Starting phenix.real_space_refine on Sat Feb 17 23:10:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/02_2024/6kz3_0784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/02_2024/6kz3_0784.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/02_2024/6kz3_0784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/02_2024/6kz3_0784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/02_2024/6kz3_0784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/02_2024/6kz3_0784.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 12702 2.51 5 N 3396 2.21 5 O 3900 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A GLU 89": "OE1" <-> "OE2" Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A ASP 370": "OD1" <-> "OD2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A GLU 443": "OE1" <-> "OE2" Residue "A ASP 487": "OD1" <-> "OD2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 78": "OD1" <-> "OD2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B GLU 257": "OE1" <-> "OE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B ASP 370": "OD1" <-> "OD2" Residue "B ARG 374": "NH1" <-> "NH2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B ASP 487": "OD1" <-> "OD2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 241": "OE1" <-> "OE2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C ASP 370": "OD1" <-> "OD2" Residue "C ARG 374": "NH1" <-> "NH2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C ASP 487": "OD1" <-> "OD2" Residue "D GLU 72": "OE1" <-> "OE2" Residue "D ASP 78": "OD1" <-> "OD2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ASP 370": "OD1" <-> "OD2" Residue "D ARG 374": "NH1" <-> "NH2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D ASP 487": "OD1" <-> "OD2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 241": "OE1" <-> "OE2" Residue "E GLU 257": "OE1" <-> "OE2" Residue "E GLU 265": "OE1" <-> "OE2" Residue "E ASP 370": "OD1" <-> "OD2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E GLU 443": "OE1" <-> "OE2" Residue "E ASP 487": "OD1" <-> "OD2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "F ASP 78": "OD1" <-> "OD2" Residue "F GLU 89": "OE1" <-> "OE2" Residue "F PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 241": "OE1" <-> "OE2" Residue "F GLU 257": "OE1" <-> "OE2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F ASP 370": "OD1" <-> "OD2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F GLU 443": "OE1" <-> "OE2" Residue "F ASP 487": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20046 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3341 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3341 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3341 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3341 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3341 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3341 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 10.31, per 1000 atoms: 0.51 Number of scatterers: 20046 At special positions: 0 Unit cell: (110.39, 110.39, 138.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 3900 8.00 N 3396 7.00 C 12702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.49 Conformation dependent library (CDL) restraints added in 3.6 seconds 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4764 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 36 sheets defined 8.4% alpha, 33.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.684A pdb=" N LEU A 126 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 127 " --> pdb=" O ASP A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 127' Processing helix chain 'A' and resid 209 through 212 Processing helix chain 'A' and resid 243 through 249 Processing helix chain 'A' and resid 331 through 335 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.527A pdb=" N THR A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 361 " --> pdb=" O ALA A 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 356 through 361' Processing helix chain 'A' and resid 500 through 506 removed outlier: 3.787A pdb=" N ALA A 504 " --> pdb=" O ASN A 500 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 506 " --> pdb=" O GLU A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 509 No H-bonds generated for 'chain 'A' and resid 507 through 509' Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.684A pdb=" N LEU B 126 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 127 " --> pdb=" O ASP B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 127' Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 331 through 335 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.527A pdb=" N THR B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY B 361 " --> pdb=" O ALA B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 361' Processing helix chain 'B' and resid 500 through 506 removed outlier: 3.787A pdb=" N ALA B 504 " --> pdb=" O ASN B 500 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU B 506 " --> pdb=" O GLU B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 509 No H-bonds generated for 'chain 'B' and resid 507 through 509' Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.683A pdb=" N LEU C 126 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 127 " --> pdb=" O ASP C 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 123 through 127' Processing helix chain 'C' and resid 209 through 212 Processing helix chain 'C' and resid 243 through 249 Processing helix chain 'C' and resid 331 through 335 Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.528A pdb=" N THR C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY C 361 " --> pdb=" O ALA C 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 356 through 361' Processing helix chain 'C' and resid 500 through 506 removed outlier: 3.787A pdb=" N ALA C 504 " --> pdb=" O ASN C 500 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU C 506 " --> pdb=" O GLU C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 509 No H-bonds generated for 'chain 'C' and resid 507 through 509' Processing helix chain 'D' and resid 123 through 127 removed outlier: 3.684A pdb=" N LEU D 126 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D 127 " --> pdb=" O ASP D 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 123 through 127' Processing helix chain 'D' and resid 209 through 212 Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 331 through 335 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.527A pdb=" N THR D 360 " --> pdb=" O SER D 356 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY D 361 " --> pdb=" O ALA D 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 356 through 361' Processing helix chain 'D' and resid 500 through 506 removed outlier: 3.787A pdb=" N ALA D 504 " --> pdb=" O ASN D 500 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU D 506 " --> pdb=" O GLU D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 509 No H-bonds generated for 'chain 'D' and resid 507 through 509' Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.683A pdb=" N LEU E 126 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL E 127 " --> pdb=" O ASP E 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 127' Processing helix chain 'E' and resid 209 through 212 Processing helix chain 'E' and resid 243 through 249 Processing helix chain 'E' and resid 331 through 335 Processing helix chain 'E' and resid 356 through 361 removed outlier: 3.527A pdb=" N THR E 360 " --> pdb=" O SER E 356 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY E 361 " --> pdb=" O ALA E 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 356 through 361' Processing helix chain 'E' and resid 500 through 506 removed outlier: 3.787A pdb=" N ALA E 504 " --> pdb=" O ASN E 500 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU E 506 " --> pdb=" O GLU E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 507 through 509 No H-bonds generated for 'chain 'E' and resid 507 through 509' Processing helix chain 'F' and resid 123 through 127 removed outlier: 3.683A pdb=" N LEU F 126 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL F 127 " --> pdb=" O ASP F 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 123 through 127' Processing helix chain 'F' and resid 209 through 212 Processing helix chain 'F' and resid 243 through 249 Processing helix chain 'F' and resid 331 through 335 Processing helix chain 'F' and resid 356 through 361 removed outlier: 3.528A pdb=" N THR F 360 " --> pdb=" O SER F 356 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY F 361 " --> pdb=" O ALA F 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 356 through 361' Processing helix chain 'F' and resid 500 through 506 removed outlier: 3.787A pdb=" N ALA F 504 " --> pdb=" O ASN F 500 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU F 506 " --> pdb=" O GLU F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 507 through 509 No H-bonds generated for 'chain 'F' and resid 507 through 509' Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.022A pdb=" N TYR A 68 " --> pdb=" O GLU A 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS A 91 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE A 79 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU A 89 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR A 50 " --> pdb=" O PHE A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 110 Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 167 removed outlier: 6.687A pdb=" N VAL A 202 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR A 192 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP A 204 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL A 179 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU A 178 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE A 253 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR A 180 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE A 221 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE A 268 " --> pdb=" O MET A 162 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS A 164 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU A 270 " --> pdb=" O HIS A 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN A 166 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 229 removed outlier: 3.665A pdb=" N VAL A 227 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU B 240 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 229 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 240 removed outlier: 3.572A pdb=" N ALA F 229 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU A 240 " --> pdb=" O VAL F 227 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL F 227 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 340 through 344 removed outlier: 6.184A pdb=" N LEU A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU A 324 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU A 313 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR A 322 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 321 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N PHE A 377 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS A 284 " --> pdb=" O PHE A 377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 399 removed outlier: 6.479A pdb=" N THR A 432 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG A 424 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR A 434 " --> pdb=" O ILE A 422 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU A 411 " --> pdb=" O VAL A 418 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE A 483 " --> pdb=" O PRO A 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 412 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE A 451 " --> pdb=" O TYR A 498 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TYR A 495 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR A 396 " --> pdb=" O TYR A 495 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU A 497 " --> pdb=" O THR A 396 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR A 398 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.022A pdb=" N TYR B 68 " --> pdb=" O GLU B 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU B 72 " --> pdb=" O TYR B 68 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS B 91 " --> pdb=" O GLN B 77 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE B 79 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU B 89 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR B 50 " --> pdb=" O PHE B 145 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 107 through 110 Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 167 removed outlier: 6.687A pdb=" N VAL B 202 " --> pdb=" O TYR B 192 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR B 192 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP B 204 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL B 179 " --> pdb=" O VAL B 186 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU B 178 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE B 253 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR B 180 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE B 221 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE B 268 " --> pdb=" O MET B 162 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS B 164 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 270 " --> pdb=" O HIS B 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN B 166 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 227 through 229 removed outlier: 3.669A pdb=" N VAL B 227 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LEU C 240 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA B 229 " --> pdb=" O VAL C 238 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 340 through 344 removed outlier: 6.185A pdb=" N LEU B 300 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU B 324 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU B 313 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N THR B 322 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL B 321 " --> pdb=" O LEU B 287 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N PHE B 377 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS B 284 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 393 through 399 removed outlier: 6.478A pdb=" N THR B 432 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG B 424 " --> pdb=" O THR B 432 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR B 434 " --> pdb=" O ILE B 422 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU B 411 " --> pdb=" O VAL B 418 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE B 483 " --> pdb=" O PRO B 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 412 " --> pdb=" O ILE B 483 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE B 451 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N TYR B 495 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR B 396 " --> pdb=" O TYR B 495 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 497 " --> pdb=" O THR B 396 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR B 398 " --> pdb=" O LEU B 497 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.022A pdb=" N TYR C 68 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU C 72 " --> pdb=" O TYR C 68 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS C 91 " --> pdb=" O GLN C 77 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE C 79 " --> pdb=" O GLU C 89 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU C 89 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR C 50 " --> pdb=" O PHE C 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 107 through 110 Processing sheet with id=AB7, first strand: chain 'C' and resid 161 through 167 removed outlier: 6.687A pdb=" N VAL C 202 " --> pdb=" O TYR C 192 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR C 192 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP C 204 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL C 179 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU C 178 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE C 253 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR C 180 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE C 221 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE C 268 " --> pdb=" O MET C 162 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS C 164 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU C 270 " --> pdb=" O HIS C 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN C 166 " --> pdb=" O LEU C 270 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 227 through 229 removed outlier: 3.676A pdb=" N VAL C 227 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU D 240 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA C 229 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 340 through 344 removed outlier: 6.185A pdb=" N LEU C 300 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU C 324 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU C 313 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR C 322 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL C 321 " --> pdb=" O LEU C 287 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N PHE C 377 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS C 284 " --> pdb=" O PHE C 377 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 393 through 399 removed outlier: 6.478A pdb=" N THR C 432 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG C 424 " --> pdb=" O THR C 432 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR C 434 " --> pdb=" O ILE C 422 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU C 411 " --> pdb=" O VAL C 418 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE C 483 " --> pdb=" O PRO C 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 412 " --> pdb=" O ILE C 483 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE C 451 " --> pdb=" O TYR C 498 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TYR C 495 " --> pdb=" O THR C 394 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR C 396 " --> pdb=" O TYR C 495 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 497 " --> pdb=" O THR C 396 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR C 398 " --> pdb=" O LEU C 497 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 65 through 68 removed outlier: 6.022A pdb=" N TYR D 68 " --> pdb=" O GLU D 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU D 72 " --> pdb=" O TYR D 68 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS D 91 " --> pdb=" O GLN D 77 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE D 79 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N GLU D 89 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR D 50 " --> pdb=" O PHE D 145 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 107 through 110 Processing sheet with id=AC4, first strand: chain 'D' and resid 161 through 167 removed outlier: 6.687A pdb=" N VAL D 202 " --> pdb=" O TYR D 192 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR D 192 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP D 204 " --> pdb=" O TYR D 190 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL D 179 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU D 178 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE D 253 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR D 180 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE D 221 " --> pdb=" O TYR D 271 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE D 268 " --> pdb=" O MET D 162 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS D 164 " --> pdb=" O PHE D 268 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU D 270 " --> pdb=" O HIS D 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN D 166 " --> pdb=" O LEU D 270 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 227 through 229 removed outlier: 3.683A pdb=" N VAL D 227 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LEU E 240 " --> pdb=" O VAL D 227 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 229 " --> pdb=" O VAL E 238 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 340 through 344 removed outlier: 6.184A pdb=" N LEU D 300 " --> pdb=" O VAL D 307 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU D 324 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU D 313 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR D 322 " --> pdb=" O LEU D 313 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL D 321 " --> pdb=" O LEU D 287 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N PHE D 377 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS D 284 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 393 through 399 removed outlier: 6.479A pdb=" N THR D 432 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG D 424 " --> pdb=" O THR D 432 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N THR D 434 " --> pdb=" O ILE D 422 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU D 411 " --> pdb=" O VAL D 418 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE D 483 " --> pdb=" O PRO D 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE D 412 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE D 451 " --> pdb=" O TYR D 498 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TYR D 495 " --> pdb=" O THR D 394 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR D 396 " --> pdb=" O TYR D 495 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU D 497 " --> pdb=" O THR D 396 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR D 398 " --> pdb=" O LEU D 497 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 65 through 68 removed outlier: 6.022A pdb=" N TYR E 68 " --> pdb=" O GLU E 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU E 72 " --> pdb=" O TYR E 68 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LYS E 91 " --> pdb=" O GLN E 77 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ILE E 79 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU E 89 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR E 50 " --> pdb=" O PHE E 145 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 107 through 110 Processing sheet with id=AD1, first strand: chain 'E' and resid 161 through 167 removed outlier: 6.687A pdb=" N VAL E 202 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR E 192 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP E 204 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL E 179 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LEU E 178 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE E 253 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR E 180 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE E 221 " --> pdb=" O TYR E 271 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE E 268 " --> pdb=" O MET E 162 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS E 164 " --> pdb=" O PHE E 268 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU E 270 " --> pdb=" O HIS E 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN E 166 " --> pdb=" O LEU E 270 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 227 through 229 removed outlier: 3.678A pdb=" N VAL E 227 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU F 240 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA E 229 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.185A pdb=" N LEU E 300 " --> pdb=" O VAL E 307 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU E 324 " --> pdb=" O THR E 311 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU E 313 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR E 322 " --> pdb=" O LEU E 313 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL E 321 " --> pdb=" O LEU E 287 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N PHE E 377 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS E 284 " --> pdb=" O PHE E 377 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 393 through 399 removed outlier: 6.478A pdb=" N THR E 432 " --> pdb=" O ARG E 424 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG E 424 " --> pdb=" O THR E 432 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR E 434 " --> pdb=" O ILE E 422 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU E 411 " --> pdb=" O VAL E 418 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE E 483 " --> pdb=" O PRO E 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE E 412 " --> pdb=" O ILE E 483 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N PHE E 451 " --> pdb=" O TYR E 498 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N TYR E 495 " --> pdb=" O THR E 394 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR E 396 " --> pdb=" O TYR E 495 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU E 497 " --> pdb=" O THR E 396 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR E 398 " --> pdb=" O LEU E 497 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 65 through 68 removed outlier: 6.021A pdb=" N TYR F 68 " --> pdb=" O GLU F 72 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N GLU F 72 " --> pdb=" O TYR F 68 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS F 91 " --> pdb=" O GLN F 77 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE F 79 " --> pdb=" O GLU F 89 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N GLU F 89 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR F 50 " --> pdb=" O PHE F 145 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 107 through 110 Processing sheet with id=AD7, first strand: chain 'F' and resid 161 through 167 removed outlier: 6.687A pdb=" N VAL F 202 " --> pdb=" O TYR F 192 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N TYR F 192 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP F 204 " --> pdb=" O TYR F 190 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 179 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU F 178 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N PHE F 253 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TYR F 180 " --> pdb=" O PHE F 253 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE F 221 " --> pdb=" O TYR F 271 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N PHE F 268 " --> pdb=" O MET F 162 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N HIS F 164 " --> pdb=" O PHE F 268 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU F 270 " --> pdb=" O HIS F 164 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN F 166 " --> pdb=" O LEU F 270 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 340 through 344 removed outlier: 6.185A pdb=" N LEU F 300 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU F 324 " --> pdb=" O THR F 311 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU F 313 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N THR F 322 " --> pdb=" O LEU F 313 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL F 321 " --> pdb=" O LEU F 287 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N PHE F 377 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS F 284 " --> pdb=" O PHE F 377 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 393 through 399 removed outlier: 6.478A pdb=" N THR F 432 " --> pdb=" O ARG F 424 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG F 424 " --> pdb=" O THR F 432 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N THR F 434 " --> pdb=" O ILE F 422 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU F 411 " --> pdb=" O VAL F 418 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE F 483 " --> pdb=" O PRO F 410 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE F 412 " --> pdb=" O ILE F 483 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N PHE F 451 " --> pdb=" O TYR F 498 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N TYR F 495 " --> pdb=" O THR F 394 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N THR F 396 " --> pdb=" O TYR F 495 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU F 497 " --> pdb=" O THR F 396 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR F 398 " --> pdb=" O LEU F 497 " (cutoff:3.500A) 474 hydrogen bonds defined for protein. 1080 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: 6.69 Time building geometry restraints manager: 8.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6648 1.34 - 1.45: 2299 1.45 - 1.57: 11333 1.57 - 1.69: 0 1.69 - 1.80: 96 Bond restraints: 20376 Sorted by residual: bond pdb=" C GLU D 286 " pdb=" N LEU D 287 " ideal model delta sigma weight residual 1.329 1.231 0.098 3.03e-02 1.09e+03 1.04e+01 bond pdb=" C GLU A 286 " pdb=" N LEU A 287 " ideal model delta sigma weight residual 1.329 1.231 0.098 3.03e-02 1.09e+03 1.04e+01 bond pdb=" C GLU C 286 " pdb=" N LEU C 287 " ideal model delta sigma weight residual 1.329 1.231 0.098 3.03e-02 1.09e+03 1.04e+01 bond pdb=" C GLU B 286 " pdb=" N LEU B 287 " ideal model delta sigma weight residual 1.329 1.232 0.097 3.03e-02 1.09e+03 1.03e+01 bond pdb=" C GLU F 286 " pdb=" N LEU F 287 " ideal model delta sigma weight residual 1.329 1.232 0.097 3.03e-02 1.09e+03 1.03e+01 ... (remaining 20371 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.72: 678 106.72 - 113.53: 11631 113.53 - 120.33: 6920 120.33 - 127.14: 8191 127.14 - 133.95: 192 Bond angle restraints: 27612 Sorted by residual: angle pdb=" C VAL F 421 " pdb=" N ILE F 422 " pdb=" CA ILE F 422 " ideal model delta sigma weight residual 123.16 119.01 4.15 1.06e+00 8.90e-01 1.53e+01 angle pdb=" C VAL C 421 " pdb=" N ILE C 422 " pdb=" CA ILE C 422 " ideal model delta sigma weight residual 123.16 119.01 4.15 1.06e+00 8.90e-01 1.53e+01 angle pdb=" C VAL E 421 " pdb=" N ILE E 422 " pdb=" CA ILE E 422 " ideal model delta sigma weight residual 123.16 119.02 4.14 1.06e+00 8.90e-01 1.53e+01 angle pdb=" C VAL B 421 " pdb=" N ILE B 422 " pdb=" CA ILE B 422 " ideal model delta sigma weight residual 123.16 119.02 4.14 1.06e+00 8.90e-01 1.53e+01 angle pdb=" C VAL A 421 " pdb=" N ILE A 422 " pdb=" CA ILE A 422 " ideal model delta sigma weight residual 123.16 119.03 4.13 1.06e+00 8.90e-01 1.52e+01 ... (remaining 27607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.69: 11170 15.69 - 31.38: 951 31.38 - 47.07: 221 47.07 - 62.76: 36 62.76 - 78.45: 30 Dihedral angle restraints: 12408 sinusoidal: 4944 harmonic: 7464 Sorted by residual: dihedral pdb=" CA GLN F 420 " pdb=" C GLN F 420 " pdb=" N VAL F 421 " pdb=" CA VAL F 421 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLN C 420 " pdb=" C GLN C 420 " pdb=" N VAL C 421 " pdb=" CA VAL C 421 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA GLN E 420 " pdb=" C GLN E 420 " pdb=" N VAL E 421 " pdb=" CA VAL E 421 " ideal model delta harmonic sigma weight residual 180.00 160.25 19.75 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 12405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1772 0.029 - 0.059: 863 0.059 - 0.088: 267 0.088 - 0.117: 272 0.117 - 0.146: 54 Chirality restraints: 3228 Sorted by residual: chirality pdb=" CA ILE F 184 " pdb=" N ILE F 184 " pdb=" C ILE F 184 " pdb=" CB ILE F 184 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ILE C 184 " pdb=" N ILE C 184 " pdb=" C ILE C 184 " pdb=" CB ILE C 184 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE B 184 " pdb=" N ILE B 184 " pdb=" C ILE B 184 " pdb=" CB ILE B 184 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 3225 not shown) Planarity restraints: 3588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 195 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO C 196 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 196 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 196 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN F 195 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO F 196 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 196 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO F 196 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 195 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO D 196 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 196 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 196 " 0.026 5.00e-02 4.00e+02 ... (remaining 3585 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1935 2.73 - 3.28: 19585 3.28 - 3.82: 30920 3.82 - 4.36: 38685 4.36 - 4.90: 66653 Nonbonded interactions: 157778 Sorted by model distance: nonbonded pdb=" OG1 THR E 294 " pdb=" O ASP E 296 " model vdw 2.194 2.440 nonbonded pdb=" OG1 THR B 294 " pdb=" O ASP B 296 " model vdw 2.194 2.440 nonbonded pdb=" OG1 THR D 294 " pdb=" O ASP D 296 " model vdw 2.194 2.440 nonbonded pdb=" OG1 THR A 294 " pdb=" O ASP A 296 " model vdw 2.194 2.440 nonbonded pdb=" OG1 THR C 294 " pdb=" O ASP C 296 " model vdw 2.194 2.440 ... (remaining 157773 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.240 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 51.390 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.006 0.098 20376 Z= 0.395 Angle : 0.676 6.770 27612 Z= 0.369 Chirality : 0.047 0.146 3228 Planarity : 0.004 0.047 3588 Dihedral : 13.186 78.448 7644 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 0.82 % Allowed : 6.20 % Favored : 92.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.13), residues: 2622 helix: -4.79 (0.13), residues: 186 sheet: -2.54 (0.14), residues: 816 loop : -2.73 (0.13), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 222 HIS 0.002 0.000 HIS F 388 PHE 0.012 0.001 PHE B 253 TYR 0.010 0.001 TYR B 131 ARG 0.002 0.000 ARG A 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 228 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8246 (mtp85) cc_final: 0.7911 (ttm-80) REVERT: A 365 GLU cc_start: 0.8248 (tp30) cc_final: 0.7902 (tp30) REVERT: B 190 TYR cc_start: 0.8551 (t80) cc_final: 0.8276 (t80) REVERT: B 314 ASP cc_start: 0.7737 (m-30) cc_final: 0.7338 (m-30) REVERT: B 325 MET cc_start: 0.8690 (ttm) cc_final: 0.8421 (ttp) REVERT: C 63 ARG cc_start: 0.8404 (mtp85) cc_final: 0.8127 (ttm-80) REVERT: C 135 MET cc_start: 0.8322 (tpp) cc_final: 0.7636 (mmm) REVERT: C 190 TYR cc_start: 0.8738 (t80) cc_final: 0.8491 (t80) REVERT: C 314 ASP cc_start: 0.7808 (m-30) cc_final: 0.7427 (m-30) REVERT: D 63 ARG cc_start: 0.8248 (mtp85) cc_final: 0.7913 (ttm-80) REVERT: D 365 GLU cc_start: 0.8256 (tp30) cc_final: 0.7907 (tp30) REVERT: E 190 TYR cc_start: 0.8560 (t80) cc_final: 0.8282 (t80) REVERT: E 314 ASP cc_start: 0.7754 (m-30) cc_final: 0.7354 (m-30) REVERT: E 325 MET cc_start: 0.8730 (ttm) cc_final: 0.8404 (ttp) REVERT: F 63 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8121 (ttm-80) REVERT: F 135 MET cc_start: 0.8322 (tpp) cc_final: 0.7630 (mmm) REVERT: F 190 TYR cc_start: 0.8746 (t80) cc_final: 0.8510 (t80) REVERT: F 314 ASP cc_start: 0.7815 (m-30) cc_final: 0.7174 (m-30) outliers start: 18 outliers final: 9 residues processed: 246 average time/residue: 0.3907 time to fit residues: 141.1957 Evaluate side-chains 164 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 155 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 360 THR Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 360 THR Chi-restraints excluded: chain D residue 434 THR Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 434 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.5980 chunk 200 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 134 optimal weight: 0.3980 chunk 106 optimal weight: 9.9990 chunk 206 optimal weight: 0.0770 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 239 optimal weight: 2.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 ASN B 316 ASN C 316 ASN C 420 GLN D 316 ASN E 316 ASN F 316 ASN F 420 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20376 Z= 0.234 Angle : 0.594 10.274 27612 Z= 0.292 Chirality : 0.046 0.142 3228 Planarity : 0.005 0.054 3588 Dihedral : 5.321 44.234 2811 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 1.54 % Allowed : 9.65 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.15), residues: 2622 helix: -3.67 (0.28), residues: 186 sheet: -1.94 (0.15), residues: 858 loop : -2.28 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 222 HIS 0.002 0.000 HIS A 276 PHE 0.009 0.001 PHE B 433 TYR 0.010 0.001 TYR B 131 ARG 0.006 0.000 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 188 time to evaluate : 2.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7861 (ttm-80) REVERT: B 63 ARG cc_start: 0.8423 (mtp85) cc_final: 0.8076 (ttm-80) REVERT: B 325 MET cc_start: 0.8655 (ttm) cc_final: 0.8417 (ttp) REVERT: B 487 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7582 (p0) REVERT: C 63 ARG cc_start: 0.8412 (mtp85) cc_final: 0.8161 (ttm-80) REVERT: C 491 MET cc_start: 0.8586 (tpp) cc_final: 0.8335 (mmt) REVERT: D 63 ARG cc_start: 0.8185 (mtp85) cc_final: 0.7863 (ttm-80) REVERT: E 63 ARG cc_start: 0.8424 (mtp85) cc_final: 0.8081 (ttm-80) REVERT: E 190 TYR cc_start: 0.8424 (t80) cc_final: 0.8104 (t80) REVERT: E 325 MET cc_start: 0.8655 (ttm) cc_final: 0.8414 (ttp) REVERT: F 63 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8154 (ttm-80) REVERT: F 491 MET cc_start: 0.8576 (tpp) cc_final: 0.8332 (mmt) outliers start: 34 outliers final: 14 residues processed: 208 average time/residue: 0.3380 time to fit residues: 107.1792 Evaluate side-chains 176 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 434 THR Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 434 THR Chi-restraints excluded: chain F residue 213 ASP Chi-restraints excluded: chain F residue 434 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 199 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 259 optimal weight: 0.7980 chunk 213 optimal weight: 0.7980 chunk 238 optimal weight: 0.0670 chunk 81 optimal weight: 2.9990 chunk 192 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 20376 Z= 0.228 Angle : 0.567 9.837 27612 Z= 0.278 Chirality : 0.045 0.141 3228 Planarity : 0.004 0.052 3588 Dihedral : 4.766 21.309 2806 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 2.58 % Allowed : 10.82 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.15), residues: 2622 helix: -3.38 (0.30), residues: 186 sheet: -1.53 (0.16), residues: 858 loop : -1.99 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 222 HIS 0.002 0.001 HIS D 276 PHE 0.009 0.001 PHE E 253 TYR 0.015 0.001 TYR A 68 ARG 0.004 0.000 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 175 time to evaluate : 2.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8218 (mtp85) cc_final: 0.7910 (ttm-80) REVERT: A 365 GLU cc_start: 0.8265 (tp30) cc_final: 0.8055 (tp30) REVERT: B 63 ARG cc_start: 0.8469 (mtp85) cc_final: 0.8150 (ttm-80) REVERT: B 98 MET cc_start: 0.8345 (ttm) cc_final: 0.8072 (ttt) REVERT: C 63 ARG cc_start: 0.8309 (mtp85) cc_final: 0.8075 (ttm-80) REVERT: C 491 MET cc_start: 0.8568 (tpp) cc_final: 0.8259 (mmt) REVERT: D 63 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7910 (ttm-80) REVERT: D 365 GLU cc_start: 0.8175 (tp30) cc_final: 0.7728 (tp30) REVERT: E 63 ARG cc_start: 0.8458 (mtp85) cc_final: 0.8124 (ttm-80) REVERT: E 98 MET cc_start: 0.8343 (ttm) cc_final: 0.8065 (ttt) REVERT: E 190 TYR cc_start: 0.8395 (t80) cc_final: 0.8038 (t80) REVERT: E 325 MET cc_start: 0.8693 (ttm) cc_final: 0.8461 (ttp) REVERT: F 63 ARG cc_start: 0.8307 (mtp85) cc_final: 0.8074 (ttm-80) REVERT: F 491 MET cc_start: 0.8564 (tpp) cc_final: 0.8259 (mmt) outliers start: 57 outliers final: 36 residues processed: 208 average time/residue: 0.3185 time to fit residues: 102.4573 Evaluate side-chains 205 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 2.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 1.9990 chunk 180 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 241 optimal weight: 2.9990 chunk 255 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 228 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 20376 Z= 0.303 Angle : 0.587 10.035 27612 Z= 0.288 Chirality : 0.046 0.146 3228 Planarity : 0.005 0.050 3588 Dihedral : 4.812 21.856 2802 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 2.63 % Allowed : 13.27 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.16), residues: 2622 helix: -3.22 (0.31), residues: 186 sheet: -1.41 (0.16), residues: 828 loop : -1.80 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 222 HIS 0.003 0.001 HIS A 276 PHE 0.010 0.001 PHE E 253 TYR 0.014 0.001 TYR D 131 ARG 0.003 0.000 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 171 time to evaluate : 2.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8170 (mtp85) cc_final: 0.7870 (ttm-80) REVERT: A 365 GLU cc_start: 0.8265 (tp30) cc_final: 0.7837 (tp30) REVERT: B 63 ARG cc_start: 0.8479 (mtp85) cc_final: 0.8152 (ttm-80) REVERT: B 98 MET cc_start: 0.8286 (ttm) cc_final: 0.8029 (ttt) REVERT: C 63 ARG cc_start: 0.8328 (mtp85) cc_final: 0.8081 (ttm-80) REVERT: D 63 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7850 (ttm-80) REVERT: D 365 GLU cc_start: 0.8277 (tp30) cc_final: 0.7845 (tp30) REVERT: E 63 ARG cc_start: 0.8464 (mtp85) cc_final: 0.8124 (ttm-80) REVERT: E 98 MET cc_start: 0.8281 (ttm) cc_final: 0.8021 (ttt) REVERT: F 63 ARG cc_start: 0.8322 (mtp85) cc_final: 0.8079 (ttm-80) outliers start: 58 outliers final: 34 residues processed: 200 average time/residue: 0.3310 time to fit residues: 101.4905 Evaluate side-chains 201 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 314 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 212 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 190 optimal weight: 0.0370 chunk 105 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 GLN E 199 GLN F 199 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 20376 Z= 0.391 Angle : 0.628 10.498 27612 Z= 0.307 Chirality : 0.047 0.150 3228 Planarity : 0.005 0.048 3588 Dihedral : 5.027 22.149 2802 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 2.45 % Allowed : 15.44 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.16), residues: 2622 helix: -3.58 (0.26), residues: 186 sheet: -1.46 (0.16), residues: 852 loop : -1.55 (0.16), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 222 HIS 0.003 0.001 HIS A 276 PHE 0.011 0.002 PHE E 253 TYR 0.020 0.001 TYR C 131 ARG 0.003 0.000 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 163 time to evaluate : 2.522 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8142 (mtp85) cc_final: 0.7780 (ttm-80) REVERT: B 63 ARG cc_start: 0.8475 (mtp85) cc_final: 0.8153 (ttm-80) REVERT: B 98 MET cc_start: 0.8354 (ttm) cc_final: 0.8070 (ttt) REVERT: C 63 ARG cc_start: 0.8352 (mtp85) cc_final: 0.8090 (ttm-80) REVERT: D 63 ARG cc_start: 0.8144 (mtp85) cc_final: 0.7783 (ttm-80) REVERT: E 63 ARG cc_start: 0.8478 (mtp85) cc_final: 0.8152 (ttm-80) REVERT: E 98 MET cc_start: 0.8349 (ttm) cc_final: 0.8061 (ttt) REVERT: F 63 ARG cc_start: 0.8347 (mtp85) cc_final: 0.8088 (ttm-80) outliers start: 54 outliers final: 44 residues processed: 190 average time/residue: 0.3135 time to fit residues: 92.9393 Evaluate side-chains 202 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 158 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 356 SER Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 1.9990 chunk 229 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 0.0270 chunk 62 optimal weight: 4.9990 chunk 255 optimal weight: 0.5980 chunk 212 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20376 Z= 0.353 Angle : 0.621 10.215 27612 Z= 0.301 Chirality : 0.046 0.145 3228 Planarity : 0.005 0.051 3588 Dihedral : 4.980 21.966 2802 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 2.72 % Allowed : 16.35 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.16), residues: 2622 helix: -3.30 (0.27), residues: 222 sheet: -1.34 (0.16), residues: 852 loop : -1.58 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 222 HIS 0.003 0.001 HIS D 276 PHE 0.012 0.001 PHE B 253 TYR 0.015 0.001 TYR C 131 ARG 0.003 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 160 time to evaluate : 2.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7772 (ttm-80) REVERT: B 63 ARG cc_start: 0.8439 (mtp85) cc_final: 0.8108 (ttm-80) REVERT: B 98 MET cc_start: 0.8351 (ttm) cc_final: 0.8080 (ttt) REVERT: B 134 MET cc_start: 0.8926 (ttp) cc_final: 0.8661 (ttt) REVERT: C 63 ARG cc_start: 0.8299 (mtp85) cc_final: 0.7999 (ttm-80) REVERT: D 63 ARG cc_start: 0.8131 (mtp85) cc_final: 0.7775 (ttm-80) REVERT: E 63 ARG cc_start: 0.8442 (mtp85) cc_final: 0.8109 (ttm-80) REVERT: E 98 MET cc_start: 0.8346 (ttm) cc_final: 0.8070 (ttt) REVERT: E 134 MET cc_start: 0.8897 (ttp) cc_final: 0.8623 (ttt) REVERT: F 63 ARG cc_start: 0.8355 (mtp85) cc_final: 0.8130 (ttm-80) outliers start: 60 outliers final: 43 residues processed: 192 average time/residue: 0.3181 time to fit residues: 94.9401 Evaluate side-chains 197 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 154 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 370 ASP Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 145 optimal weight: 0.9990 chunk 186 optimal weight: 0.9990 chunk 144 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 254 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20376 Z= 0.275 Angle : 0.602 10.306 27612 Z= 0.289 Chirality : 0.046 0.143 3228 Planarity : 0.005 0.049 3588 Dihedral : 4.817 21.679 2802 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.95 % Favored : 90.05 % Rotamer: Outliers : 2.49 % Allowed : 16.67 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.16), residues: 2622 helix: -3.22 (0.27), residues: 222 sheet: -1.11 (0.16), residues: 948 loop : -1.47 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 222 HIS 0.002 0.000 HIS D 276 PHE 0.011 0.001 PHE B 253 TYR 0.013 0.001 TYR C 131 ARG 0.008 0.000 ARG D 155 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 164 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7757 (ttm-80) REVERT: B 63 ARG cc_start: 0.8377 (mtp85) cc_final: 0.8091 (ttm-80) REVERT: B 98 MET cc_start: 0.8408 (ttm) cc_final: 0.8142 (ttt) REVERT: C 63 ARG cc_start: 0.8298 (mtp85) cc_final: 0.7992 (ttm-80) REVERT: D 63 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7757 (ttm-80) REVERT: E 63 ARG cc_start: 0.8375 (mtp85) cc_final: 0.8086 (ttm-80) REVERT: E 98 MET cc_start: 0.8404 (ttm) cc_final: 0.8141 (ttt) REVERT: E 134 MET cc_start: 0.8889 (ttp) cc_final: 0.8628 (ttt) REVERT: F 63 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8013 (ttm-80) outliers start: 55 outliers final: 42 residues processed: 191 average time/residue: 0.3198 time to fit residues: 93.9128 Evaluate side-chains 202 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 160 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 370 ASP Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 151 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 231 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20376 Z= 0.283 Angle : 0.612 10.262 27612 Z= 0.293 Chirality : 0.046 0.144 3228 Planarity : 0.005 0.049 3588 Dihedral : 4.797 21.778 2802 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.03 % Favored : 89.97 % Rotamer: Outliers : 2.54 % Allowed : 16.58 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.16), residues: 2622 helix: -3.14 (0.27), residues: 222 sheet: -1.02 (0.16), residues: 948 loop : -1.44 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 222 HIS 0.002 0.001 HIS D 276 PHE 0.010 0.001 PHE B 253 TYR 0.012 0.001 TYR C 131 ARG 0.008 0.000 ARG A 155 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 160 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8111 (mtp85) cc_final: 0.7759 (ttm-80) REVERT: A 417 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.7771 (tp40) REVERT: B 63 ARG cc_start: 0.8381 (mtp85) cc_final: 0.8095 (ttm-80) REVERT: B 98 MET cc_start: 0.8379 (ttm) cc_final: 0.8126 (ttt) REVERT: C 63 ARG cc_start: 0.8498 (mtp85) cc_final: 0.8016 (ttm-80) REVERT: D 63 ARG cc_start: 0.8109 (mtp85) cc_final: 0.7757 (ttm-80) REVERT: D 417 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.7781 (tp40) REVERT: E 63 ARG cc_start: 0.8382 (mtp85) cc_final: 0.8090 (ttm-80) REVERT: E 98 MET cc_start: 0.8381 (ttm) cc_final: 0.8125 (ttt) REVERT: E 134 MET cc_start: 0.8911 (ttp) cc_final: 0.8669 (ttt) REVERT: F 63 ARG cc_start: 0.8335 (mtp85) cc_final: 0.8017 (ttm-80) outliers start: 56 outliers final: 46 residues processed: 189 average time/residue: 0.3204 time to fit residues: 93.9539 Evaluate side-chains 206 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 158 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 162 MET Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 162 MET Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 314 ASP Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 0.7980 chunk 222 optimal weight: 0.0050 chunk 237 optimal weight: 0.6980 chunk 142 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 chunk 186 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 214 optimal weight: 0.9990 chunk 224 optimal weight: 0.9990 chunk 236 optimal weight: 0.6980 chunk 155 optimal weight: 0.8980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 417 GLN E 417 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20376 Z= 0.198 Angle : 0.593 10.513 27612 Z= 0.279 Chirality : 0.045 0.146 3228 Planarity : 0.004 0.049 3588 Dihedral : 4.568 21.222 2802 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 1.99 % Allowed : 16.80 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.17), residues: 2622 helix: -3.07 (0.28), residues: 222 sheet: -0.82 (0.16), residues: 948 loop : -1.35 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 222 HIS 0.002 0.000 HIS A 164 PHE 0.010 0.001 PHE B 253 TYR 0.011 0.001 TYR C 131 ARG 0.005 0.000 ARG B 155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 166 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7799 (ttm-80) REVERT: A 417 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.7761 (tp40) REVERT: B 63 ARG cc_start: 0.8395 (mtp85) cc_final: 0.8120 (ttm-80) REVERT: B 98 MET cc_start: 0.8375 (ttm) cc_final: 0.8131 (ttt) REVERT: C 63 ARG cc_start: 0.8482 (mtp85) cc_final: 0.8008 (ttm-80) REVERT: C 417 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7564 (tp40) REVERT: D 63 ARG cc_start: 0.8117 (mtp85) cc_final: 0.7799 (ttm-80) REVERT: D 417 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7768 (tp40) REVERT: E 63 ARG cc_start: 0.8385 (mtp85) cc_final: 0.8110 (ttm-80) REVERT: E 98 MET cc_start: 0.8380 (ttm) cc_final: 0.8136 (ttt) REVERT: E 134 MET cc_start: 0.8899 (ttp) cc_final: 0.8663 (ttt) REVERT: F 63 ARG cc_start: 0.8471 (mtp85) cc_final: 0.8004 (ttm-80) REVERT: F 417 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7582 (tp40) outliers start: 44 outliers final: 34 residues processed: 186 average time/residue: 0.3150 time to fit residues: 91.4578 Evaluate side-chains 194 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 417 GLN Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 174 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 209 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 420 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 20376 Z= 0.407 Angle : 0.658 10.211 27612 Z= 0.317 Chirality : 0.047 0.174 3228 Planarity : 0.005 0.050 3588 Dihedral : 4.988 22.253 2802 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 1.86 % Allowed : 16.94 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.16), residues: 2622 helix: -3.27 (0.28), residues: 186 sheet: -0.95 (0.16), residues: 948 loop : -1.29 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 222 HIS 0.003 0.001 HIS A 276 PHE 0.011 0.002 PHE E 253 TYR 0.013 0.001 TYR C 131 ARG 0.004 0.000 ARG B 155 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 151 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8185 (mmt) cc_final: 0.7951 (mmm) REVERT: A 63 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7787 (ttm-80) REVERT: A 417 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7885 (tp40) REVERT: B 63 ARG cc_start: 0.8380 (mtp85) cc_final: 0.8102 (ttm-80) REVERT: B 98 MET cc_start: 0.8332 (ttm) cc_final: 0.8087 (ttt) REVERT: C 63 ARG cc_start: 0.8380 (mtp85) cc_final: 0.8040 (ttm-80) REVERT: C 417 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7604 (tp40) REVERT: D 54 MET cc_start: 0.8189 (mmt) cc_final: 0.7951 (mmm) REVERT: D 63 ARG cc_start: 0.8143 (mtp85) cc_final: 0.7790 (ttm-80) REVERT: D 417 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.7922 (tp40) REVERT: E 63 ARG cc_start: 0.8413 (mtp85) cc_final: 0.8134 (ttm-80) REVERT: E 98 MET cc_start: 0.8329 (ttm) cc_final: 0.8078 (ttt) REVERT: E 134 MET cc_start: 0.8887 (ttp) cc_final: 0.8654 (ttt) REVERT: F 63 ARG cc_start: 0.8357 (mtp85) cc_final: 0.8030 (ttm-80) REVERT: F 417 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.7565 (tp40) outliers start: 41 outliers final: 34 residues processed: 174 average time/residue: 0.3204 time to fit residues: 87.1466 Evaluate side-chains 187 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 149 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 370 ASP Chi-restraints excluded: chain A residue 417 GLN Chi-restraints excluded: chain B residue 83 ASP Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 162 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 314 ASP Chi-restraints excluded: chain B residue 376 GLU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 417 GLN Chi-restraints excluded: chain C residue 505 LEU Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 83 ASP Chi-restraints excluded: chain D residue 163 ILE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 370 ASP Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 162 MET Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 314 ASP Chi-restraints excluded: chain E residue 376 GLU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain F residue 83 ASP Chi-restraints excluded: chain F residue 287 LEU Chi-restraints excluded: chain F residue 314 ASP Chi-restraints excluded: chain F residue 417 GLN Chi-restraints excluded: chain F residue 505 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 193 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 209 optimal weight: 0.2980 chunk 87 optimal weight: 2.9990 chunk 215 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.114580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.078555 restraints weight = 29667.797| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.06 r_work: 0.2779 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20376 Z= 0.190 Angle : 0.595 10.315 27612 Z= 0.280 Chirality : 0.045 0.154 3228 Planarity : 0.004 0.053 3588 Dihedral : 4.588 21.022 2802 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 1.77 % Allowed : 17.12 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.17), residues: 2622 helix: -2.99 (0.28), residues: 222 sheet: -0.74 (0.17), residues: 948 loop : -1.30 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 222 HIS 0.002 0.000 HIS A 276 PHE 0.009 0.001 PHE E 253 TYR 0.011 0.001 TYR C 131 ARG 0.004 0.000 ARG B 155 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3696.50 seconds wall clock time: 68 minutes 34.23 seconds (4114.23 seconds total)