Starting phenix.real_space_refine on Tue Dec 12 04:02:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/12_2023/6kz3_0784.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/12_2023/6kz3_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_0784/12_2023/6kz3_0784.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/12_2023/6kz3_0784.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/12_2023/6kz3_0784.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6kz3_0784/12_2023/6kz3_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 10.39, per 1000 atoms: 0.52 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: 7.89 Conformation dependent library (CDL) restraints added in 3.5 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: 2.51 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: 6.62 Time building geometry restraints manager: 8.40 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: 0.010 Normalize map: mean=0, sd=1: 2.390 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: 10.400 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 51.680 Find NCS groups from input model: 1.450 Set up NCS constraints: 0.110 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.140 ------------------------------------------------------------------------------- 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 : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 246 average time/residue: 0.3833 time to fit residues: 138.0066 Evaluate side-chains 171 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1802 time to fit residues: 6.3041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 222 optimal weight: 0.9990 chunk 200 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 206 optimal weight: 0.0770 chunk 80 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 239 optimal weight: 10.0000 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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: 0.8357 moved from start: 0.1095 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= 0.229 Angle : 0.595 10.258 27612 Z= 0.293 Chirality : 0.046 0.147 3228 Planarity : 0.004 0.053 3588 Dihedral : 4.936 20.145 2802 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 1.22 % Allowed : 9.92 % Favored : 88.86 % 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: -3.39 (0.15), residues: 2622 helix: -3.65 (0.28), residues: 186 sheet: -1.98 (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 E 253 TYR 0.010 0.001 TYR E 131 ARG 0.007 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 229 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 216 average time/residue: 0.3493 time to fit residues: 113.9299 Evaluate side-chains 183 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 2.598 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1914 time to fit residues: 8.2922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 0.0770 chunk 199 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 259 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 238 optimal weight: 0.5980 chunk 81 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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: 0.8357 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 20376 Z= 0.252 Angle : 0.580 9.750 27612 Z= 0.286 Chirality : 0.046 0.143 3228 Planarity : 0.004 0.052 3588 Dihedral : 4.833 21.518 2802 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 2.04 % Allowed : 10.87 % Favored : 87.09 % 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: -2.96 (0.15), residues: 2622 helix: -3.41 (0.29), residues: 186 sheet: -1.63 (0.15), residues: 858 loop : -2.01 (0.15), residues: 1578 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 433 TYR 0.015 0.001 TYR D 131 ARG 0.005 0.000 ARG F 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 229 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 184 time to evaluate : 2.407 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 25 residues processed: 214 average time/residue: 0.3372 time to fit residues: 111.2830 Evaluate side-chains 202 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.1724 time to fit residues: 11.4659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 237 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 chunk 161 optimal weight: 0.0370 chunk 241 optimal weight: 0.9980 chunk 255 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 228 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- 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: 0.8357 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 20376 Z= 0.270 Angle : 0.580 9.679 27612 Z= 0.285 Chirality : 0.046 0.143 3228 Planarity : 0.004 0.050 3588 Dihedral : 4.828 21.596 2802 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 1.09 % Allowed : 13.41 % Favored : 85.51 % 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: -2.72 (0.15), residues: 2622 helix: -3.26 (0.30), residues: 186 sheet: -1.44 (0.16), residues: 858 loop : -1.86 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 222 HIS 0.002 0.000 HIS D 276 PHE 0.009 0.001 PHE B 433 TYR 0.013 0.001 TYR D 131 ARG 0.004 0.000 ARG F 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 209 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 199 average time/residue: 0.3472 time to fit residues: 104.6406 Evaluate side-chains 180 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 172 time to evaluate : 2.263 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1782 time to fit residues: 5.4806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 105 optimal weight: 0.9990 chunk 217 optimal weight: 0.6980 chunk 176 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 chunk 64 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 199 GLN F 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20376 Z= 0.346 Angle : 0.616 10.318 27612 Z= 0.301 Chirality : 0.047 0.148 3228 Planarity : 0.005 0.048 3588 Dihedral : 4.994 22.072 2802 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 1.09 % Allowed : 15.99 % Favored : 82.93 % 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: -2.67 (0.16), residues: 2622 helix: -3.42 (0.26), residues: 222 sheet: -1.43 (0.16), residues: 882 loop : -1.71 (0.16), residues: 1518 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 0.001 PHE B 253 TYR 0.019 0.001 TYR F 131 ARG 0.003 0.000 ARG A 63 *********************** 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 183 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 174 average time/residue: 0.3465 time to fit residues: 92.0536 Evaluate side-chains 169 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 2.555 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1794 time to fit residues: 9.0848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 85 optimal weight: 0.9990 chunk 229 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 255 optimal weight: 0.2980 chunk 212 optimal weight: 0.9980 chunk 118 optimal weight: 0.0970 chunk 21 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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: 0.8344 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20376 Z= 0.215 Angle : 0.581 10.159 27612 Z= 0.278 Chirality : 0.045 0.143 3228 Planarity : 0.004 0.047 3588 Dihedral : 4.716 21.323 2802 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 0.95 % Allowed : 16.94 % 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: -2.30 (0.16), residues: 2622 helix: -3.01 (0.31), residues: 186 sheet: -1.20 (0.16), residues: 948 loop : -1.52 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 222 HIS 0.002 0.000 HIS D 276 PHE 0.010 0.001 PHE E 253 TYR 0.013 0.001 TYR F 131 ARG 0.003 0.000 ARG D 63 *********************** 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 192 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 171 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 182 average time/residue: 0.3207 time to fit residues: 91.7791 Evaluate side-chains 171 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 162 time to evaluate : 2.500 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1863 time to fit residues: 6.4792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 246 optimal weight: 0.3980 chunk 28 optimal weight: 0.3980 chunk 145 optimal weight: 0.5980 chunk 186 optimal weight: 2.9990 chunk 144 optimal weight: 0.5980 chunk 215 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 254 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 117 optimal weight: 0.0870 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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: 0.8327 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20376 Z= 0.176 Angle : 0.576 10.330 27612 Z= 0.273 Chirality : 0.045 0.140 3228 Planarity : 0.004 0.046 3588 Dihedral : 4.525 21.192 2802 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.50 % Favored : 90.50 % Rotamer: Outliers : 1.00 % Allowed : 17.12 % Favored : 81.88 % 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: -2.16 (0.16), residues: 2622 helix: -3.24 (0.27), residues: 222 sheet: -0.91 (0.17), residues: 822 loop : -1.45 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 222 HIS 0.001 0.000 HIS D 164 PHE 0.009 0.001 PHE B 433 TYR 0.011 0.001 TYR C 131 ARG 0.004 0.000 ARG D 63 *********************** 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 190 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 2.359 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 7 residues processed: 187 average time/residue: 0.3144 time to fit residues: 92.7214 Evaluate side-chains 164 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 157 time to evaluate : 2.391 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1895 time to fit residues: 5.5717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 157 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 151 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 161 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 231 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20376 Z= 0.352 Angle : 0.629 10.114 27612 Z= 0.304 Chirality : 0.047 0.153 3228 Planarity : 0.005 0.046 3588 Dihedral : 4.897 22.096 2802 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 0.82 % Allowed : 17.03 % Favored : 82.16 % 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: -2.22 (0.16), residues: 2622 helix: -3.19 (0.27), residues: 222 sheet: -1.08 (0.17), residues: 852 loop : -1.42 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 222 HIS 0.003 0.001 HIS D 276 PHE 0.010 0.001 PHE B 433 TYR 0.013 0.001 TYR F 131 ARG 0.003 0.000 ARG A 63 *********************** 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 182 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 164 time to evaluate : 2.340 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 168 average time/residue: 0.3303 time to fit residues: 86.6176 Evaluate side-chains 172 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 2.627 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1698 time to fit residues: 6.7131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 243 optimal weight: 1.9990 chunk 222 optimal weight: 0.4980 chunk 237 optimal weight: 0.6980 chunk 142 optimal weight: 0.3980 chunk 103 optimal weight: 0.8980 chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 214 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 236 optimal weight: 0.2980 chunk 155 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.8338 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20376 Z= 0.207 Angle : 0.592 10.384 27612 Z= 0.280 Chirality : 0.045 0.143 3228 Planarity : 0.004 0.047 3588 Dihedral : 4.651 21.258 2802 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 0.41 % Allowed : 17.35 % Favored : 82.25 % 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: -2.02 (0.16), residues: 2622 helix: -3.13 (0.27), residues: 222 sheet: -0.80 (0.18), residues: 822 loop : -1.36 (0.16), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 222 HIS 0.002 0.000 HIS D 276 PHE 0.009 0.001 PHE B 253 TYR 0.011 0.001 TYR C 131 ARG 0.004 0.000 ARG A 63 *********************** 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 169 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 167 average time/residue: 0.3408 time to fit residues: 90.3691 Evaluate side-chains 163 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 158 time to evaluate : 2.374 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1786 time to fit residues: 4.9307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 250 optimal weight: 0.0470 chunk 153 optimal weight: 0.5980 chunk 118 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 263 optimal weight: 0.7980 chunk 242 optimal weight: 1.9990 chunk 209 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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: 0.8343 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20376 Z= 0.236 Angle : 0.605 10.185 27612 Z= 0.287 Chirality : 0.045 0.142 3228 Planarity : 0.004 0.047 3588 Dihedral : 4.658 21.543 2802 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 0.23 % Allowed : 17.80 % Favored : 81.97 % 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: -1.98 (0.16), residues: 2622 helix: -3.05 (0.28), residues: 222 sheet: -0.82 (0.17), residues: 852 loop : -1.32 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 222 HIS 0.002 0.000 HIS A 276 PHE 0.009 0.001 PHE E 433 TYR 0.012 0.001 TYR C 131 ARG 0.004 0.000 ARG D 63 ********************** 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 167 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 162 time to evaluate : 2.409 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 164 average time/residue: 0.3359 time to fit residues: 86.2248 Evaluate side-chains 161 residues out of total 2214 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 157 time to evaluate : 2.467 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1797 time to fit residues: 4.7533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 264 random chunks: chunk 223 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 209 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 38 optimal weight: 0.4980 chunk 184 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 420 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.077974 restraints weight = 29763.313| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 3.04 r_work: 0.2768 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20376 Z= 0.254 Angle : 0.607 10.205 27612 Z= 0.288 Chirality : 0.046 0.142 3228 Planarity : 0.004 0.048 3588 Dihedral : 4.692 21.500 2802 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.41 % Allowed : 17.66 % Favored : 81.93 % 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: -1.96 (0.16), residues: 2622 helix: -2.99 (0.28), residues: 222 sheet: -0.81 (0.17), residues: 852 loop : -1.31 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 222 HIS 0.002 0.001 HIS A 276 PHE 0.010 0.001 PHE B 253 TYR 0.012 0.001 TYR C 131 ARG 0.004 0.000 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3668.97 seconds wall clock time: 68 minutes 3.37 seconds (4083.37 seconds total)