Starting phenix.real_space_refine on Wed Feb 21 11:27:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nal_24273/02_2024/7nal_24273_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nal_24273/02_2024/7nal_24273.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nal_24273/02_2024/7nal_24273_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nal_24273/02_2024/7nal_24273_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nal_24273/02_2024/7nal_24273_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nal_24273/02_2024/7nal_24273.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nal_24273/02_2024/7nal_24273.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nal_24273/02_2024/7nal_24273_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nal_24273/02_2024/7nal_24273_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 136 5.16 5 C 19056 2.51 5 N 5544 2.21 5 O 5656 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 340": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "B GLU 196": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "C GLU 111": "OE1" <-> "OE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C GLU 435": "OE1" <-> "OE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D GLU 520": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E GLU 340": "OE1" <-> "OE2" Residue "E GLU 435": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F GLU 340": "OE1" <-> "OE2" Residue "F GLU 520": "OE1" <-> "OE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G GLU 340": "OE1" <-> "OE2" Residue "G GLU 435": "OE1" <-> "OE2" Residue "H GLU 196": "OE1" <-> "OE2" Residue "H GLU 340": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 30400 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "B" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "C" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "D" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "E" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "F" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "G" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "H" Number of atoms: 3778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3778 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 15, 'TRANS': 470} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.65, per 1000 atoms: 0.48 Number of scatterers: 30400 At special positions: 0 Unit cell: (194.394, 194.394, 70.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 136 16.00 P 8 15.00 O 5656 8.00 N 5544 7.00 C 19056 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: 12.15 Conformation dependent library (CDL) restraints added in 5.5 seconds 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7232 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 265 helices and 0 sheets defined 72.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.17 Creating SS restraints... Processing helix chain 'A' and resid 63 through 80 Proline residue: A 70 - end of helix Processing helix chain 'A' and resid 85 through 103 removed outlier: 3.643A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 121 removed outlier: 4.368A pdb=" N LEU A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.764A pdb=" N GLN A 143 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN A 150 " --> pdb=" O ARG A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 removed outlier: 3.991A pdb=" N ARG A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.674A pdb=" N LYS A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 191 Processing helix chain 'A' and resid 196 through 204 Processing helix chain 'A' and resid 207 through 216 removed outlier: 4.489A pdb=" N ARG A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 236 Processing helix chain 'A' and resid 239 through 247 Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.605A pdb=" N LEU A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 281 through 290 removed outlier: 5.483A pdb=" N ARG A 285 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU A 286 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.289A pdb=" N GLU A 297 " --> pdb=" O ALA A 294 " (cutoff:3.500A) Proline residue: A 298 - end of helix removed outlier: 3.648A pdb=" N ALA A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.568A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Proline residue: A 332 - end of helix removed outlier: 4.219A pdb=" N ASP A 335 " --> pdb=" O VAL A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 359 removed outlier: 3.547A pdb=" N LEU A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.633A pdb=" N ILE A 368 " --> pdb=" O PHE A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 385 through 396 Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 414 through 424 Processing helix chain 'A' and resid 427 through 435 removed outlier: 3.507A pdb=" N CYS A 430 " --> pdb=" O SER A 427 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N GLU A 431 " --> pdb=" O LYS A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 443 No H-bonds generated for 'chain 'A' and resid 440 through 443' Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 460 through 475 removed outlier: 3.605A pdb=" N GLU A 472 " --> pdb=" O ARG A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.580A pdb=" N LEU A 494 " --> pdb=" O TRP A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 508 removed outlier: 4.320A pdb=" N GLN A 500 " --> pdb=" O ARG A 497 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N TYR A 503 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 506 " --> pdb=" O TYR A 503 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 507 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 532 through 543 Processing helix chain 'B' and resid 63 through 81 Proline residue: B 70 - end of helix Processing helix chain 'B' and resid 85 through 103 Processing helix chain 'B' and resid 109 through 121 removed outlier: 3.797A pdb=" N LEU B 116 " --> pdb=" O VAL B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 138 through 149 removed outlier: 3.825A pdb=" N GLN B 143 " --> pdb=" O GLU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 162 removed outlier: 3.981A pdb=" N ARG B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 160 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 removed outlier: 3.687A pdb=" N LYS B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 191 Processing helix chain 'B' and resid 196 through 204 Processing helix chain 'B' and resid 207 through 216 removed outlier: 4.270A pdb=" N ARG B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 236 Processing helix chain 'B' and resid 239 through 247 Processing helix chain 'B' and resid 250 through 259 removed outlier: 3.730A pdb=" N LEU B 254 " --> pdb=" O ALA B 250 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Proline residue: B 256 - end of helix Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 281 through 290 removed outlier: 5.496A pdb=" N ARG B 285 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 286 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 300 removed outlier: 4.320A pdb=" N GLU B 297 " --> pdb=" O ALA B 294 " (cutoff:3.500A) Proline residue: B 298 - end of helix Processing helix chain 'B' and resid 305 through 310 Processing helix chain 'B' and resid 324 through 335 removed outlier: 3.567A pdb=" N GLN B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Proline residue: B 332 - end of helix removed outlier: 4.308A pdb=" N ASP B 335 " --> pdb=" O VAL B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 359 removed outlier: 3.527A pdb=" N LEU B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.656A pdb=" N ILE B 368 " --> pdb=" O PHE B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 385 through 396 Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 414 through 424 Processing helix chain 'B' and resid 427 through 436 removed outlier: 3.540A pdb=" N CYS B 430 " --> pdb=" O SER B 427 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU B 431 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER B 432 " --> pdb=" O TYR B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 443 No H-bonds generated for 'chain 'B' and resid 440 through 443' Processing helix chain 'B' and resid 448 through 453 Processing helix chain 'B' and resid 460 through 475 removed outlier: 3.570A pdb=" N GLU B 472 " --> pdb=" O ARG B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 494 removed outlier: 3.600A pdb=" N LEU B 494 " --> pdb=" O TRP B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 508 removed outlier: 4.468A pdb=" N GLN B 500 " --> pdb=" O ARG B 497 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N TYR B 503 " --> pdb=" O GLN B 500 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL B 506 " --> pdb=" O TYR B 503 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N SER B 507 " --> pdb=" O GLY B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 517 No H-bonds generated for 'chain 'B' and resid 515 through 517' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 532 through 543 Processing helix chain 'C' and resid 63 through 80 Proline residue: C 70 - end of helix Processing helix chain 'C' and resid 85 through 104 removed outlier: 3.527A pdb=" N ALA C 102 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 121 removed outlier: 4.312A pdb=" N LEU C 116 " --> pdb=" O VAL C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 138 through 149 removed outlier: 3.776A pdb=" N GLN C 143 " --> pdb=" O GLU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 162 removed outlier: 4.514A pdb=" N ARG C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 160 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 removed outlier: 3.666A pdb=" N LYS C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 196 through 204 Processing helix chain 'C' and resid 207 through 216 removed outlier: 4.335A pdb=" N ARG C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 236 Processing helix chain 'C' and resid 239 through 247 Processing helix chain 'C' and resid 250 through 259 removed outlier: 3.778A pdb=" N LEU C 254 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Proline residue: C 256 - end of helix Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 281 through 290 removed outlier: 5.518A pdb=" N ARG C 285 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU C 286 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 302 removed outlier: 4.286A pdb=" N GLU C 297 " --> pdb=" O ALA C 294 " (cutoff:3.500A) Proline residue: C 298 - end of helix removed outlier: 3.648A pdb=" N ALA C 301 " --> pdb=" O PRO C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 324 through 335 removed outlier: 3.596A pdb=" N ARG C 329 " --> pdb=" O ASP C 325 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Proline residue: C 332 - end of helix removed outlier: 4.215A pdb=" N ASP C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 359 removed outlier: 3.540A pdb=" N LEU C 358 " --> pdb=" O ALA C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.645A pdb=" N ILE C 368 " --> pdb=" O PHE C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 385 through 396 Processing helix chain 'C' and resid 409 through 411 No H-bonds generated for 'chain 'C' and resid 409 through 411' Processing helix chain 'C' and resid 414 through 424 Processing helix chain 'C' and resid 427 through 435 removed outlier: 3.509A pdb=" N CYS C 430 " --> pdb=" O SER C 427 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N GLU C 431 " --> pdb=" O LYS C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 443 No H-bonds generated for 'chain 'C' and resid 440 through 443' Processing helix chain 'C' and resid 448 through 453 Processing helix chain 'C' and resid 460 through 475 removed outlier: 3.626A pdb=" N GLU C 472 " --> pdb=" O ARG C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 494 removed outlier: 3.583A pdb=" N LEU C 494 " --> pdb=" O TRP C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 508 removed outlier: 4.343A pdb=" N GLN C 500 " --> pdb=" O ARG C 497 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N TYR C 503 " --> pdb=" O GLN C 500 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL C 506 " --> pdb=" O TYR C 503 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER C 507 " --> pdb=" O GLY C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 532 through 543 Processing helix chain 'D' and resid 63 through 80 Proline residue: D 70 - end of helix Processing helix chain 'D' and resid 85 through 103 Processing helix chain 'D' and resid 109 through 121 removed outlier: 3.800A pdb=" N LEU D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 133 Processing helix chain 'D' and resid 138 through 149 removed outlier: 3.785A pdb=" N GLN D 143 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 3.971A pdb=" N ARG D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 removed outlier: 3.702A pdb=" N LYS D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 191 Processing helix chain 'D' and resid 196 through 204 Processing helix chain 'D' and resid 207 through 216 removed outlier: 4.107A pdb=" N ARG D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 236 Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 250 through 259 removed outlier: 3.815A pdb=" N LEU D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) Proline residue: D 256 - end of helix Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 281 through 290 removed outlier: 5.508A pdb=" N ARG D 285 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU D 286 " --> pdb=" O VAL D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 4.304A pdb=" N GLU D 297 " --> pdb=" O ALA D 294 " (cutoff:3.500A) Proline residue: D 298 - end of helix Processing helix chain 'D' and resid 305 through 310 Processing helix chain 'D' and resid 324 through 335 removed outlier: 3.563A pdb=" N GLN D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG D 329 " --> pdb=" O ASP D 325 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU D 330 " --> pdb=" O ASP D 326 " (cutoff:3.500A) Proline residue: D 332 - end of helix removed outlier: 4.312A pdb=" N ASP D 335 " --> pdb=" O VAL D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 359 removed outlier: 3.527A pdb=" N LEU D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 368 removed outlier: 3.650A pdb=" N ILE D 368 " --> pdb=" O PHE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 385 through 396 Processing helix chain 'D' and resid 409 through 411 No H-bonds generated for 'chain 'D' and resid 409 through 411' Processing helix chain 'D' and resid 414 through 424 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.540A pdb=" N CYS D 430 " --> pdb=" O SER D 427 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU D 431 " --> pdb=" O LYS D 428 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER D 432 " --> pdb=" O TYR D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 443 No H-bonds generated for 'chain 'D' and resid 440 through 443' Processing helix chain 'D' and resid 448 through 453 Processing helix chain 'D' and resid 460 through 475 removed outlier: 3.584A pdb=" N GLU D 472 " --> pdb=" O ARG D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 494 removed outlier: 3.604A pdb=" N LEU D 494 " --> pdb=" O TRP D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 508 removed outlier: 4.416A pdb=" N GLN D 500 " --> pdb=" O ARG D 497 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N TYR D 503 " --> pdb=" O GLN D 500 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL D 506 " --> pdb=" O TYR D 503 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N SER D 507 " --> pdb=" O GLY D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 515 through 517 No H-bonds generated for 'chain 'D' and resid 515 through 517' Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 532 through 543 Processing helix chain 'E' and resid 63 through 80 Proline residue: E 70 - end of helix Processing helix chain 'E' and resid 85 through 103 removed outlier: 3.593A pdb=" N ALA E 102 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 121 removed outlier: 4.370A pdb=" N LEU E 116 " --> pdb=" O VAL E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 125 through 133 Processing helix chain 'E' and resid 138 through 150 removed outlier: 3.919A pdb=" N GLN E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLN E 150 " --> pdb=" O ARG E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.998A pdb=" N ARG E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 removed outlier: 3.664A pdb=" N LYS E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 191 Processing helix chain 'E' and resid 196 through 204 Processing helix chain 'E' and resid 207 through 216 removed outlier: 4.397A pdb=" N ARG E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 236 Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 250 through 253 No H-bonds generated for 'chain 'E' and resid 250 through 253' Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 281 through 290 removed outlier: 5.497A pdb=" N ARG E 285 " --> pdb=" O GLU E 282 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU E 286 " --> pdb=" O VAL E 283 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 302 removed outlier: 4.286A pdb=" N GLU E 297 " --> pdb=" O ALA E 294 " (cutoff:3.500A) Proline residue: E 298 - end of helix removed outlier: 3.646A pdb=" N ALA E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 Processing helix chain 'E' and resid 324 through 335 removed outlier: 3.568A pdb=" N GLN E 328 " --> pdb=" O PRO E 324 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG E 329 " --> pdb=" O ASP E 325 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU E 330 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Proline residue: E 332 - end of helix removed outlier: 4.189A pdb=" N ASP E 335 " --> pdb=" O VAL E 331 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 359 removed outlier: 3.553A pdb=" N LEU E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 368 removed outlier: 3.648A pdb=" N ILE E 368 " --> pdb=" O PHE E 365 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 385 through 396 Processing helix chain 'E' and resid 409 through 411 No H-bonds generated for 'chain 'E' and resid 409 through 411' Processing helix chain 'E' and resid 414 through 424 Processing helix chain 'E' and resid 427 through 435 removed outlier: 3.507A pdb=" N CYS E 430 " --> pdb=" O SER E 427 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU E 431 " --> pdb=" O LYS E 428 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 443 No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'E' and resid 448 through 453 Processing helix chain 'E' and resid 460 through 475 removed outlier: 3.612A pdb=" N GLU E 472 " --> pdb=" O ARG E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 487 through 494 removed outlier: 3.579A pdb=" N LEU E 494 " --> pdb=" O TRP E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 508 removed outlier: 4.497A pdb=" N GLN E 500 " --> pdb=" O ARG E 497 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR E 503 " --> pdb=" O GLN E 500 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL E 506 " --> pdb=" O TYR E 503 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N SER E 507 " --> pdb=" O GLY E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 515 through 517 No H-bonds generated for 'chain 'E' and resid 515 through 517' Processing helix chain 'E' and resid 520 through 525 Processing helix chain 'E' and resid 532 through 543 Processing helix chain 'F' and resid 63 through 80 Proline residue: F 70 - end of helix Processing helix chain 'F' and resid 85 through 104 Processing helix chain 'F' and resid 109 through 121 Processing helix chain 'F' and resid 125 through 133 Processing helix chain 'F' and resid 138 through 151 removed outlier: 3.833A pdb=" N GLN F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN F 150 " --> pdb=" O ARG F 146 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE F 151 " --> pdb=" O LEU F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 162 removed outlier: 3.943A pdb=" N ARG F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 160 " --> pdb=" O ASN F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 removed outlier: 3.707A pdb=" N LYS F 173 " --> pdb=" O LEU F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 191 Processing helix chain 'F' and resid 196 through 204 Processing helix chain 'F' and resid 207 through 216 removed outlier: 4.107A pdb=" N ARG F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 236 Processing helix chain 'F' and resid 239 through 247 Processing helix chain 'F' and resid 250 through 259 removed outlier: 3.692A pdb=" N LEU F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE F 255 " --> pdb=" O ALA F 251 " (cutoff:3.500A) Proline residue: F 256 - end of helix Processing helix chain 'F' and resid 264 through 278 Processing helix chain 'F' and resid 281 through 290 removed outlier: 5.492A pdb=" N ARG F 285 " --> pdb=" O GLU F 282 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU F 286 " --> pdb=" O VAL F 283 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 300 removed outlier: 4.318A pdb=" N GLU F 297 " --> pdb=" O ALA F 294 " (cutoff:3.500A) Proline residue: F 298 - end of helix Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 324 through 335 removed outlier: 3.584A pdb=" N GLN F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG F 329 " --> pdb=" O ASP F 325 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU F 330 " --> pdb=" O ASP F 326 " (cutoff:3.500A) Proline residue: F 332 - end of helix removed outlier: 4.309A pdb=" N ASP F 335 " --> pdb=" O VAL F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 359 removed outlier: 3.527A pdb=" N LEU F 358 " --> pdb=" O ALA F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 368 removed outlier: 3.656A pdb=" N ILE F 368 " --> pdb=" O PHE F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 385 through 396 Processing helix chain 'F' and resid 409 through 411 No H-bonds generated for 'chain 'F' and resid 409 through 411' Processing helix chain 'F' and resid 414 through 424 Processing helix chain 'F' and resid 427 through 436 removed outlier: 3.541A pdb=" N CYS F 430 " --> pdb=" O SER F 427 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU F 431 " --> pdb=" O LYS F 428 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER F 432 " --> pdb=" O TYR F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 443 No H-bonds generated for 'chain 'F' and resid 440 through 443' Processing helix chain 'F' and resid 448 through 453 Processing helix chain 'F' and resid 460 through 475 removed outlier: 3.562A pdb=" N GLU F 472 " --> pdb=" O ARG F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 487 through 494 removed outlier: 3.603A pdb=" N LEU F 494 " --> pdb=" O TRP F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 508 removed outlier: 4.379A pdb=" N GLN F 500 " --> pdb=" O ARG F 497 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR F 503 " --> pdb=" O GLN F 500 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL F 506 " --> pdb=" O TYR F 503 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER F 507 " --> pdb=" O GLY F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 515 through 517 No H-bonds generated for 'chain 'F' and resid 515 through 517' Processing helix chain 'F' and resid 520 through 525 Processing helix chain 'F' and resid 532 through 543 Processing helix chain 'G' and resid 63 through 80 Proline residue: G 70 - end of helix Processing helix chain 'G' and resid 85 through 103 removed outlier: 3.600A pdb=" N ALA G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 121 removed outlier: 4.315A pdb=" N LEU G 116 " --> pdb=" O VAL G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 133 Processing helix chain 'G' and resid 138 through 149 removed outlier: 3.876A pdb=" N GLN G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 162 removed outlier: 4.106A pdb=" N ARG G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL G 160 " --> pdb=" O ASN G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 173 removed outlier: 3.673A pdb=" N LYS G 173 " --> pdb=" O LEU G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 191 Processing helix chain 'G' and resid 196 through 204 Processing helix chain 'G' and resid 207 through 216 removed outlier: 4.365A pdb=" N ARG G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 236 Processing helix chain 'G' and resid 239 through 247 Processing helix chain 'G' and resid 250 through 259 removed outlier: 3.574A pdb=" N LEU G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Proline residue: G 256 - end of helix Processing helix chain 'G' and resid 264 through 278 Processing helix chain 'G' and resid 281 through 290 removed outlier: 5.468A pdb=" N ARG G 285 " --> pdb=" O GLU G 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU G 286 " --> pdb=" O VAL G 283 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 302 removed outlier: 4.288A pdb=" N GLU G 297 " --> pdb=" O ALA G 294 " (cutoff:3.500A) Proline residue: G 298 - end of helix removed outlier: 3.645A pdb=" N ALA G 301 " --> pdb=" O PRO G 298 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 310 Processing helix chain 'G' and resid 324 through 335 removed outlier: 3.622A pdb=" N ARG G 329 " --> pdb=" O ASP G 325 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU G 330 " --> pdb=" O ASP G 326 " (cutoff:3.500A) Proline residue: G 332 - end of helix removed outlier: 4.221A pdb=" N ASP G 335 " --> pdb=" O VAL G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 359 removed outlier: 3.547A pdb=" N LEU G 358 " --> pdb=" O ALA G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 368 removed outlier: 3.654A pdb=" N ILE G 368 " --> pdb=" O PHE G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 385 through 396 Processing helix chain 'G' and resid 409 through 411 No H-bonds generated for 'chain 'G' and resid 409 through 411' Processing helix chain 'G' and resid 414 through 424 Processing helix chain 'G' and resid 427 through 435 removed outlier: 3.506A pdb=" N CYS G 430 " --> pdb=" O SER G 427 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU G 431 " --> pdb=" O LYS G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 440 through 443 No H-bonds generated for 'chain 'G' and resid 440 through 443' Processing helix chain 'G' and resid 448 through 453 Processing helix chain 'G' and resid 460 through 475 removed outlier: 3.600A pdb=" N GLU G 472 " --> pdb=" O ARG G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 487 through 494 removed outlier: 3.578A pdb=" N LEU G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 508 removed outlier: 4.436A pdb=" N GLN G 500 " --> pdb=" O ARG G 497 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR G 503 " --> pdb=" O GLN G 500 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL G 506 " --> pdb=" O TYR G 503 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER G 507 " --> pdb=" O GLY G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 515 through 517 No H-bonds generated for 'chain 'G' and resid 515 through 517' Processing helix chain 'G' and resid 520 through 525 Processing helix chain 'G' and resid 532 through 543 Processing helix chain 'H' and resid 63 through 81 Proline residue: H 70 - end of helix Processing helix chain 'H' and resid 85 through 104 Processing helix chain 'H' and resid 109 through 121 removed outlier: 3.695A pdb=" N LEU H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 133 Processing helix chain 'H' and resid 138 through 149 removed outlier: 3.794A pdb=" N GLN H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 162 removed outlier: 4.018A pdb=" N ARG H 159 " --> pdb=" O GLU H 155 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL H 160 " --> pdb=" O ASN H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 173 removed outlier: 3.656A pdb=" N LYS H 173 " --> pdb=" O LEU H 169 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 191 Processing helix chain 'H' and resid 196 through 204 Processing helix chain 'H' and resid 207 through 216 removed outlier: 4.107A pdb=" N ARG H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 236 Processing helix chain 'H' and resid 239 through 247 Processing helix chain 'H' and resid 250 through 259 removed outlier: 3.651A pdb=" N LEU H 254 " --> pdb=" O ALA H 250 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE H 255 " --> pdb=" O ALA H 251 " (cutoff:3.500A) Proline residue: H 256 - end of helix Processing helix chain 'H' and resid 264 through 278 Processing helix chain 'H' and resid 281 through 290 removed outlier: 5.485A pdb=" N ARG H 285 " --> pdb=" O GLU H 282 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU H 286 " --> pdb=" O VAL H 283 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 302 removed outlier: 4.322A pdb=" N GLU H 297 " --> pdb=" O ALA H 294 " (cutoff:3.500A) Proline residue: H 298 - end of helix removed outlier: 3.685A pdb=" N ALA H 301 " --> pdb=" O PRO H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 305 through 310 Processing helix chain 'H' and resid 324 through 335 removed outlier: 3.594A pdb=" N GLN H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG H 329 " --> pdb=" O ASP H 325 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU H 330 " --> pdb=" O ASP H 326 " (cutoff:3.500A) Proline residue: H 332 - end of helix removed outlier: 4.302A pdb=" N ASP H 335 " --> pdb=" O VAL H 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 359 removed outlier: 3.528A pdb=" N LEU H 358 " --> pdb=" O ALA H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 368 removed outlier: 3.652A pdb=" N ILE H 368 " --> pdb=" O PHE H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 379 Processing helix chain 'H' and resid 385 through 396 Processing helix chain 'H' and resid 409 through 411 No H-bonds generated for 'chain 'H' and resid 409 through 411' Processing helix chain 'H' and resid 414 through 424 Processing helix chain 'H' and resid 427 through 436 removed outlier: 3.542A pdb=" N CYS H 430 " --> pdb=" O SER H 427 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N GLU H 431 " --> pdb=" O LYS H 428 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER H 432 " --> pdb=" O TYR H 429 " (cutoff:3.500A) Processing helix chain 'H' and resid 440 through 443 No H-bonds generated for 'chain 'H' and resid 440 through 443' Processing helix chain 'H' and resid 448 through 453 Processing helix chain 'H' and resid 460 through 475 removed outlier: 3.572A pdb=" N GLU H 472 " --> pdb=" O ARG H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 487 through 494 removed outlier: 3.604A pdb=" N LEU H 494 " --> pdb=" O TRP H 490 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 508 removed outlier: 4.414A pdb=" N GLN H 500 " --> pdb=" O ARG H 497 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR H 503 " --> pdb=" O GLN H 500 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL H 506 " --> pdb=" O TYR H 503 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER H 507 " --> pdb=" O GLY H 504 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 517 No H-bonds generated for 'chain 'H' and resid 515 through 517' Processing helix chain 'H' and resid 520 through 525 Processing helix chain 'H' and resid 532 through 543 1499 hydrogen bonds defined for protein. 4026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.46 Time building geometry restraints manager: 12.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5198 1.32 - 1.44: 7456 1.44 - 1.57: 18010 1.57 - 1.69: 8 1.69 - 1.81: 168 Bond restraints: 30840 Sorted by residual: bond pdb=" C3R NMN A 801 " pdb=" C4R NMN A 801 " ideal model delta sigma weight residual 1.304 1.528 -0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3R NMN G 801 " pdb=" C4R NMN G 801 " ideal model delta sigma weight residual 1.304 1.528 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C3R NMN E 801 " pdb=" C4R NMN E 801 " ideal model delta sigma weight residual 1.304 1.528 -0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C3R NMN C 801 " pdb=" C4R NMN C 801 " ideal model delta sigma weight residual 1.304 1.527 -0.223 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C3R NMN F 801 " pdb=" C4R NMN F 801 " ideal model delta sigma weight residual 1.304 1.527 -0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 30835 not shown) Histogram of bond angle deviations from ideal: 99.69 - 106.65: 704 106.65 - 113.60: 17114 113.60 - 120.55: 13761 120.55 - 127.51: 9872 127.51 - 134.46: 253 Bond angle restraints: 41704 Sorted by residual: angle pdb=" CA ASP G 483 " pdb=" CB ASP G 483 " pdb=" CG ASP G 483 " ideal model delta sigma weight residual 112.60 116.59 -3.99 1.00e+00 1.00e+00 1.59e+01 angle pdb=" N ASP C 326 " pdb=" CA ASP C 326 " pdb=" C ASP C 326 " ideal model delta sigma weight residual 113.28 108.43 4.85 1.22e+00 6.72e-01 1.58e+01 angle pdb=" N VAL A 211 " pdb=" CA VAL A 211 " pdb=" C VAL A 211 " ideal model delta sigma weight residual 110.72 106.71 4.01 1.01e+00 9.80e-01 1.57e+01 angle pdb=" N ASP H 326 " pdb=" CA ASP H 326 " pdb=" C ASP H 326 " ideal model delta sigma weight residual 113.28 108.53 4.75 1.22e+00 6.72e-01 1.51e+01 angle pdb=" CA PRO H 106 " pdb=" C PRO H 106 " pdb=" O PRO H 106 " ideal model delta sigma weight residual 121.23 117.07 4.16 1.07e+00 8.73e-01 1.51e+01 ... (remaining 41699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 17404 17.23 - 34.45: 1240 34.45 - 51.68: 179 51.68 - 68.90: 43 68.90 - 86.13: 14 Dihedral angle restraints: 18880 sinusoidal: 7712 harmonic: 11168 Sorted by residual: dihedral pdb=" C ASP G 483 " pdb=" N ASP G 483 " pdb=" CA ASP G 483 " pdb=" CB ASP G 483 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" CA LEU G 406 " pdb=" C LEU G 406 " pdb=" N PRO G 407 " pdb=" CA PRO G 407 " ideal model delta harmonic sigma weight residual -180.00 -163.14 -16.86 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA LEU A 406 " pdb=" C LEU A 406 " pdb=" N PRO A 407 " pdb=" CA PRO A 407 " ideal model delta harmonic sigma weight residual -180.00 -163.17 -16.83 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 18877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 4028 0.051 - 0.103: 543 0.103 - 0.154: 184 0.154 - 0.206: 42 0.206 - 0.257: 19 Chirality restraints: 4816 Sorted by residual: chirality pdb=" C3R NMN D 801 " pdb=" C2R NMN D 801 " pdb=" C4R NMN D 801 " pdb=" O3R NMN D 801 " both_signs ideal model delta sigma weight residual False -2.39 -2.65 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C3R NMN H 801 " pdb=" C2R NMN H 801 " pdb=" C4R NMN H 801 " pdb=" O3R NMN H 801 " both_signs ideal model delta sigma weight residual False -2.39 -2.65 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" C3R NMN A 801 " pdb=" C2R NMN A 801 " pdb=" C4R NMN A 801 " pdb=" O3R NMN A 801 " both_signs ideal model delta sigma weight residual False -2.39 -2.65 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4813 not shown) Planarity restraints: 5424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP E 214 " 0.019 2.00e-02 2.50e+03 1.71e-02 7.29e+00 pdb=" CG TRP E 214 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP E 214 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP E 214 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 214 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 214 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 214 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 214 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 214 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP E 214 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 328 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.63e+00 pdb=" C GLN A 328 " -0.045 2.00e-02 2.50e+03 pdb=" O GLN A 328 " 0.016 2.00e-02 2.50e+03 pdb=" N ARG A 329 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 214 " 0.018 2.00e-02 2.50e+03 1.58e-02 6.26e+00 pdb=" CG TRP B 214 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP B 214 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 214 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 214 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 214 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 214 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 214 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 214 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 214 " -0.000 2.00e-02 2.50e+03 ... (remaining 5421 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2732 2.74 - 3.28: 31931 3.28 - 3.82: 48050 3.82 - 4.36: 60422 4.36 - 4.90: 101436 Nonbonded interactions: 244571 Sorted by model distance: nonbonded pdb=" OD1 ASP B 441 " pdb=" OH TYR B 503 " model vdw 2.197 2.440 nonbonded pdb=" OD1 ASP H 441 " pdb=" OH TYR H 503 " model vdw 2.198 2.440 nonbonded pdb=" OD1 ASP F 441 " pdb=" OH TYR F 503 " model vdw 2.198 2.440 nonbonded pdb=" OD1 ASP D 441 " pdb=" OH TYR D 503 " model vdw 2.199 2.440 nonbonded pdb=" O ASP B 483 " pdb=" OD1 ASP B 483 " model vdw 2.216 3.040 ... (remaining 244566 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' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 7.450 Check model and map are aligned: 0.430 Set scattering table: 0.290 Process input model: 76.550 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 0.008 0.224 30840 Z= 0.493 Angle : 0.791 6.355 41704 Z= 0.531 Chirality : 0.046 0.257 4816 Planarity : 0.004 0.045 5424 Dihedral : 12.139 86.127 11648 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 1.51 (0.15), residues: 3872 helix: 1.37 (0.10), residues: 2792 sheet: None (None), residues: 0 loop : 0.23 (0.22), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP E 214 HIS 0.008 0.001 HIS A 190 PHE 0.011 0.001 PHE E 192 TYR 0.008 0.001 TYR C 348 ARG 0.008 0.000 ARG G 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 457 time to evaluate : 3.522 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.8121 (tt0) cc_final: 0.7775 (pp30) REVERT: B 239 GLN cc_start: 0.8032 (tt0) cc_final: 0.7746 (pp30) REVERT: C 239 GLN cc_start: 0.8058 (tt0) cc_final: 0.7691 (tm-30) REVERT: C 253 TRP cc_start: 0.6694 (m100) cc_final: 0.5766 (m100) REVERT: E 239 GLN cc_start: 0.8106 (tt0) cc_final: 0.7771 (pp30) REVERT: F 239 GLN cc_start: 0.8117 (tt0) cc_final: 0.7788 (pp30) REVERT: G 239 GLN cc_start: 0.8146 (tt0) cc_final: 0.7787 (pp30) REVERT: H 239 GLN cc_start: 0.7959 (tt0) cc_final: 0.7657 (pp30) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 1.5022 time to fit residues: 799.5803 Evaluate side-chains 301 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 3.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 300 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 chunk 348 optimal weight: 8.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 200 GLN A 239 GLN A 418 GLN A 478 ASN A 521 GLN B 134 GLN C 134 GLN C 200 GLN C 239 GLN C 418 GLN C 478 ASN C 521 GLN D 134 GLN D 337 ASN D 521 GLN E 134 GLN E 239 GLN E 418 GLN E 478 ASN E 500 GLN E 521 GLN F 134 GLN F 337 ASN F 521 GLN G 134 GLN G 239 GLN G 418 GLN G 478 ASN G 500 GLN G 521 GLN H 134 GLN H 521 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 30840 Z= 0.242 Angle : 0.580 7.662 41704 Z= 0.280 Chirality : 0.037 0.140 4816 Planarity : 0.004 0.040 5424 Dihedral : 5.988 65.914 4352 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.61 % Allowed : 7.65 % Favored : 89.74 % 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: 1.27 (0.14), residues: 3872 helix: 1.16 (0.10), residues: 2792 sheet: None (None), residues: 0 loop : 0.26 (0.22), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 214 HIS 0.007 0.001 HIS B 190 PHE 0.011 0.001 PHE F 308 TYR 0.007 0.001 TYR B 213 ARG 0.006 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 349 time to evaluate : 3.365 Fit side-chains REVERT: A 239 GLN cc_start: 0.8183 (tt0) cc_final: 0.7769 (pp30) REVERT: B 239 GLN cc_start: 0.8175 (tt0) cc_final: 0.7519 (pp30) REVERT: C 171 LEU cc_start: 0.8261 (tp) cc_final: 0.8032 (tt) REVERT: C 239 GLN cc_start: 0.8262 (tt0) cc_final: 0.7809 (pp30) REVERT: C 253 TRP cc_start: 0.6775 (m100) cc_final: 0.6164 (m100) REVERT: E 239 GLN cc_start: 0.8172 (tt0) cc_final: 0.7666 (pp30) REVERT: F 132 LEU cc_start: 0.8310 (mp) cc_final: 0.8109 (mp) REVERT: F 239 GLN cc_start: 0.8207 (tt0) cc_final: 0.7521 (pp30) REVERT: G 171 LEU cc_start: 0.8265 (tp) cc_final: 0.8052 (tt) REVERT: G 239 GLN cc_start: 0.8175 (tt0) cc_final: 0.7770 (pp30) REVERT: G 310 ARG cc_start: 0.7342 (tpp80) cc_final: 0.7017 (tpp80) REVERT: H 239 GLN cc_start: 0.8131 (tt0) cc_final: 0.7478 (pp30) REVERT: H 318 THR cc_start: 0.8405 (p) cc_final: 0.7977 (t) REVERT: H 484 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.7108 (mpt90) outliers start: 83 outliers final: 44 residues processed: 391 average time/residue: 1.2702 time to fit residues: 593.4362 Evaluate side-chains 337 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 292 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain C residue 72 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 484 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 290 optimal weight: 30.0000 chunk 237 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 349 optimal weight: 5.9990 chunk 377 optimal weight: 1.9990 chunk 311 optimal weight: 0.1980 chunk 346 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 478 ASN C 190 HIS C 239 GLN C 280 ASN C 478 ASN D 337 ASN E 190 HIS E 200 GLN E 478 ASN F 337 ASN G 190 HIS G 478 ASN H 190 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 : 0.003 0.031 30840 Z= 0.222 Angle : 0.565 15.690 41704 Z= 0.268 Chirality : 0.037 0.186 4816 Planarity : 0.004 0.042 5424 Dihedral : 5.950 65.590 4352 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.90 % Allowed : 9.54 % Favored : 87.56 % 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: 1.22 (0.15), residues: 3872 helix: 1.09 (0.10), residues: 2784 sheet: None (None), residues: 0 loop : 0.33 (0.22), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 214 HIS 0.007 0.001 HIS B 190 PHE 0.010 0.001 PHE H 192 TYR 0.006 0.001 TYR C 429 ARG 0.006 0.000 ARG E 121 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 327 time to evaluate : 3.548 Fit side-chains REVERT: A 239 GLN cc_start: 0.8221 (tt0) cc_final: 0.7832 (pp30) REVERT: B 239 GLN cc_start: 0.8096 (tt0) cc_final: 0.7895 (pp30) REVERT: B 318 THR cc_start: 0.8524 (p) cc_final: 0.8118 (t) REVERT: C 239 GLN cc_start: 0.8322 (tt0) cc_final: 0.7819 (pp30) REVERT: D 318 THR cc_start: 0.8529 (p) cc_final: 0.8144 (t) REVERT: E 239 GLN cc_start: 0.8166 (tt0) cc_final: 0.7724 (pp30) REVERT: F 132 LEU cc_start: 0.8317 (mp) cc_final: 0.8067 (mp) REVERT: F 239 GLN cc_start: 0.8126 (tt0) cc_final: 0.7873 (pp30) REVERT: F 318 THR cc_start: 0.8502 (p) cc_final: 0.8122 (t) REVERT: G 239 GLN cc_start: 0.8217 (tt0) cc_final: 0.7759 (pp30) REVERT: G 244 ARG cc_start: 0.8036 (tmt-80) cc_final: 0.7761 (tmt-80) REVERT: H 167 VAL cc_start: 0.7370 (OUTLIER) cc_final: 0.7163 (p) REVERT: H 239 GLN cc_start: 0.8177 (tt0) cc_final: 0.7832 (pp30) REVERT: H 318 THR cc_start: 0.8489 (p) cc_final: 0.8108 (t) REVERT: H 484 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7084 (mpt90) outliers start: 92 outliers final: 51 residues processed: 380 average time/residue: 1.1965 time to fit residues: 547.7277 Evaluate side-chains 350 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 297 time to evaluate : 3.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain E residue 72 LEU Chi-restraints excluded: chain E residue 128 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 189 GLU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 531 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 189 GLU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 358 LEU Chi-restraints excluded: chain H residue 484 ARG Chi-restraints excluded: chain H residue 531 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 6.9990 chunk 262 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 38 optimal weight: 0.4980 chunk 166 optimal weight: 0.0370 chunk 234 optimal weight: 2.9990 chunk 350 optimal weight: 6.9990 chunk 371 optimal weight: 0.6980 chunk 183 optimal weight: 1.9990 chunk 332 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 200 GLN A 478 ASN C 190 HIS C 239 GLN C 280 ASN C 337 ASN C 478 ASN E 190 HIS E 478 ASN F 337 ASN G 190 HIS G 478 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30840 Z= 0.162 Angle : 0.548 15.352 41704 Z= 0.254 Chirality : 0.035 0.136 4816 Planarity : 0.003 0.035 5424 Dihedral : 5.887 65.571 4352 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.80 % Allowed : 11.24 % Favored : 85.96 % 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: 1.29 (0.15), residues: 3872 helix: 1.19 (0.10), residues: 2784 sheet: None (None), residues: 0 loop : 0.21 (0.22), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 214 HIS 0.005 0.001 HIS B 190 PHE 0.011 0.001 PHE B 192 TYR 0.004 0.001 TYR F 380 ARG 0.003 0.000 ARG G 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 310 time to evaluate : 3.337 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.8214 (tt0) cc_final: 0.7778 (pp30) REVERT: A 318 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7898 (t) REVERT: B 318 THR cc_start: 0.8511 (p) cc_final: 0.8113 (t) REVERT: C 171 LEU cc_start: 0.8260 (tp) cc_final: 0.8003 (tt) REVERT: C 239 GLN cc_start: 0.8152 (tt0) cc_final: 0.7782 (pp30) REVERT: C 253 TRP cc_start: 0.6825 (m100) cc_final: 0.6610 (m100) REVERT: C 318 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7750 (t) REVERT: D 167 VAL cc_start: 0.7232 (OUTLIER) cc_final: 0.7031 (p) REVERT: D 318 THR cc_start: 0.8529 (p) cc_final: 0.8132 (t) REVERT: E 159 ARG cc_start: 0.7358 (mtp85) cc_final: 0.7138 (mtp85) REVERT: E 310 ARG cc_start: 0.7087 (tpp80) cc_final: 0.6883 (tpp80) REVERT: E 318 THR cc_start: 0.8211 (OUTLIER) cc_final: 0.7894 (t) REVERT: F 132 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8026 (mp) REVERT: F 239 GLN cc_start: 0.8152 (tt0) cc_final: 0.7920 (pp30) REVERT: F 318 THR cc_start: 0.8531 (p) cc_final: 0.8121 (t) REVERT: G 171 LEU cc_start: 0.8299 (tp) cc_final: 0.8044 (tt) REVERT: G 239 GLN cc_start: 0.8113 (tt0) cc_final: 0.7730 (pp30) REVERT: G 318 THR cc_start: 0.8191 (OUTLIER) cc_final: 0.7903 (t) REVERT: H 239 GLN cc_start: 0.8076 (tt0) cc_final: 0.7856 (pp30) REVERT: H 318 THR cc_start: 0.8540 (p) cc_final: 0.8120 (t) outliers start: 89 outliers final: 44 residues processed: 360 average time/residue: 1.1839 time to fit residues: 514.0727 Evaluate side-chains 333 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 283 time to evaluate : 3.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 167 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 358 LEU Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 531 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 189 GLU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 531 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 276 optimal weight: 0.8980 chunk 153 optimal weight: 6.9990 chunk 316 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 189 optimal weight: 0.0000 chunk 333 optimal weight: 0.6980 chunk 93 optimal weight: 0.0060 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS A 200 GLN A 478 ASN C 239 GLN C 280 ASN C 337 ASN C 478 ASN E 478 ASN F 337 ASN G 200 GLN G 478 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30840 Z= 0.153 Angle : 0.535 14.995 41704 Z= 0.247 Chirality : 0.035 0.171 4816 Planarity : 0.003 0.031 5424 Dihedral : 5.888 65.758 4352 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.71 % Allowed : 12.59 % Favored : 84.70 % 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: 1.30 (0.15), residues: 3872 helix: 1.14 (0.10), residues: 2824 sheet: None (None), residues: 0 loop : 0.38 (0.23), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 214 HIS 0.005 0.000 HIS C 190 PHE 0.014 0.001 PHE D 192 TYR 0.004 0.001 TYR G 429 ARG 0.005 0.000 ARG B 159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 299 time to evaluate : 3.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 MET cc_start: 0.8100 (tpp) cc_final: 0.7863 (mmm) REVERT: A 239 GLN cc_start: 0.8089 (tt0) cc_final: 0.7758 (pp30) REVERT: A 318 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7847 (t) REVERT: B 318 THR cc_start: 0.8587 (p) cc_final: 0.8172 (t) REVERT: C 239 GLN cc_start: 0.8229 (tt0) cc_final: 0.7829 (pp30) REVERT: C 318 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7761 (t) REVERT: D 318 THR cc_start: 0.8630 (p) cc_final: 0.8213 (t) REVERT: E 159 ARG cc_start: 0.7296 (mtp85) cc_final: 0.7090 (mtp85) REVERT: E 318 THR cc_start: 0.8138 (OUTLIER) cc_final: 0.7860 (t) REVERT: F 132 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.8012 (mp) REVERT: F 239 GLN cc_start: 0.8153 (tt0) cc_final: 0.7853 (pp30) REVERT: F 318 THR cc_start: 0.8566 (p) cc_final: 0.8154 (t) REVERT: G 239 GLN cc_start: 0.8091 (tt0) cc_final: 0.7743 (pp30) REVERT: G 318 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7851 (t) REVERT: H 239 GLN cc_start: 0.8083 (tt0) cc_final: 0.7655 (pp30) REVERT: H 318 THR cc_start: 0.8556 (p) cc_final: 0.8149 (t) outliers start: 86 outliers final: 50 residues processed: 349 average time/residue: 1.1840 time to fit residues: 500.6228 Evaluate side-chains 339 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 284 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 484 ARG Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 531 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 484 ARG Chi-restraints excluded: chain H residue 531 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 7.9990 chunk 334 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 217 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 371 optimal weight: 1.9990 chunk 308 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN C 239 GLN C 280 ASN C 337 ASN C 478 ASN E 478 ASN F 337 ASN G 478 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30840 Z= 0.197 Angle : 0.552 14.012 41704 Z= 0.255 Chirality : 0.036 0.235 4816 Planarity : 0.003 0.030 5424 Dihedral : 5.963 66.529 4352 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.93 % Allowed : 13.04 % Favored : 84.04 % 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: 1.20 (0.15), residues: 3872 helix: 1.06 (0.10), residues: 2832 sheet: None (None), residues: 0 loop : 0.34 (0.23), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 214 HIS 0.007 0.001 HIS A 190 PHE 0.012 0.001 PHE F 192 TYR 0.006 0.001 TYR A 429 ARG 0.006 0.000 ARG E 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 292 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.8097 (tt0) cc_final: 0.7759 (pp30) REVERT: A 318 THR cc_start: 0.8212 (OUTLIER) cc_final: 0.7967 (t) REVERT: B 318 THR cc_start: 0.8614 (p) cc_final: 0.8204 (t) REVERT: C 159 ARG cc_start: 0.7319 (mtp85) cc_final: 0.7113 (mtp85) REVERT: C 239 GLN cc_start: 0.8153 (tt0) cc_final: 0.7768 (pp30) REVERT: C 253 TRP cc_start: 0.6895 (m100) cc_final: 0.6669 (m100) REVERT: C 318 THR cc_start: 0.8069 (OUTLIER) cc_final: 0.7784 (t) REVERT: D 318 THR cc_start: 0.8615 (p) cc_final: 0.8213 (t) REVERT: E 318 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7950 (t) REVERT: F 132 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7989 (mp) REVERT: F 192 PHE cc_start: 0.8146 (m-80) cc_final: 0.7931 (m-80) REVERT: F 239 GLN cc_start: 0.8174 (tt0) cc_final: 0.7865 (pp30) REVERT: F 318 THR cc_start: 0.8611 (p) cc_final: 0.8216 (t) REVERT: G 239 GLN cc_start: 0.8099 (tt0) cc_final: 0.7747 (pp30) REVERT: G 318 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7924 (t) REVERT: H 239 GLN cc_start: 0.8075 (tt0) cc_final: 0.7748 (pp30) REVERT: H 318 THR cc_start: 0.8608 (p) cc_final: 0.8210 (t) outliers start: 93 outliers final: 60 residues processed: 347 average time/residue: 1.2095 time to fit residues: 509.0652 Evaluate side-chains 347 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 282 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 484 ARG Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 337 ASN Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 202 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 337 ASN Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 531 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 189 GLU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 481 THR Chi-restraints excluded: chain H residue 484 ARG Chi-restraints excluded: chain H residue 531 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 211 optimal weight: 0.7980 chunk 271 optimal weight: 1.9990 chunk 210 optimal weight: 7.9990 chunk 312 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 370 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 chunk 225 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN C 239 GLN C 280 ASN C 337 ASN C 478 ASN D 337 ASN F 337 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30840 Z= 0.177 Angle : 0.541 13.493 41704 Z= 0.251 Chirality : 0.035 0.153 4816 Planarity : 0.003 0.029 5424 Dihedral : 5.908 67.210 4352 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.24 % Allowed : 13.10 % Favored : 83.66 % 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: 1.26 (0.15), residues: 3872 helix: 1.10 (0.10), residues: 2824 sheet: None (None), residues: 0 loop : 0.37 (0.23), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 214 HIS 0.006 0.001 HIS A 190 PHE 0.014 0.001 PHE B 192 TYR 0.005 0.001 TYR E 429 ARG 0.006 0.000 ARG G 146 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 281 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 239 GLN cc_start: 0.8085 (tt0) cc_final: 0.7750 (pp30) REVERT: A 318 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7930 (t) REVERT: B 318 THR cc_start: 0.8621 (p) cc_final: 0.8212 (t) REVERT: C 239 GLN cc_start: 0.8276 (tt0) cc_final: 0.7875 (pp30) REVERT: C 253 TRP cc_start: 0.6996 (m100) cc_final: 0.6721 (m100) REVERT: C 295 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7144 (tt) REVERT: C 318 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7829 (t) REVERT: D 318 THR cc_start: 0.8630 (p) cc_final: 0.8217 (t) REVERT: E 159 ARG cc_start: 0.7249 (mtp85) cc_final: 0.6992 (mtp85) REVERT: E 295 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7130 (tt) REVERT: E 318 THR cc_start: 0.8201 (OUTLIER) cc_final: 0.7939 (t) REVERT: F 132 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7976 (mp) REVERT: F 239 GLN cc_start: 0.8190 (tt0) cc_final: 0.7807 (pp30) REVERT: F 318 THR cc_start: 0.8620 (p) cc_final: 0.8224 (t) REVERT: G 239 GLN cc_start: 0.8053 (tt0) cc_final: 0.7741 (pp30) REVERT: G 295 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7086 (tt) REVERT: G 318 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7947 (t) REVERT: H 239 GLN cc_start: 0.8075 (tt0) cc_final: 0.7621 (pp30) REVERT: H 253 TRP cc_start: 0.6846 (m100) cc_final: 0.6476 (m100) REVERT: H 318 THR cc_start: 0.8611 (p) cc_final: 0.8230 (t) outliers start: 103 outliers final: 63 residues processed: 349 average time/residue: 1.1508 time to fit residues: 487.1015 Evaluate side-chains 345 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 274 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 358 LEU Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain B residue 335 ASP Chi-restraints excluded: chain B residue 484 ARG Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 531 LEU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 531 LEU Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 318 THR Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 189 GLU Chi-restraints excluded: chain H residue 335 ASP Chi-restraints excluded: chain H residue 481 THR Chi-restraints excluded: chain H residue 484 ARG Chi-restraints excluded: chain H residue 531 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.0000 chunk 147 optimal weight: 4.9990 chunk 221 optimal weight: 0.0050 chunk 111 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 235 optimal weight: 0.2980 chunk 252 optimal weight: 3.9990 chunk 182 optimal weight: 0.7980 chunk 34 optimal weight: 0.0060 chunk 290 optimal weight: 0.0770 overall best weight: 0.0772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN C 478 ASN D 337 ASN E 239 GLN E 280 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30840 Z= 0.128 Angle : 0.534 13.290 41704 Z= 0.246 Chirality : 0.034 0.290 4816 Planarity : 0.003 0.064 5424 Dihedral : 5.620 67.966 4352 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.74 % Allowed : 13.89 % Favored : 83.38 % 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: 1.51 (0.15), residues: 3872 helix: 1.30 (0.11), residues: 2800 sheet: None (None), residues: 0 loop : 0.45 (0.22), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 214 HIS 0.005 0.000 HIS A 190 PHE 0.010 0.000 PHE A 96 TYR 0.004 0.000 TYR C 213 ARG 0.012 0.000 ARG G 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 307 time to evaluate : 3.466 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 VAL cc_start: 0.6861 (OUTLIER) cc_final: 0.6579 (p) REVERT: A 191 MET cc_start: 0.7998 (tpp) cc_final: 0.7761 (mmm) REVERT: A 239 GLN cc_start: 0.8047 (tt0) cc_final: 0.7673 (pp30) REVERT: A 318 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7905 (t) REVERT: B 318 THR cc_start: 0.8569 (p) cc_final: 0.8165 (t) REVERT: C 239 GLN cc_start: 0.8186 (tt0) cc_final: 0.7825 (pp30) REVERT: C 253 TRP cc_start: 0.6955 (m100) cc_final: 0.6697 (m100) REVERT: C 318 THR cc_start: 0.8058 (OUTLIER) cc_final: 0.7820 (t) REVERT: D 318 THR cc_start: 0.8599 (p) cc_final: 0.8178 (t) REVERT: E 159 ARG cc_start: 0.7308 (mtp85) cc_final: 0.7067 (mtp85) REVERT: E 167 VAL cc_start: 0.7028 (OUTLIER) cc_final: 0.6759 (p) REVERT: E 318 THR cc_start: 0.8143 (OUTLIER) cc_final: 0.7902 (t) REVERT: F 132 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7965 (mp) REVERT: F 318 THR cc_start: 0.8592 (p) cc_final: 0.8187 (t) REVERT: G 239 GLN cc_start: 0.8062 (tt0) cc_final: 0.7647 (pp30) REVERT: G 318 THR cc_start: 0.8094 (p) cc_final: 0.7880 (t) REVERT: H 253 TRP cc_start: 0.6750 (m100) cc_final: 0.6437 (m100) REVERT: H 318 THR cc_start: 0.8589 (p) cc_final: 0.8188 (t) outliers start: 87 outliers final: 44 residues processed: 366 average time/residue: 1.1426 time to fit residues: 519.6991 Evaluate side-chains 330 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 280 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 189 GLU Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 337 ASN Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 481 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 20.0000 chunk 354 optimal weight: 2.9990 chunk 323 optimal weight: 0.9990 chunk 344 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 311 optimal weight: 0.9990 chunk 326 optimal weight: 0.9990 chunk 343 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN E 239 GLN E 280 ASN F 239 GLN H 239 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 30840 Z= 0.265 Angle : 0.599 12.882 41704 Z= 0.279 Chirality : 0.038 0.225 4816 Planarity : 0.003 0.032 5424 Dihedral : 5.823 70.085 4352 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.52 % Allowed : 14.45 % Favored : 83.03 % 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: 1.28 (0.15), residues: 3872 helix: 1.14 (0.10), residues: 2776 sheet: None (None), residues: 0 loop : 0.35 (0.22), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 214 HIS 0.008 0.001 HIS A 190 PHE 0.014 0.001 PHE F 192 TYR 0.011 0.001 TYR E 429 ARG 0.007 0.000 ARG G 159 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 272 time to evaluate : 3.087 Fit side-chains revert: symmetry clash REVERT: A 191 MET cc_start: 0.8087 (tpp) cc_final: 0.7853 (mmm) REVERT: A 239 GLN cc_start: 0.8081 (tt0) cc_final: 0.7776 (pp30) REVERT: A 295 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7105 (tt) REVERT: A 318 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7920 (t) REVERT: B 239 GLN cc_start: 0.8244 (tt0) cc_final: 0.7772 (pp30) REVERT: B 318 THR cc_start: 0.8661 (p) cc_final: 0.8262 (t) REVERT: C 126 LEU cc_start: 0.7784 (tp) cc_final: 0.7380 (tm) REVERT: C 239 GLN cc_start: 0.8219 (tt0) cc_final: 0.7874 (pp30) REVERT: C 295 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7151 (tt) REVERT: C 318 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7876 (t) REVERT: D 318 THR cc_start: 0.8664 (p) cc_final: 0.8271 (t) REVERT: E 159 ARG cc_start: 0.7248 (mtp85) cc_final: 0.6993 (mtp85) REVERT: E 295 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7136 (tt) REVERT: E 318 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7958 (t) REVERT: F 132 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8036 (mp) REVERT: F 239 GLN cc_start: 0.8223 (tt0) cc_final: 0.7611 (pp30) REVERT: F 318 THR cc_start: 0.8625 (p) cc_final: 0.8240 (t) REVERT: G 239 GLN cc_start: 0.8062 (tt0) cc_final: 0.7734 (pp30) REVERT: G 295 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7153 (tt) REVERT: G 318 THR cc_start: 0.8215 (p) cc_final: 0.7968 (t) REVERT: H 239 GLN cc_start: 0.8185 (tt0) cc_final: 0.7546 (pp30) REVERT: H 253 TRP cc_start: 0.6829 (m100) cc_final: 0.6531 (m100) REVERT: H 318 THR cc_start: 0.8608 (p) cc_final: 0.8238 (t) outliers start: 80 outliers final: 50 residues processed: 333 average time/residue: 1.1133 time to fit residues: 455.2942 Evaluate side-chains 317 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 259 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 189 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 481 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 0.6980 chunk 364 optimal weight: 0.9990 chunk 222 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 382 optimal weight: 1.9990 chunk 352 optimal weight: 5.9990 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN B 280 ASN B 337 ASN E 239 GLN E 280 ASN H 337 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30840 Z= 0.213 Angle : 0.582 12.664 41704 Z= 0.271 Chirality : 0.037 0.202 4816 Planarity : 0.003 0.040 5424 Dihedral : 5.714 71.848 4352 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.14 % Allowed : 14.99 % Favored : 82.87 % 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: 1.21 (0.15), residues: 3872 helix: 1.10 (0.10), residues: 2776 sheet: None (None), residues: 0 loop : 0.29 (0.22), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 253 HIS 0.007 0.001 HIS A 190 PHE 0.013 0.001 PHE B 192 TYR 0.009 0.001 TYR C 429 ARG 0.010 0.000 ARG A 146 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7744 Ramachandran restraints generated. 3872 Oldfield, 0 Emsley, 3872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 272 time to evaluate : 3.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7028 (tt) REVERT: A 318 THR cc_start: 0.8133 (OUTLIER) cc_final: 0.7914 (t) REVERT: B 239 GLN cc_start: 0.8233 (tt0) cc_final: 0.7775 (pp30) REVERT: B 318 THR cc_start: 0.8664 (p) cc_final: 0.8266 (t) REVERT: C 239 GLN cc_start: 0.8237 (tt0) cc_final: 0.7878 (pp30) REVERT: C 295 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7086 (tt) REVERT: C 318 THR cc_start: 0.8184 (OUTLIER) cc_final: 0.7923 (t) REVERT: D 318 THR cc_start: 0.8672 (p) cc_final: 0.8277 (t) REVERT: E 295 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7064 (tt) REVERT: E 318 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7941 (t) REVERT: F 132 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.8033 (mp) REVERT: F 253 TRP cc_start: 0.6808 (m100) cc_final: 0.6395 (m100) REVERT: F 318 THR cc_start: 0.8618 (p) cc_final: 0.8239 (t) REVERT: G 239 GLN cc_start: 0.8134 (tt0) cc_final: 0.7739 (pp30) REVERT: G 295 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7076 (tt) REVERT: G 318 THR cc_start: 0.8180 (p) cc_final: 0.7949 (t) REVERT: H 253 TRP cc_start: 0.6766 (m100) cc_final: 0.6520 (m100) REVERT: H 318 THR cc_start: 0.8627 (p) cc_final: 0.8244 (t) outliers start: 68 outliers final: 48 residues processed: 317 average time/residue: 1.1001 time to fit residues: 428.0845 Evaluate side-chains 320 residues out of total 3176 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 264 time to evaluate : 3.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 318 THR Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 295 LEU Chi-restraints excluded: chain C residue 318 THR Chi-restraints excluded: chain C residue 335 ASP Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 531 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 481 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 335 ASP Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 481 THR Chi-restraints excluded: chain F residue 518 VAL Chi-restraints excluded: chain G residue 130 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 295 LEU Chi-restraints excluded: chain G residue 335 ASP Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 337 ASN Chi-restraints excluded: chain H residue 481 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 9.9990 chunk 324 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 280 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 84 optimal weight: 0.0980 chunk 305 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 313 optimal weight: 0.0870 chunk 38 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 239 GLN E 280 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.211962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157350 restraints weight = 33985.112| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 1.67 r_work: 0.3546 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3420 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30840 Z= 0.132 Angle : 0.564 18.427 41704 Z= 0.258 Chirality : 0.035 0.180 4816 Planarity : 0.003 0.037 5424 Dihedral : 5.452 72.113 4352 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.95 % Allowed : 15.30 % Favored : 82.75 % 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: 1.46 (0.15), residues: 3872 helix: 1.24 (0.11), residues: 2784 sheet: None (None), residues: 0 loop : 0.53 (0.23), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 214 HIS 0.005 0.000 HIS A 190 PHE 0.006 0.001 PHE F 192 TYR 0.010 0.001 TYR C 429 ARG 0.010 0.000 ARG A 146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9355.89 seconds wall clock time: 167 minutes 44.44 seconds (10064.44 seconds total)