125 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 91 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 94 LYS Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 105 optimal weight: 0.0670 chunk 44 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14968 Z= 0.323 Angle : 0.571 5.899 20284 Z= 0.309 Chirality : 0.041 0.183 2388 Planarity : 0.003 0.035 2562 Dihedral : 4.909 59.804 2043 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.43 % Favored : 93.35 % Rotamer: Outliers : 2.31 % Allowed : 28.51 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % 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: -0.89 (0.19), residues: 1866 helix: 1.09 (0.26), residues: 423 sheet: -0.08 (0.25), residues: 437 loop : -1.62 (0.18), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 32 HIS 0.005 0.001 HIS B 414 PHE 0.015 0.001 PHE A 378 TYR 0.012 0.001 TYR C 235 ARG 0.002 0.000 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 93 time to evaluate : 2.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8516 (pp) REVERT: H 61 ASP cc_start: 0.7819 (p0) cc_final: 0.7573 (p0) REVERT: L 105 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.4835 (tp30) REVERT: B 435 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7662 (tp) outliers start: 38 outliers final: 34 residues processed: 128 average time/residue: 0.7709 time to fit residues: 135.8954 Evaluate side-chains 123 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 86 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 6 GLU Chi-restraints excluded: chain G residue 17 ASP Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain H residue 94 LYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 101 optimal weight: 7.9990 chunk 151 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14968 Z= 0.246 Angle : 0.542 5.509 20284 Z= 0.291 Chirality : 0.041 0.172 2388 Planarity : 0.003 0.037 2562 Dihedral : 4.857 58.491 2043 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.73 % Favored : 94.11 % Rotamer: Outliers : 2.67 % Allowed : 28.39 % Favored : 68.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % 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: -0.78 (0.19), residues: 1866 helix: 1.26 (0.26), residues: 425 sheet: -0.06 (0.25), residues: 436 loop : -1.57 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 32 HIS 0.004 0.001 HIS B 414 PHE 0.010 0.001 PHE A 378 TYR 0.011 0.001 TYR C 235 ARG 0.004 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 86 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8476 (pp) REVERT: L 105 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.4764 (tp30) REVERT: B 435 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7674 (tp) outliers start: 44 outliers final: 33 residues processed: 124 average time/residue: 0.7195 time to fit residues: 123.5460 Evaluate side-chains 118 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 82 time to evaluate : 2.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14968 Z= 0.215 Angle : 0.528 5.648 20284 Z= 0.283 Chirality : 0.041 0.171 2388 Planarity : 0.003 0.034 2562 Dihedral : 4.809 59.987 2043 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.06 % Favored : 93.84 % Rotamer: Outliers : 2.25 % Allowed : 28.39 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % 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: -0.68 (0.20), residues: 1866 helix: 1.37 (0.26), residues: 425 sheet: -0.05 (0.25), residues: 436 loop : -1.50 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 32 HIS 0.004 0.001 HIS B 414 PHE 0.010 0.001 PHE A 378 TYR 0.011 0.001 TYR C 235 ARG 0.006 0.000 ARG B 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 84 time to evaluate : 2.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8455 (pp) REVERT: L 105 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.4863 (tp30) REVERT: B 435 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7648 (tp) outliers start: 37 outliers final: 32 residues processed: 116 average time/residue: 0.7081 time to fit residues: 114.7134 Evaluate side-chains 116 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 81 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 93 THR Chi-restraints excluded: chain E residue 95 SER Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 407 GLN Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 419 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 432 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.0980 chunk 171 optimal weight: 4.9990 chunk 156 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 158 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14968 Z= 0.154 Angle : 0.516 6.206 20284 Z= 0.273 Chirality : 0.041 0.168 2388 Planarity : 0.003 0.087 2562 Dihedral : 4.692 58.630 2043 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.20 % Favored : 94.69 % Rotamer: Outliers : 1.88 % Allowed : 28.88 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % 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: -0.47 (0.20), residues: 1866 helix: 1.59 (0.26), residues: 425 sheet: 0.03 (0.25), residues: 436 loop : -1.36 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 32 HIS 0.002 0.000 HIS B 414 PHE 0.007 0.001 PHE A 378 TYR 0.010 0.001 TYR C 235 ARG 0.010 0.000 ARG C 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 116 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 85 time to evaluate : 2.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8485 (pp) REVERT: L 105 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.4734 (tp30) REVERT: B 435 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7628 (tp) outliers start: 31 outliers final: 28 residues processed: 111 average time/residue: 0.7382 time to fit residues: 114.0947 Evaluate side-chains 111 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 80 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 432 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 185 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14968 Z= 0.174 Angle : 0.511 6.361 20284 Z= 0.271 Chirality : 0.041 0.168 2388 Planarity : 0.003 0.052 2562 Dihedral : 4.603 57.502 2042 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.52 % Favored : 94.37 % Rotamer: Outliers : 1.95 % Allowed : 28.69 % Favored : 69.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % 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: -0.40 (0.20), residues: 1866 helix: 1.69 (0.26), residues: 420 sheet: 0.03 (0.25), residues: 445 loop : -1.30 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 32 HIS 0.003 0.000 HIS B 414 PHE 0.008 0.001 PHE A 378 TYR 0.011 0.001 TYR C 235 ARG 0.006 0.000 ARG C 236 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3732 Ramachandran restraints generated. 1866 Oldfield, 0 Emsley, 1866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LEU 108 is missing expected H atoms. Skipping. Residue THR 93 is missing expected H atoms. Skipping. Residue SER 95 is missing expected H atoms. Skipping. Residue VAL 104 is missing expected H atoms. Skipping. Residue LYS 72 is missing expected H atoms. Skipping. Residue LYS 90 is missing expected H atoms. Skipping. Residue SER 337 is missing expected H atoms. Skipping. Residue LYS 431 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 82 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 46 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8487 (pp) REVERT: L 105 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.4743 (tp30) REVERT: B 435 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7628 (tp) outliers start: 32 outliers final: 28 residues processed: 108 average time/residue: 0.7539 time to fit residues: 113.6681 Evaluate side-chains 110 residues out of total 1666 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 79 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain F residue 85 GLU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 214 PHE Chi-restraints excluded: chain A residue 236 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 342 SER Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 465 SER Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain C residue 162 CYS Chi-restraints excluded: chain C residue 209 GLU Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 302 ASN Chi-restraints excluded: chain C residue 352 MET Chi-restraints excluded: chain C residue 401 ILE Chi-restraints excluded: chain C residue 422 ILE Chi-restraints excluded: chain C residue 432 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 6.9990 chunk 157 optimal weight: 0.0370 chunk 45 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 147 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 362 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.055246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.043743 restraints weight = 207802.607| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.84 r_work: 0.2791 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14968 Z= 0.293 Angle : 0.549 6.304 20284 Z= 0.296 Chirality : 0.041 0.171 2388 Planarity : 0.003 0.058 2562 Dihedral : 4.754 57.495 2042 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.65 % Favored : 93.25 % Rotamer: Outliers : 2.07 % Allowed : 28.33 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.05 % 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: -0.65 (0.20), residues: 1866 helix: 1.39 (0.26), residues: 420 sheet: -0.09 (0.25), residues: 445 loop : -1.45 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 32 HIS 0.005 0.001 HIS B 414 PHE 0.012 0.001 PHE A 378 TYR 0.013 0.001 TYR C 235 ARG 0.007 0.000 ARG C 236 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5445.00 seconds wall clock time: 96 minutes 23.47 seconds (5783.47 seconds total)