Starting phenix.real_space_refine on Mon Mar 18 18:11:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjx_25939/03_2024/7tjx_25939_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjx_25939/03_2024/7tjx_25939.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjx_25939/03_2024/7tjx_25939.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjx_25939/03_2024/7tjx_25939.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjx_25939/03_2024/7tjx_25939_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tjx_25939/03_2024/7tjx_25939_updated.pdb" } resolution = 4.0 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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 5 5.21 5 S 25 5.16 5 C 13686 2.51 5 N 3896 2.21 5 O 4036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21663 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3384 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 450} Chain breaks: 1 Unresolved non-hydrogen bonds: 202 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 156 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 21, 'ARG:plan': 3, 'PHE:plan': 2, 'ASP:plan': 8} Unresolved non-hydrogen planarities: 143 Chain: "B" Number of atoms: 3375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3375 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 456} Chain breaks: 2 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 312 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 23, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 171 Chain: "C" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3523 Classifications: {'peptide': 484} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 18, 'TRANS': 463} Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 121 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 17, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 130 Chain: "D" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3206 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 430} Chain breaks: 1 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 271 Unresolved non-hydrogen dihedrals: 170 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 14, 'GLU:plan': 17, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 157 Chain: "E" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3105 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 433} Chain breaks: 2 Unresolved non-hydrogen bonds: 351 Unresolved non-hydrogen angles: 430 Unresolved non-hydrogen dihedrals: 284 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 28, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 243 Chain: "F" Number of atoms: 3349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3349 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 443} Unresolved non-hydrogen bonds: 181 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 23, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 127 Chain: "G" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1560 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 513 Unresolved non-hydrogen angles: 640 Unresolved non-hydrogen dihedrals: 423 Unresolved non-hydrogen chiralities: 43 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 14, 'ASP:plan': 10, 'PHE:plan': 7, 'GLU:plan': 11, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 247 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.03, per 1000 atoms: 0.56 Number of scatterers: 21663 At special positions: 0 Unit cell: (126.665, 126.665, 154.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 15 15.00 Mg 5 11.99 O 4036 8.00 N 3896 7.00 C 13686 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: 8.42 Conformation dependent library (CDL) restraints added in 4.7 seconds 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5580 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 126 helices and 23 sheets defined 43.5% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 177 through 192 removed outlier: 3.889A pdb=" N ALA A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS A 189 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ARG A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N TRP A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 199 No H-bonds generated for 'chain 'A' and resid 197 through 199' Processing helix chain 'A' and resid 212 through 224 Processing helix chain 'A' and resid 227 through 230 Processing helix chain 'A' and resid 242 through 261 Proline residue: A 249 - end of helix removed outlier: 3.637A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N PHE A 259 " --> pdb=" O ILE A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 Processing helix chain 'A' and resid 293 through 295 No H-bonds generated for 'chain 'A' and resid 293 through 295' Processing helix chain 'A' and resid 298 through 310 removed outlier: 4.173A pdb=" N PHE A 301 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A 305 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG A 306 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU A 309 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 361 Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 377 through 380 Processing helix chain 'A' and resid 383 through 401 removed outlier: 3.596A pdb=" N VAL A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N SER A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 440 through 452 Proline residue: A 445 - end of helix Processing helix chain 'A' and resid 454 through 457 Processing helix chain 'A' and resid 460 through 477 removed outlier: 4.124A pdb=" N GLY A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 468 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 493 through 507 Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 155 through 158 No H-bonds generated for 'chain 'B' and resid 155 through 158' Processing helix chain 'B' and resid 177 through 192 removed outlier: 3.874A pdb=" N ALA B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS B 189 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ARG B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TRP B 191 " --> pdb=" O ASN B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 199 No H-bonds generated for 'chain 'B' and resid 197 through 199' Processing helix chain 'B' and resid 212 through 224 Processing helix chain 'B' and resid 228 through 230 No H-bonds generated for 'chain 'B' and resid 228 through 230' Processing helix chain 'B' and resid 242 through 261 Proline residue: B 249 - end of helix removed outlier: 3.530A pdb=" N TRP B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N PHE B 259 " --> pdb=" O ILE B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 298 through 310 removed outlier: 4.093A pdb=" N PHE B 301 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG B 306 " --> pdb=" O LEU B 303 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU B 309 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 385 through 388 No H-bonds generated for 'chain 'B' and resid 385 through 388' Processing helix chain 'B' and resid 392 through 405 removed outlier: 4.225A pdb=" N GLN B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ARG B 400 " --> pdb=" O LEU B 396 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 430 removed outlier: 3.620A pdb=" N VAL B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLU B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ARG B 425 " --> pdb=" O VAL B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 451 removed outlier: 3.894A pdb=" N VAL B 444 " --> pdb=" O THR B 440 " (cutoff:3.500A) Proline residue: B 445 - end of helix removed outlier: 4.152A pdb=" N GLY B 450 " --> pdb=" O LEU B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 475 removed outlier: 3.530A pdb=" N SER B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 488 removed outlier: 4.460A pdb=" N GLU B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 507 removed outlier: 3.686A pdb=" N GLU B 504 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL B 507 " --> pdb=" O THR B 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 153 through 158 Processing helix chain 'C' and resid 177 through 192 removed outlier: 3.966A pdb=" N ALA C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS C 189 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ARG C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N TRP C 191 " --> pdb=" O ASN C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 224 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 242 through 261 Proline residue: C 249 - end of helix removed outlier: 3.657A pdb=" N TRP C 258 " --> pdb=" O SER C 254 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 286 Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 300 through 310 removed outlier: 3.635A pdb=" N ARG C 306 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG C 310 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 383 through 406 removed outlier: 5.587A pdb=" N SER C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LEU C 392 " --> pdb=" O VAL C 388 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS C 393 " --> pdb=" O ALA C 389 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N LEU C 394 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ALA C 404 " --> pdb=" O ARG C 400 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N PHE C 405 " --> pdb=" O GLU C 401 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 429 removed outlier: 4.237A pdb=" N THR C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG C 425 " --> pdb=" O VAL C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 452 Proline residue: C 445 - end of helix Processing helix chain 'C' and resid 454 through 457 removed outlier: 4.243A pdb=" N GLY C 457 " --> pdb=" O HIS C 454 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'C' and resid 460 through 477 removed outlier: 5.394A pdb=" N GLY C 464 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE C 470 " --> pdb=" O GLU C 467 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU C 471 " --> pdb=" O SER C 468 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS C 475 " --> pdb=" O SER C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 488 removed outlier: 3.634A pdb=" N ARG C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 508 removed outlier: 3.510A pdb=" N ALA C 497 " --> pdb=" O LYS C 493 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA C 508 " --> pdb=" O GLU C 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 139 through 144 Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.830A pdb=" N LYS D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA D 177 " --> pdb=" O ASN D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 204 removed outlier: 3.645A pdb=" N LYS D 202 " --> pdb=" O TYR D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 245 removed outlier: 5.007A pdb=" N ALA D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LEU D 234 " --> pdb=" O ALA D 230 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE D 239 " --> pdb=" O THR D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 272 Processing helix chain 'D' and resid 285 through 295 removed outlier: 3.671A pdb=" N LEU D 291 " --> pdb=" O THR D 287 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG D 295 " --> pdb=" O LEU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 328 removed outlier: 4.020A pdb=" N ALA D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N HIS D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 341 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 360 through 363 No H-bonds generated for 'chain 'D' and resid 360 through 363' Processing helix chain 'D' and resid 365 through 387 removed outlier: 3.606A pdb=" N LYS D 373 " --> pdb=" O ASP D 369 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER D 383 " --> pdb=" O GLN D 379 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP D 386 " --> pdb=" O LYS D 382 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE D 387 " --> pdb=" O SER D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 414 removed outlier: 3.743A pdb=" N LYS D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 420 through 425 Processing helix chain 'D' and resid 434 through 445 Processing helix chain 'D' and resid 463 through 474 removed outlier: 3.887A pdb=" N ALA D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 139 through 144 Processing helix chain 'E' and resid 163 through 178 Processing helix chain 'E' and resid 191 through 204 Processing helix chain 'E' and resid 226 through 245 removed outlier: 5.148A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU E 234 " --> pdb=" O ALA E 230 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 272 removed outlier: 3.567A pdb=" N THR E 262 " --> pdb=" O ILE E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 280 No H-bonds generated for 'chain 'E' and resid 278 through 280' Processing helix chain 'E' and resid 285 through 293 removed outlier: 3.756A pdb=" N GLY E 290 " --> pdb=" O ALA E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 315 No H-bonds generated for 'chain 'E' and resid 313 through 315' Processing helix chain 'E' and resid 320 through 327 removed outlier: 3.871A pdb=" N ALA E 327 " --> pdb=" O ALA E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 342 removed outlier: 3.704A pdb=" N LEU E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 363 No H-bonds generated for 'chain 'E' and resid 360 through 363' Processing helix chain 'E' and resid 365 through 386 removed outlier: 3.677A pdb=" N GLN E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASP E 386 " --> pdb=" O LYS E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 413 Processing helix chain 'E' and resid 421 through 425 Processing helix chain 'E' and resid 434 through 445 Processing helix chain 'E' and resid 462 through 473 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 124 through 126 No H-bonds generated for 'chain 'F' and resid 124 through 126' Processing helix chain 'F' and resid 139 through 144 Processing helix chain 'F' and resid 163 through 177 removed outlier: 4.807A pdb=" N LYS F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA F 177 " --> pdb=" O ASN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 204 removed outlier: 3.598A pdb=" N LYS F 202 " --> pdb=" O TYR F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 245 removed outlier: 4.891A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU F 234 " --> pdb=" O ALA F 230 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 239 " --> pdb=" O THR F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 272 removed outlier: 3.625A pdb=" N VAL F 268 " --> pdb=" O GLY F 265 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ALA F 270 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 280 No H-bonds generated for 'chain 'F' and resid 278 through 280' Processing helix chain 'F' and resid 283 through 295 removed outlier: 4.570A pdb=" N ALA F 286 " --> pdb=" O PRO F 283 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU F 294 " --> pdb=" O LEU F 291 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG F 295 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 320 through 328 removed outlier: 4.303A pdb=" N ALA F 327 " --> pdb=" O ALA F 323 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N HIS F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 341 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 360 through 363 No H-bonds generated for 'chain 'F' and resid 360 through 363' Processing helix chain 'F' and resid 365 through 391 removed outlier: 3.897A pdb=" N VAL F 370 " --> pdb=" O GLU F 366 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP F 386 " --> pdb=" O LYS F 382 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ILE F 387 " --> pdb=" O SER F 383 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE F 390 " --> pdb=" O ASP F 386 " (cutoff:3.500A) Processing helix chain 'F' and resid 393 through 395 No H-bonds generated for 'chain 'F' and resid 393 through 395' Processing helix chain 'F' and resid 398 through 413 removed outlier: 3.603A pdb=" N ARG F 412 " --> pdb=" O ARG F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 425 removed outlier: 4.065A pdb=" N VAL F 423 " --> pdb=" O VAL F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 445 Processing helix chain 'F' and resid 454 through 457 Processing helix chain 'F' and resid 463 through 474 Processing helix chain 'G' and resid 3 through 55 removed outlier: 4.351A pdb=" N SER G 32 " --> pdb=" O SER G 28 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS G 33 " --> pdb=" O THR G 29 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA G 55 " --> pdb=" O PHE G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 100 removed outlier: 4.105A pdb=" N LEU G 91 " --> pdb=" O HIS G 88 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL G 95 " --> pdb=" O ALA G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 119 Processing helix chain 'G' and resid 140 through 152 Processing helix chain 'G' and resid 156 through 158 No H-bonds generated for 'chain 'G' and resid 156 through 158' Processing helix chain 'G' and resid 185 through 190 Processing helix chain 'G' and resid 204 through 275 removed outlier: 3.540A pdb=" N ASP G 208 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR G 212 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER G 275 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 30 through 32 removed outlier: 6.660A pdb=" N GLY A 74 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU A 68 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N GLN A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE A 44 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL A 33 " --> pdb=" O PHE A 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 98 through 101 Processing sheet with id= C, first strand: chain 'A' and resid 351 through 354 removed outlier: 6.606A pdb=" N LEU A 168 " --> pdb=" O ILE A 352 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N LEU A 354 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE A 170 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 231 through 236 removed outlier: 6.502A pdb=" N CYS A 203 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL A 234 " --> pdb=" O CYS A 203 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR A 205 " --> pdb=" O VAL A 234 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ALA A 236 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ALA A 207 " --> pdb=" O ALA A 236 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N SER A 322 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE A 268 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N THR A 324 " --> pdb=" O ILE A 268 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYR A 270 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU A 326 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 30 through 32 removed outlier: 3.693A pdb=" N GLY B 31 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N GLY B 74 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU B 68 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLN B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE B 44 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N VAL B 33 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 98 through 101 Processing sheet with id= G, first strand: chain 'B' and resid 351 through 354 removed outlier: 6.517A pdb=" N LEU B 168 " --> pdb=" O ILE B 352 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N LEU B 354 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE B 170 " --> pdb=" O LEU B 354 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 231 through 236 removed outlier: 6.609A pdb=" N CYS B 203 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N VAL B 234 " --> pdb=" O CYS B 203 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N TYR B 205 " --> pdb=" O VAL B 234 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ALA B 236 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ALA B 207 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 30 through 32 removed outlier: 6.786A pdb=" N GLY C 74 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 35 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N PHE C 44 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N VAL C 33 " --> pdb=" O PHE C 44 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 98 through 101 Processing sheet with id= K, first strand: chain 'C' and resid 108 through 110 removed outlier: 3.871A pdb=" N ARG C 108 " --> pdb=" O SER C 231 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N CYS C 203 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N VAL C 234 " --> pdb=" O CYS C 203 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR C 205 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ALA C 236 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA C 207 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N SER C 322 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N ILE C 268 " --> pdb=" O SER C 322 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR C 324 " --> pdb=" O ILE C 268 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N TYR C 270 " --> pdb=" O THR C 324 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU C 326 " --> pdb=" O TYR C 270 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 350 through 353 Processing sheet with id= M, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.481A pdb=" N ASP D 22 " --> pdb=" O THR D 14 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL D 16 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ILE D 20 " --> pdb=" O VAL D 16 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 84 through 86 Processing sheet with id= O, first strand: chain 'D' and resid 331 through 334 removed outlier: 8.301A pdb=" N ILE D 153 " --> pdb=" O VAL D 304 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER D 306 " --> pdb=" O ILE D 153 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LEU D 155 " --> pdb=" O SER D 306 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLN D 308 " --> pdb=" O LEU D 155 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N GLY D 157 " --> pdb=" O GLN D 308 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D 310 " --> pdb=" O GLY D 157 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.834A pdb=" N ASP E 22 " --> pdb=" O THR E 14 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N VAL E 16 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ILE E 20 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLY E 81 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N GLU E 38 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N THR E 79 " --> pdb=" O GLU E 38 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= R, first strand: chain 'E' and resid 331 through 335 removed outlier: 8.595A pdb=" N ILE E 153 " --> pdb=" O VAL E 304 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER E 306 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU E 155 " --> pdb=" O SER E 306 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN E 308 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N GLY E 157 " --> pdb=" O GLN E 308 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 12 through 17 removed outlier: 6.391A pdb=" N ASP F 22 " --> pdb=" O THR F 14 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL F 16 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE F 20 " --> pdb=" O VAL F 16 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 84 through 86 Processing sheet with id= U, first strand: chain 'F' and resid 152 through 157 removed outlier: 7.684A pdb=" N ILE F 153 " --> pdb=" O VAL F 304 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER F 306 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU F 155 " --> pdb=" O SER F 306 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLN F 308 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLY F 157 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL F 310 " --> pdb=" O GLY F 157 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL F 251 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N VAL F 307 " --> pdb=" O VAL F 251 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU F 253 " --> pdb=" O VAL F 307 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N ALA F 309 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE F 255 " --> pdb=" O ALA F 309 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N TYR F 311 " --> pdb=" O ILE F 255 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 331 through 333 Processing sheet with id= W, first strand: chain 'G' and resid 105 through 109 removed outlier: 5.954A pdb=" N GLU G 72 " --> pdb=" O ASP G 106 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N VAL G 108 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE G 74 " --> pdb=" O VAL G 108 " (cutoff:3.500A) 948 hydrogen bonds defined for protein. 2412 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.86 Time building geometry restraints manager: 9.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7304 1.34 - 1.46: 3262 1.46 - 1.58: 11347 1.58 - 1.69: 18 1.69 - 1.81: 47 Bond restraints: 21978 Sorted by residual: bond pdb=" O3 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.569 1.510 0.059 2.00e-02 2.50e+03 8.68e+00 bond pdb=" O4 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.568 1.510 0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" O2 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.567 1.510 0.057 2.00e-02 2.50e+03 8.10e+00 bond pdb=" O1 PO4 D 602 " pdb=" P PO4 D 602 " ideal model delta sigma weight residual 1.565 1.509 0.056 2.00e-02 2.50e+03 7.92e+00 bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.466 0.024 2.00e-02 2.50e+03 1.46e+00 ... (remaining 21973 not shown) Histogram of bond angle deviations from ideal: 99.43 - 107.52: 754 107.52 - 115.61: 13813 115.61 - 123.70: 14998 123.70 - 131.79: 397 131.79 - 139.88: 21 Bond angle restraints: 29983 Sorted by residual: angle pdb=" N ILE F 103 " pdb=" CA ILE F 103 " pdb=" C ILE F 103 " ideal model delta sigma weight residual 113.20 109.78 3.42 9.60e-01 1.09e+00 1.27e+01 angle pdb=" C ASP E 256 " pdb=" N ASN E 257 " pdb=" CA ASN E 257 " ideal model delta sigma weight residual 121.70 127.90 -6.20 1.80e+00 3.09e-01 1.19e+01 angle pdb=" C ASP F 256 " pdb=" N ASN F 257 " pdb=" CA ASN F 257 " ideal model delta sigma weight residual 121.70 127.34 -5.64 1.80e+00 3.09e-01 9.83e+00 angle pdb=" C3' ATP A 600 " pdb=" C4' ATP A 600 " pdb=" O4' ATP A 600 " ideal model delta sigma weight residual 105.22 101.23 3.99 1.30e+00 5.94e-01 9.43e+00 angle pdb=" C3' ATP F 600 " pdb=" C4' ATP F 600 " pdb=" O4' ATP F 600 " ideal model delta sigma weight residual 105.22 101.51 3.71 1.30e+00 5.94e-01 8.15e+00 ... (remaining 29978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.80: 12735 21.80 - 43.61: 381 43.61 - 65.41: 79 65.41 - 87.22: 19 87.22 - 109.02: 2 Dihedral angle restraints: 13216 sinusoidal: 4505 harmonic: 8711 Sorted by residual: dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 -169.02 109.02 1 2.00e+01 2.50e-03 3.18e+01 dihedral pdb=" O1B ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PB ADP D 600 " pdb=" PA ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 43.60 -103.60 1 2.00e+01 2.50e-03 2.96e+01 dihedral pdb=" CA GLY E 157 " pdb=" C GLY E 157 " pdb=" N GLY E 158 " pdb=" CA GLY E 158 " ideal model delta harmonic sigma weight residual -180.00 -153.63 -26.37 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 13213 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3130 0.059 - 0.117: 455 0.117 - 0.176: 83 0.176 - 0.234: 3 0.234 - 0.293: 10 Chirality restraints: 3681 Sorted by residual: chirality pdb=" C3' ATP F 600 " pdb=" C2' ATP F 600 " pdb=" C4' ATP F 600 " pdb=" O3' ATP F 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.93 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' ATP A 600 " pdb=" C1' ATP A 600 " pdb=" C3' ATP A 600 " pdb=" O2' ATP A 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C2' ATP F 600 " pdb=" C1' ATP F 600 " pdb=" C3' ATP F 600 " pdb=" O2' ATP F 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 3678 not shown) Planarity restraints: 3859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 41 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO D 42 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 42 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 42 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 102 " -0.031 5.00e-02 4.00e+02 4.64e-02 3.45e+00 pdb=" N PRO A 103 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 146 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO A 147 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 147 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 147 " -0.023 5.00e-02 4.00e+02 ... (remaining 3856 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 54 2.47 - 3.07: 16113 3.07 - 3.68: 31394 3.68 - 4.29: 46674 4.29 - 4.90: 77001 Nonbonded interactions: 171236 Sorted by model distance: nonbonded pdb="MG MG D 601 " pdb=" O2 PO4 D 602 " model vdw 1.858 2.170 nonbonded pdb=" O1G ATP F 600 " pdb="MG MG F 601 " model vdw 1.886 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.911 2.170 nonbonded pdb=" O1G ATP B 600 " pdb="MG MG B 601 " model vdw 1.936 2.170 nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 1.983 2.170 ... (remaining 171231 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' and (resid 29 through 51 or (resid 52 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 55 or (resid 56 and (na \ me N or name CA or name C or name O or name CB )) or resid 57 through 80 or (res \ id 81 and (name N or name CA or name C or name O or name CB )) or resid 82 throu \ gh 155 or (resid 156 through 157 and (name N or name CA or name C or name O or n \ ame CB )) or resid 158 through 164 or (resid 165 and (name N or name CA or name \ C or name O or name CB )) or resid 166 through 167 or (resid 168 and (name N or \ name CA or name C or name O or name CB )) or resid 169 through 171 or (resid 172 \ and (name N or name CA or name C or name O or name CB )) or resid 173 through 1 \ 87 or (resid 188 and (name N or name CA or name C or name O or name CB )) or res \ id 189 through 192 or (resid 193 and (name N or name CA or name C or name O or n \ ame CB )) or resid 194 through 195 or (resid 196 through 197 and (name N or name \ CA or name C or name O or name CB )) or resid 198 through 239 or (resid 240 thr \ ough 242 and (name N or name CA or name C or name O or name CB )) or resid 243 t \ hrough 306 or (resid 307 through 309 and (name N or name CA or name C or name O \ or name CB )) or resid 310 through 325 or (resid 326 and (name N or name CA or n \ ame C or name O or name CB )) or resid 327 through 382 or (resid 383 through 384 \ and (name N or name CA or name C or name O or name CB )) or resid 385 or (resid \ 386 and (name N or name CA or name C or name O or name CB )) or resid 387 throu \ gh 417 or (resid 418 and (name N or name CA or name C or name O or name CB )) or \ resid 419 through 420 or (resid 421 through 422 and (name N or name CA or name \ C or name O or name CB )) or resid 423 through 428 or (resid 429 and (name N or \ name CA or name C or name O or name CB )) or resid 430 through 431 or (resid 432 \ and (name N or name CA or name C or name O or name CB )) or resid 433 through 4 \ 42 or (resid 443 through 444 and (name N or name CA or name C or name O or name \ CB )) or resid 445 through 453 or (resid 454 and (name N or name CA or name C or \ name O or name CB )) or resid 455 through 464 or (resid 465 through 467 and (na \ me N or name CA or name C or name O or name CB )) or resid 468 through 474 or (r \ esid 475 through 477 and (name N or name CA or name C or name O or name CB )) or \ (resid 480 through 481 and (name N or name CA or name C or name O or name CB )) \ or resid 482 through 491 or (resid 492 through 508 and (name N or name CA or na \ me C or name O or name CB )) or resid 600 through 601)) selection = (chain 'B' and (resid 29 through 51 or (resid 52 through 53 and (name N or name \ CA or name C or name O or name CB )) or resid 54 through 65 or (resid 66 and (na \ me N or name CA or name C or name O or name CB )) or resid 67 through 145 or (re \ sid 146 and (name N or name CA or name C or name O or name CB )) or resid 147 th \ rough 164 or (resid 165 and (name N or name CA or name C or name O or name CB )) \ or resid 166 through 173 or (resid 174 and (name N or name CA or name C or name \ O or name CB )) or resid 175 through 187 or (resid 188 and (name N or name CA o \ r name C or name O or name CB )) or resid 189 through 293 or (resid 294 through \ 295 and (name N or name CA or name C or name O or name CB )) or resid 296 throug \ h 306 or (resid 307 through 309 and (name N or name CA or name C or name O or na \ me CB )) or resid 310 through 316 or (resid 317 through 318 and (name N or name \ CA or name C or name O or name CB )) or resid 319 through 325 or (resid 326 and \ (name N or name CA or name C or name O or name CB )) or resid 327 through 334 or \ (resid 335 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 6 through 352 or (resid 353 and (name N or name CA or name C or name O or name C \ B )) or resid 354 through 356 or (resid 357 through 358 and (name N or name CA o \ r name C or name O or name CB )) or resid 359 through 392 or (resid 393 through \ 395 and (name N or name CA or name C or name O or name CB )) or resid 396 throug \ h 399 or (resid 400 through 402 and (name N or name CA or name C or name O or na \ me CB )) or (resid 413 through 418 and (name N or name CA or name C or name O or \ name CB )) or resid 419 through 425 or (resid 426 and (name N or name CA or nam \ e C or name O or name CB )) or resid 427 through 450 or (resid 451 and (name N o \ r name CA or name C or name O or name CB )) or resid 452 through 461 or (resid 4 \ 62 and (name N or name CA or name C or name O or name CB )) or resid 463 through \ 476 or (resid 479 through 481 and (name N or name CA or name C or name O or nam \ e CB )) or resid 482 through 508 or resid 600 through 601)) selection = (chain 'C' and (resid 29 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 55 or (resid 56 and (name N or nam \ e CA or name C or name O or name CB )) or resid 57 through 65 or (resid 66 and ( \ name N or name CA or name C or name O or name CB )) or resid 67 through 68 or (r \ esid 69 and (name N or name CA or name C or name O or name CB )) or resid 70 thr \ ough 80 or (resid 81 and (name N or name CA or name C or name O or name CB )) or \ resid 82 through 85 or (resid 86 and (name N or name CA or name C or name O or \ name CB )) or resid 87 through 145 or (resid 146 and (name N or name CA or name \ C or name O or name CB )) or resid 147 through 155 or (resid 156 through 157 and \ (name N or name CA or name C or name O or name CB )) or resid 158 through 167 o \ r (resid 168 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 69 through 173 or (resid 174 and (name N or name CA or name C or name O or name \ CB )) or resid 175 through 192 or (resid 193 and (name N or name CA or name C or \ name O or name CB )) or resid 194 through 195 or (resid 196 through 197 and (na \ me N or name CA or name C or name O or name CB )) or resid 198 through 239 or (r \ esid 240 through 242 and (name N or name CA or name C or name O or name CB )) or \ resid 243 through 270 or (resid 271 through 272 and (name N or name CA or name \ C or name O or name CB )) or resid 273 through 293 or (resid 294 through 295 and \ (name N or name CA or name C or name O or name CB )) or resid 296 through 315 o \ r (resid 316 through 318 and (name N or name CA or name C or name O or name CB ) \ ) or resid 319 through 352 or (resid 353 and (name N or name CA or name C or nam \ e O or name CB )) or resid 354 through 357 or (resid 358 and (name N or name CA \ or name C or name O or name CB )) or resid 359 through 382 or (resid 383 through \ 384 and (name N or name CA or name C or name O or name CB )) or resid 385 or (r \ esid 386 and (name N or name CA or name C or name O or name CB )) or resid 387 t \ hrough 392 or (resid 393 through 395 and (name N or name CA or name C or name O \ or name CB )) or resid 396 through 399 or (resid 400 through 402 and (name N or \ name CA or name C or name O or name CB )) or (resid 413 through 418 and (name N \ or name CA or name C or name O or name CB )) or resid 419 through 420 or (resid \ 421 through 422 and (name N or name CA or name C or name O or name CB )) or resi \ d 423 or (resid 424 through 426 and (name N or name CA or name C or name O or na \ me CB )) or resid 427 through 428 or (resid 429 and (name N or name CA or name C \ or name O or name CB )) or resid 430 through 431 or (resid 432 and (name N or n \ ame CA or name C or name O or name CB )) or resid 433 or (resid 434 and (name N \ or name CA or name C or name O or name CB )) or resid 435 through 441 or (resid \ 442 through 444 and (name N or name CA or name C or name O or name CB )) or resi \ d 445 through 450 or (resid 451 and (name N or name CA or name C or name O or na \ me CB )) or resid 452 through 453 or (resid 454 and (name N or name CA or name C \ or name O or name CB )) or resid 455 through 457 or (resid 458 through 459 and \ (name N or name CA or name C or name O or name CB )) or resid 460 through 465 or \ (resid 466 through 467 and (name N or name CA or name C or name O or name CB )) \ or resid 468 through 470 or (resid 471 and (name N or name CA or name C or name \ O or name CB )) or resid 472 through 474 or (resid 475 through 477 and (name N \ or name CA or name C or name O or name CB )) or (resid 480 through 481 and (name \ N or name CA or name C or name O or name CB )) or resid 482 through 487 or (res \ id 488 and (name N or name CA or name C or name O or name CB )) or resid 489 or \ (resid 490 and (name N or name CA or name C or name O or name CB )) or resid 491 \ or (resid 492 through 508 and (name N or name CA or name C or name O or name CB \ )) or resid 600 through 601)) } ncs_group { reference = (chain 'D' and (resid 9 through 25 or (resid 26 through 27 and (name N or name C \ A or name C or name O or name CB )) or resid 28 through 34 or (resid 35 through \ 36 and (name N or name CA or name C or name O or name CB )) or resid 37 or (resi \ d 38 and (name N or name CA or name C or name O or name CB )) or resid 39 throug \ h 48 or (resid 49 and (name N or name CA or name C or name O or name CB )) or re \ sid 50 through 67 or (resid 68 and (name N or name CA or name C or name O or nam \ e CB )) or resid 69 through 77 or (resid 78 and (name N or name CA or name C or \ name O or name CB )) or resid 79 through 89 or (resid 90 and (name N or name CA \ or name C or name O or name CB )) or resid 91 or (resid 92 and (name N or name C \ A or name C or name O or name CB )) or resid 93 through 100 or (resid 101 and (n \ ame N or name CA or name C or name O or name CB )) or resid 102 through 103 or ( \ resid 104 through 105 and (name N or name CA or name C or name O or name CB )) o \ r resid 106 through 109 or (resid 110 and (name N or name CA or name C or name O \ or name CB )) or resid 111 through 131 or (resid 132 and (name N or name CA or \ name C or name O or name CB )) or resid 133 through 134 or (resid 135 and (name \ N or name CA or name C or name O or name CB )) or resid 136 through 142 or (resi \ d 143 and (name N or name CA or name C or name O or name CB )) or resid 144 thro \ ugh 162 or (resid 163 through 164 and (name N or name CA or name C or name O or \ name CB )) or resid 165 through 167 or (resid 168 through 169 and (name N or nam \ e CA or name C or name O or name CB )) or resid 170 through 175 or (resid 176 th \ rough 177 and (name N or name CA or name C or name O or name CB )) or resid 178 \ through 201 or (resid 202 and (name N or name CA or name C or name O or name CB \ )) or resid 203 through 208 or (resid 209 through 210 and (name N or name CA or \ name C or name O or name CB )) or resid 211 through 213 or (resid 214 and (name \ N or name CA or name C or name O or name CB )) or resid 215 through 220 or (resi \ d 221 through 222 and (name N or name CA or name C or name O or name CB )) or re \ sid 223 or (resid 224 and (name N or name CA or name C or name O or name CB )) o \ r resid 225 through 240 or (resid 241 and (name N or name CA or name C or name O \ or name CB )) or resid 242 through 255 or (resid 256 through 257 and (name N or \ name CA or name C or name O or name CB )) or resid 258 through 266 or (resid 26 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 268 through \ 281 or (resid 282 and (name N or name CA or name C or name O or name CB )) or re \ sid 283 through 293 or (resid 294 and (name N or name CA or name C or name O or \ name CB )) or resid 295 through 299 or (resid 300 through 301 and (name N or nam \ e CA or name C or name O or name CB )) or resid 302 through 307 or (resid 308 th \ rough 309 and (name N or name CA or name C or name O or name CB )) or resid 310 \ or (resid 311 and (name N or name CA or name C or name O or name CB )) or resid \ 312 through 314 or (resid 315 through 316 and (name N or name CA or name C or na \ me O or name CB )) or resid 317 through 328 or (resid 329 and (name N or name CA \ or name C or name O or name CB )) or resid 330 through 336 or (resid 337 and (n \ ame N or name CA or name C or name O or name CB )) or resid 338 through 340 or ( \ resid 341 through 342 and (name N or name CA or name C or name O or name CB )) o \ r resid 343 through 353 or (resid 354 and (name N or name CA or name C or name O \ or name CB )) or resid 355 through 372 or (resid 373 and (name N or name CA or \ name C or name O or name CB )) or resid 374 through 380 or (resid 381 through 38 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 383 through \ 386 or (resid 387 and (name N or name CA or name C or name O or name CB )) or re \ sid 403 through 407 or (resid 408 through 410 and (name N or name CA or name C o \ r name O or name CB )) or resid 411 or (resid 412 and (name N or name CA or name \ C or name O or name CB )) or resid 413 through 423 or (resid 424 and (name N or \ name CA or name C or name O or name CB )) or resid 425 through 426 or (resid 42 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 428 through \ 430 or (resid 431 and (name N or name CA or name C or name O or name CB )) or re \ sid 432 through 434 or (resid 435 through 436 and (name N or name CA or name C o \ r name O or name CB )) or resid 437 through 444 or (resid 445 through 446 and (n \ ame N or name CA or name C or name O or name CB )) or resid 447 or (resid 448 th \ rough 449 and (name N or name CA or name C or name O or name CB )) or resid 450 \ or (resid 455 through 457 and (name N or name CA or name C or name O or name CB \ )) or resid 458 through 466 or (resid 467 through 474 and (name N or name CA or \ name C or name O or name CB )))) selection = (chain 'E' and ((resid 9 and (name N or name CA or name C or name O or name CB ) \ ) or resid 10 through 28 or (resid 29 and (name N or name CA or name C or name O \ or name CB )) or resid 30 through 74 or (resid 75 and (name N or name CA or nam \ e C or name O or name CB )) or resid 76 through 100 or (resid 101 and (name N or \ name CA or name C or name O or name CB )) or resid 102 through 111 or (resid 11 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 113 through \ 126 or (resid 127 and (name N or name CA or name C or name O or name CB )) or re \ sid 128 through 131 or (resid 132 and (name N or name CA or name C or name O or \ name CB )) or resid 133 through 141 or (resid 142 through 143 and (name N or nam \ e CA or name C or name O or name CB )) or resid 144 through 162 or (resid 163 th \ rough 164 and (name N or name CA or name C or name O or name CB )) or resid 165 \ through 199 or (resid 200 and (name N or name CA or name C or name O or name CB \ )) or resid 201 through 207 or (resid 208 through 210 and (name N or name CA or \ name C or name O or name CB )) or resid 211 through 221 or (resid 222 and (name \ N or name CA or name C or name O or name CB )) or resid 223 or (resid 224 and (n \ ame N or name CA or name C or name O or name CB )) or resid 225 through 255 or ( \ resid 256 through 257 and (name N or name CA or name C or name O or name CB )) o \ r resid 258 through 287 or (resid 288 and (name N or name CA or name C or name O \ or name CB )) or resid 289 through 307 or (resid 308 through 309 and (name N or \ name CA or name C or name O or name CB )) or resid 310 through 328 or (resid 32 \ 9 and (name N or name CA or name C or name O or name CB )) or resid 330 through \ 341 or (resid 342 and (name N or name CA or name C or name O or name CB )) or re \ sid 343 through 348 or (resid 349 and (name N or name CA or name C or name O or \ name CB )) or resid 350 or (resid 351 through 352 and (name N or name CA or name \ C or name O or name CB )) or resid 353 or (resid 354 and (name N or name CA or \ name C or name O or name CB )) or resid 355 through 368 or (resid 369 and (name \ N or name CA or name C or name O or name CB )) or resid 370 through 387 or resid \ 403 through 409 or (resid 410 and (name N or name CA or name C or name O or nam \ e CB )) or resid 411 through 415 or (resid 416 and (name N or name CA or name C \ or name O or name CB )) or resid 417 through 430 or (resid 431 and (name N or na \ me CA or name C or name O or name CB )) or resid 432 through 437 or (resid 438 t \ hrough 439 and (name N or name CA or name C or name O or name CB )) or resid 440 \ through 448 or (resid 449 and (name N or name CA or name C or name O or name CB \ )) or resid 450 through 474)) selection = (chain 'F' and (resid 9 through 21 or (resid 22 and (name N or name CA or name C \ or name O or name CB )) or resid 23 through 26 or (resid 27 and (name N or name \ CA or name C or name O or name CB )) or resid 28 through 34 or (resid 35 throug \ h 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 55 or (resid 56 and (name N or name CA or name C or name O or name CB )) or re \ sid 57 through 64 or (resid 65 and (name N or name CA or name C or name O or nam \ e CB )) or resid 66 through 77 or (resid 78 and (name N or name CA or name C or \ name O or name CB )) or resid 79 through 91 or (resid 92 and (name N or name CA \ or name C or name O or name CB )) or resid 93 through 103 or (resid 104 through \ 105 and (name N or name CA or name C or name O or name CB )) or resid 106 throug \ h 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 or (resid 112 and (name N or name CA or name C or name O or name CB )) \ or resid 113 through 119 or (resid 120 and (name N or name CA or name C or name \ O or name CB )) or resid 121 through 126 or (resid 127 and (name N or name CA o \ r name C or name O or name CB )) or resid 128 through 134 or (resid 135 and (nam \ e N or name CA or name C or name O or name CB )) or resid 136 through 141 or (re \ sid 142 through 143 and (name N or name CA or name C or name O or name CB )) or \ resid 144 through 163 or (resid 164 and (name N or name CA or name C or name O o \ r name CB )) or resid 165 through 167 or (resid 168 through 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 175 or (resid 176 \ through 177 and (name N or name CA or name C or name O or name CB )) or resid 17 \ 8 through 199 or (resid 200 and (name N or name CA or name C or name O or name C \ B )) or resid 201 or (resid 202 and (name N or name CA or name C or name O or na \ me CB )) or resid 203 through 207 or (resid 208 through 210 and (name N or name \ CA or name C or name O or name CB )) or resid 211 or (resid 212 and (name N or n \ ame CA or name C or name O or name CB )) or resid 213 or (resid 214 and (name N \ or name CA or name C or name O or name CB )) or resid 215 through 240 or (resid \ 241 and (name N or name CA or name C or name O or name CB )) or resid 242 throug \ h 244 or (resid 245 through 247 and (name N or name CA or name C or name O or na \ me CB )) or resid 248 or (resid 249 through 250 and (name N or name CA or name C \ or name O or name CB )) or resid 251 through 266 or (resid 267 and (name N or n \ ame CA or name C or name O or name CB )) or resid 268 through 281 or (resid 282 \ and (name N or name CA or name C or name O or name CB )) or resid 283 through 28 \ 7 or (resid 288 and (name N or name CA or name C or name O or name CB )) or resi \ d 289 through 300 or (resid 301 and (name N or name CA or name C or name O or na \ me CB )) or resid 302 through 310 or (resid 311 and (name N or name CA or name C \ or name O or name CB )) or resid 312 through 314 or (resid 315 through 316 and \ (name N or name CA or name C or name O or name CB )) or resid 317 through 336 or \ (resid 337 and (name N or name CA or name C or name O or name CB )) or resid 33 \ 8 through 340 or (resid 341 through 342 and (name N or name CA or name C or name \ O or name CB )) or resid 343 through 348 or (resid 349 and (name N or name CA o \ r name C or name O or name CB )) or resid 350 or (resid 351 through 352 and (nam \ e N or name CA or name C or name O or name CB )) or resid 353 through 358 or (re \ sid 359 through 361 and (name N or name CA or name C or name O or name CB )) or \ resid 362 through 365 or (resid 366 and (name N or name CA or name C or name O o \ r name CB )) or resid 367 through 368 or (resid 369 and (name N or name CA or na \ me C or name O or name CB )) or resid 370 through 372 or (resid 373 and (name N \ or name CA or name C or name O or name CB )) or resid 374 through 375 or (resid \ 376 and (name N or name CA or name C or name O or name CB )) or resid 377 throug \ h 380 or (resid 381 through 382 and (name N or name CA or name C or name O or na \ me CB )) or resid 383 or (resid 384 through 387 and (name N or name CA or name C \ or name O or name CB )) or resid 403 through 405 or (resid 406 through 410 and \ (name N or name CA or name C or name O or name CB )) or resid 411 or (resid 412 \ and (name N or name CA or name C or name O or name CB )) or resid 413 through 41 \ 5 or (resid 416 and (name N or name CA or name C or name O or name CB )) or resi \ d 417 through 423 or (resid 424 and (name N or name CA or name C or name O or na \ me CB )) or resid 425 through 426 or (resid 427 and (name N or name CA or name C \ or name O or name CB )) or resid 428 through 429 or (resid 430 through 431 and \ (name N or name CA or name C or name O or name CB )) or resid 432 through 434 or \ (resid 435 through 436 and (name N or name CA or name C or name O or name CB )) \ or resid 437 or (resid 438 through 439 and (name N or name CA or name C or name \ O or name CB )) or resid 440 through 444 or (resid 445 through 446 and (name N \ or name CA or name C or name O or name CB )) or resid 447 or (resid 448 through \ 449 and (name N or name CA or name C or name O or name CB )) or resid 450 or (re \ sid 455 through 457 and (name N or name CA or name C or name O or name CB )) or \ resid 458 or (resid 459 and (name N or name CA or name C or name O or name CB )) \ or resid 460 through 464 or (resid 465 and (name N or name CA or name C or name \ O or name CB )) or resid 466 or (resid 467 through 474 and (name N or name CA o \ r name C or name O or name CB )))) } 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 group one per residue 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.960 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 58.710 Find NCS groups from input model: 1.670 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 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 : 0.003 0.059 21978 Z= 0.183 Angle : 0.619 6.741 29983 Z= 0.341 Chirality : 0.046 0.293 3681 Planarity : 0.004 0.047 3859 Dihedral : 12.053 109.023 7636 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.05 % Allowed : 0.10 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.15), residues: 3044 helix: 0.41 (0.14), residues: 1204 sheet: -0.04 (0.23), residues: 487 loop : -0.04 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 258 HIS 0.010 0.001 HIS C 145 PHE 0.020 0.001 PHE E 326 TYR 0.021 0.002 TYR G 255 ARG 0.005 0.001 ARG B 462 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 933 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 932 time to evaluate : 2.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 SER cc_start: 0.8135 (m) cc_final: 0.7486 (t) REVERT: A 199 LYS cc_start: 0.8227 (mttt) cc_final: 0.8015 (mttt) REVERT: A 246 TYR cc_start: 0.8430 (t80) cc_final: 0.8216 (t80) REVERT: A 308 LEU cc_start: 0.8225 (mt) cc_final: 0.8006 (mt) REVERT: A 466 PHE cc_start: 0.8507 (t80) cc_final: 0.8202 (t80) REVERT: A 477 ASN cc_start: 0.7900 (m-40) cc_final: 0.7417 (t0) REVERT: B 44 PHE cc_start: 0.8880 (t80) cc_final: 0.8676 (t80) REVERT: B 84 VAL cc_start: 0.9030 (t) cc_final: 0.8820 (p) REVERT: B 91 LYS cc_start: 0.8322 (mttt) cc_final: 0.8109 (mtpp) REVERT: B 146 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7856 (mm-30) REVERT: B 150 THR cc_start: 0.8242 (p) cc_final: 0.7996 (p) REVERT: B 187 ASN cc_start: 0.9155 (t0) cc_final: 0.8849 (t0) REVERT: B 228 MET cc_start: 0.8885 (tpt) cc_final: 0.8436 (tpp) REVERT: B 251 THR cc_start: 0.9275 (p) cc_final: 0.9061 (p) REVERT: B 262 ASN cc_start: 0.8614 (m-40) cc_final: 0.8401 (m-40) REVERT: B 448 TYR cc_start: 0.7986 (t80) cc_final: 0.7267 (t80) REVERT: B 480 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8297 (tm-30) REVERT: B 486 ARG cc_start: 0.8639 (ttt180) cc_final: 0.8398 (mtp85) REVERT: C 72 GLN cc_start: 0.7238 (pt0) cc_final: 0.6767 (pt0) REVERT: C 115 ASN cc_start: 0.8774 (m-40) cc_final: 0.8548 (m-40) REVERT: C 130 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7461 (ttp80) REVERT: C 152 LEU cc_start: 0.9388 (mt) cc_final: 0.9175 (mt) REVERT: C 178 THR cc_start: 0.8418 (m) cc_final: 0.8213 (m) REVERT: C 294 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8719 (mt-10) REVERT: C 364 ARG cc_start: 0.8862 (mtt180) cc_final: 0.8113 (mtt180) REVERT: C 368 ASN cc_start: 0.8266 (t0) cc_final: 0.7823 (t0) REVERT: C 369 VAL cc_start: 0.8931 (t) cc_final: 0.8562 (p) REVERT: C 383 LYS cc_start: 0.8190 (mmtm) cc_final: 0.7914 (mmmt) REVERT: C 398 GLN cc_start: 0.8867 (mt0) cc_final: 0.8350 (mt0) REVERT: C 425 ARG cc_start: 0.8592 (mtt90) cc_final: 0.8331 (mtt90) REVERT: C 455 LEU cc_start: 0.8316 (tp) cc_final: 0.7990 (tp) REVERT: C 478 HIS cc_start: 0.7668 (m-70) cc_final: 0.7326 (m-70) REVERT: D 12 LYS cc_start: 0.8633 (mptt) cc_final: 0.8142 (mtpp) REVERT: D 77 LEU cc_start: 0.8134 (tp) cc_final: 0.7909 (tt) REVERT: D 90 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7323 (mm-30) REVERT: D 110 LYS cc_start: 0.8187 (mttt) cc_final: 0.7920 (mttt) REVERT: D 176 LYS cc_start: 0.8498 (tttt) cc_final: 0.8172 (tppt) REVERT: D 198 TYR cc_start: 0.8910 (t80) cc_final: 0.8704 (t80) REVERT: D 203 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8258 (mt-10) REVERT: D 332 THR cc_start: 0.8562 (p) cc_final: 0.8322 (m) REVERT: D 356 ARG cc_start: 0.7799 (ttt90) cc_final: 0.7418 (ttm-80) REVERT: D 375 GLN cc_start: 0.7918 (mt0) cc_final: 0.7391 (tm-30) REVERT: D 412 ARG cc_start: 0.7794 (mtt90) cc_final: 0.7296 (mtt-85) REVERT: D 440 SER cc_start: 0.9096 (m) cc_final: 0.8888 (t) REVERT: E 128 SER cc_start: 0.9125 (t) cc_final: 0.8891 (p) REVERT: E 196 ASP cc_start: 0.8218 (t0) cc_final: 0.7830 (t0) REVERT: E 207 ILE cc_start: 0.9180 (mt) cc_final: 0.8863 (tt) REVERT: E 277 SER cc_start: 0.8320 (t) cc_final: 0.8097 (m) REVERT: E 308 GLN cc_start: 0.8923 (mt0) cc_final: 0.8696 (mt0) REVERT: E 352 ASP cc_start: 0.7559 (m-30) cc_final: 0.7280 (m-30) REVERT: E 353 SER cc_start: 0.8538 (m) cc_final: 0.8308 (p) REVERT: E 441 PHE cc_start: 0.8718 (m-80) cc_final: 0.8469 (m-80) REVERT: F 35 ASN cc_start: 0.9144 (m-40) cc_final: 0.8752 (m-40) REVERT: F 128 SER cc_start: 0.9222 (t) cc_final: 0.8997 (m) REVERT: F 201 MET cc_start: 0.8546 (mmt) cc_final: 0.8221 (mmt) REVERT: F 202 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8199 (mtmm) REVERT: F 237 LEU cc_start: 0.8781 (mp) cc_final: 0.8519 (mp) REVERT: F 259 PHE cc_start: 0.7704 (t80) cc_final: 0.7400 (t80) REVERT: F 262 THR cc_start: 0.8989 (m) cc_final: 0.8695 (p) REVERT: F 281 TYR cc_start: 0.8866 (m-80) cc_final: 0.8362 (m-80) REVERT: F 285 LEU cc_start: 0.8474 (tt) cc_final: 0.8043 (tp) REVERT: F 288 ASP cc_start: 0.7783 (m-30) cc_final: 0.7093 (m-30) REVERT: F 293 GLN cc_start: 0.8727 (tt0) cc_final: 0.8195 (tt0) REVERT: F 349 ASP cc_start: 0.8479 (t0) cc_final: 0.8105 (t0) REVERT: F 351 LEU cc_start: 0.9363 (mt) cc_final: 0.9094 (mt) REVERT: F 356 ARG cc_start: 0.8273 (tpt170) cc_final: 0.7986 (ttp-170) REVERT: F 369 ASP cc_start: 0.8180 (t0) cc_final: 0.7943 (t70) REVERT: F 375 GLN cc_start: 0.9037 (mt0) cc_final: 0.8537 (mm-40) REVERT: F 449 TYR cc_start: 0.8735 (m-80) cc_final: 0.8474 (m-80) REVERT: F 463 ILE cc_start: 0.7868 (tp) cc_final: 0.7566 (tp) REVERT: F 464 GLU cc_start: 0.8406 (mt-10) cc_final: 0.8138 (mt-10) REVERT: G 3 LEU cc_start: 0.6845 (tt) cc_final: 0.6538 (tp) REVERT: G 4 LYS cc_start: 0.8312 (tptt) cc_final: 0.7969 (tppp) REVERT: G 24 LYS cc_start: 0.4822 (tmtt) cc_final: 0.4323 (mtmt) REVERT: G 214 LEU cc_start: 0.8398 (tp) cc_final: 0.8126 (tp) REVERT: G 247 MET cc_start: 0.7066 (tpt) cc_final: 0.6599 (tpp) outliers start: 1 outliers final: 0 residues processed: 933 average time/residue: 0.3246 time to fit residues: 460.3166 Evaluate side-chains 747 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 747 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 0.8980 chunk 230 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 238 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 276 optimal weight: 0.0030 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN B 381 GLN C 145 HIS C 387 GLN D 52 GLN D 168 GLN E 24 HIS E 308 GLN ** F 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 263 GLN F 379 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21978 Z= 0.199 Angle : 0.577 6.258 29983 Z= 0.305 Chirality : 0.045 0.162 3681 Planarity : 0.005 0.055 3859 Dihedral : 7.525 95.019 3423 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.63 % Allowed : 15.48 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.15), residues: 3044 helix: 0.72 (0.15), residues: 1206 sheet: 0.06 (0.23), residues: 490 loop : 0.14 (0.18), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 191 HIS 0.006 0.001 HIS E 24 PHE 0.020 0.001 PHE D 441 TYR 0.019 0.002 TYR B 435 ARG 0.008 0.000 ARG F 190 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 788 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8613 (ptt) cc_final: 0.8285 (ptp) REVERT: A 105 LEU cc_start: 0.9105 (mt) cc_final: 0.8885 (mt) REVERT: A 129 SER cc_start: 0.8362 (m) cc_final: 0.7646 (t) REVERT: A 159 VAL cc_start: 0.9069 (t) cc_final: 0.8687 (m) REVERT: A 240 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7853 (mm-30) REVERT: A 309 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7370 (mm-30) REVERT: A 466 PHE cc_start: 0.8399 (t80) cc_final: 0.8182 (t80) REVERT: B 84 VAL cc_start: 0.8958 (t) cc_final: 0.8724 (p) REVERT: B 91 LYS cc_start: 0.8421 (mttt) cc_final: 0.8194 (mtpp) REVERT: B 228 MET cc_start: 0.8868 (tpt) cc_final: 0.8438 (tpp) REVERT: B 262 ASN cc_start: 0.8753 (m-40) cc_final: 0.8148 (m-40) REVERT: B 309 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7421 (mm-30) REVERT: B 317 LYS cc_start: 0.8521 (ttpt) cc_final: 0.8262 (ptmm) REVERT: B 349 ASP cc_start: 0.8110 (m-30) cc_final: 0.7174 (m-30) REVERT: B 448 TYR cc_start: 0.8016 (t80) cc_final: 0.7185 (t80) REVERT: B 480 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8549 (tm-30) REVERT: B 486 ARG cc_start: 0.8624 (ttt180) cc_final: 0.8216 (mtp85) REVERT: C 78 PHE cc_start: 0.8963 (m-80) cc_final: 0.8697 (m-10) REVERT: C 142 ARG cc_start: 0.8644 (tmm-80) cc_final: 0.8134 (tmm-80) REVERT: C 223 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8763 (mm-30) REVERT: C 383 LYS cc_start: 0.8377 (mmtm) cc_final: 0.8070 (mmmt) REVERT: C 398 GLN cc_start: 0.8722 (mt0) cc_final: 0.8510 (mt0) REVERT: C 425 ARG cc_start: 0.8764 (mtt90) cc_final: 0.8339 (mtt90) REVERT: C 428 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8626 (mm110) REVERT: C 440 THR cc_start: 0.8939 (p) cc_final: 0.8658 (t) REVERT: D 12 LYS cc_start: 0.8623 (mptt) cc_final: 0.8078 (mtpp) REVERT: D 89 ARG cc_start: 0.8238 (mmt-90) cc_final: 0.7268 (ttp80) REVERT: D 90 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7314 (mm-30) REVERT: D 110 LYS cc_start: 0.7971 (mttt) cc_final: 0.7742 (mttt) REVERT: D 132 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7651 (mt-10) REVERT: D 168 GLN cc_start: 0.8914 (mt0) cc_final: 0.8700 (tt0) REVERT: D 267 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7954 (mt-10) REVERT: D 277 SER cc_start: 0.8439 (t) cc_final: 0.7966 (m) REVERT: D 282 GLN cc_start: 0.9194 (pm20) cc_final: 0.8729 (pm20) REVERT: D 329 LEU cc_start: 0.8765 (mt) cc_final: 0.8372 (mt) REVERT: D 356 ARG cc_start: 0.7647 (ttt90) cc_final: 0.7400 (ttm-80) REVERT: D 375 GLN cc_start: 0.7946 (mt0) cc_final: 0.7473 (tm-30) REVERT: D 412 ARG cc_start: 0.7775 (mtt90) cc_final: 0.7290 (ttm110) REVERT: D 437 THR cc_start: 0.8964 (m) cc_final: 0.8759 (m) REVERT: E 101 GLU cc_start: 0.8365 (pt0) cc_final: 0.8118 (pm20) REVERT: E 128 SER cc_start: 0.9031 (t) cc_final: 0.8800 (p) REVERT: E 201 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8098 (mpp) REVERT: E 207 ILE cc_start: 0.9057 (mt) cc_final: 0.8792 (tt) REVERT: E 352 ASP cc_start: 0.7618 (m-30) cc_final: 0.7370 (m-30) REVERT: F 35 ASN cc_start: 0.9175 (m-40) cc_final: 0.8732 (m-40) REVERT: F 192 ARG cc_start: 0.8959 (ttp-110) cc_final: 0.8534 (ttp80) REVERT: F 201 MET cc_start: 0.8542 (mmt) cc_final: 0.8146 (mmt) REVERT: F 202 LYS cc_start: 0.8586 (mtpt) cc_final: 0.8114 (mtmm) REVERT: F 237 LEU cc_start: 0.8834 (mp) cc_final: 0.8504 (mp) REVERT: F 262 THR cc_start: 0.9017 (m) cc_final: 0.8674 (p) REVERT: F 281 TYR cc_start: 0.9041 (m-80) cc_final: 0.8617 (m-80) REVERT: F 282 GLN cc_start: 0.9365 (pm20) cc_final: 0.8245 (pm20) REVERT: F 288 ASP cc_start: 0.7992 (m-30) cc_final: 0.7357 (m-30) REVERT: F 293 GLN cc_start: 0.8576 (tt0) cc_final: 0.8205 (tt0) REVERT: F 349 ASP cc_start: 0.8509 (t0) cc_final: 0.8217 (t0) REVERT: F 375 GLN cc_start: 0.9002 (mt0) cc_final: 0.8615 (mm-40) REVERT: F 449 TYR cc_start: 0.8841 (m-80) cc_final: 0.8629 (m-80) REVERT: F 463 ILE cc_start: 0.7894 (tp) cc_final: 0.7614 (tp) REVERT: F 464 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7999 (mt-10) REVERT: G 4 LYS cc_start: 0.8354 (tptt) cc_final: 0.8012 (tppp) REVERT: G 24 LYS cc_start: 0.5047 (tmtt) cc_final: 0.4531 (mtpt) REVERT: G 247 MET cc_start: 0.7229 (tpt) cc_final: 0.6751 (tpp) outliers start: 52 outliers final: 37 residues processed: 809 average time/residue: 0.3324 time to fit residues: 413.4108 Evaluate side-chains 755 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 717 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 353 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain G residue 241 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 0.0270 chunk 85 optimal weight: 10.0000 chunk 229 optimal weight: 7.9990 chunk 187 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 276 optimal weight: 2.9990 chunk 298 optimal weight: 0.1980 chunk 246 optimal weight: 9.9990 chunk 274 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 221 optimal weight: 0.8980 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 245 GLN A 381 GLN A 477 ASN C 387 GLN D 52 GLN D 195 ASN E 24 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21978 Z= 0.194 Angle : 0.549 6.623 29983 Z= 0.288 Chirality : 0.044 0.171 3681 Planarity : 0.005 0.055 3859 Dihedral : 7.076 91.253 3423 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.95 % Allowed : 18.16 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3044 helix: 0.84 (0.15), residues: 1200 sheet: 0.07 (0.24), residues: 477 loop : 0.19 (0.18), residues: 1367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 191 HIS 0.006 0.001 HIS E 24 PHE 0.020 0.001 PHE F 219 TYR 0.020 0.001 TYR B 435 ARG 0.007 0.000 ARG F 433 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 745 time to evaluate : 2.348 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.8638 (ptt) cc_final: 0.8348 (ptp) REVERT: A 129 SER cc_start: 0.8353 (m) cc_final: 0.7796 (t) REVERT: A 141 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.8200 (mtt-85) REVERT: A 159 VAL cc_start: 0.9096 (t) cc_final: 0.8700 (m) REVERT: A 199 LYS cc_start: 0.8290 (mttt) cc_final: 0.7477 (mttm) REVERT: A 309 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7582 (mm-30) REVERT: A 466 PHE cc_start: 0.8313 (t80) cc_final: 0.8040 (t80) REVERT: B 84 VAL cc_start: 0.8845 (t) cc_final: 0.8629 (p) REVERT: B 91 LYS cc_start: 0.8436 (mttt) cc_final: 0.8121 (mtpp) REVERT: B 124 ASP cc_start: 0.6302 (p0) cc_final: 0.6070 (p0) REVERT: B 228 MET cc_start: 0.8846 (tpt) cc_final: 0.8327 (tpp) REVERT: B 262 ASN cc_start: 0.8695 (m-40) cc_final: 0.8058 (m-40) REVERT: B 309 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7315 (mm-30) REVERT: B 349 ASP cc_start: 0.8134 (m-30) cc_final: 0.7162 (m-30) REVERT: B 448 TYR cc_start: 0.7910 (t80) cc_final: 0.7175 (t80) REVERT: B 480 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8562 (tm-30) REVERT: B 486 ARG cc_start: 0.8695 (ttt180) cc_final: 0.8291 (mtp85) REVERT: C 43 VAL cc_start: 0.9042 (m) cc_final: 0.8798 (p) REVERT: C 78 PHE cc_start: 0.8851 (m-80) cc_final: 0.8630 (m-10) REVERT: C 106 LEU cc_start: 0.9095 (tp) cc_final: 0.8753 (mp) REVERT: C 223 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8834 (mm-30) REVERT: C 345 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8463 (mp) REVERT: C 364 ARG cc_start: 0.8816 (mtt180) cc_final: 0.8511 (mtt180) REVERT: C 398 GLN cc_start: 0.8636 (mt0) cc_final: 0.8311 (mt0) REVERT: C 425 ARG cc_start: 0.8771 (mtt90) cc_final: 0.8078 (mtt90) REVERT: C 428 GLN cc_start: 0.8917 (mm-40) cc_final: 0.8684 (mm110) REVERT: C 440 THR cc_start: 0.8901 (p) cc_final: 0.8664 (t) REVERT: C 478 HIS cc_start: 0.8105 (m-70) cc_final: 0.7769 (m-70) REVERT: D 12 LYS cc_start: 0.8613 (mptt) cc_final: 0.8121 (mtpp) REVERT: D 89 ARG cc_start: 0.8126 (mmt-90) cc_final: 0.7032 (ttp80) REVERT: D 90 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7271 (mm-30) REVERT: D 110 LYS cc_start: 0.7954 (mttt) cc_final: 0.7682 (mttt) REVERT: D 132 GLU cc_start: 0.7906 (mt-10) cc_final: 0.7653 (mt-10) REVERT: D 168 GLN cc_start: 0.8982 (mt0) cc_final: 0.8751 (tt0) REVERT: D 267 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7877 (mt-10) REVERT: D 282 GLN cc_start: 0.9083 (pm20) cc_final: 0.8630 (pm20) REVERT: D 356 ARG cc_start: 0.7648 (ttt90) cc_final: 0.7402 (ttm-80) REVERT: D 368 TYR cc_start: 0.8601 (t80) cc_final: 0.7920 (t80) REVERT: D 375 GLN cc_start: 0.7852 (mt0) cc_final: 0.7434 (tm-30) REVERT: D 464 GLU cc_start: 0.7509 (pp20) cc_final: 0.7261 (pm20) REVERT: E 101 GLU cc_start: 0.8356 (pt0) cc_final: 0.8064 (pm20) REVERT: E 128 SER cc_start: 0.9017 (t) cc_final: 0.8804 (p) REVERT: E 201 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7972 (mpp) REVERT: E 207 ILE cc_start: 0.8977 (mt) cc_final: 0.8620 (tt) REVERT: E 352 ASP cc_start: 0.7523 (m-30) cc_final: 0.5995 (t70) REVERT: F 35 ASN cc_start: 0.9157 (m-40) cc_final: 0.8699 (m-40) REVERT: F 61 THR cc_start: 0.8398 (p) cc_final: 0.8130 (t) REVERT: F 192 ARG cc_start: 0.9030 (ttp-110) cc_final: 0.8584 (ttp80) REVERT: F 201 MET cc_start: 0.8570 (mmt) cc_final: 0.8100 (mmt) REVERT: F 237 LEU cc_start: 0.8840 (mp) cc_final: 0.8483 (mp) REVERT: F 262 THR cc_start: 0.8914 (m) cc_final: 0.8583 (p) REVERT: F 281 TYR cc_start: 0.9103 (m-80) cc_final: 0.8695 (m-80) REVERT: F 282 GLN cc_start: 0.9402 (pm20) cc_final: 0.8354 (pm20) REVERT: F 288 ASP cc_start: 0.7942 (m-30) cc_final: 0.7373 (m-30) REVERT: F 349 ASP cc_start: 0.8573 (t0) cc_final: 0.8194 (t0) REVERT: F 351 LEU cc_start: 0.9308 (mt) cc_final: 0.8965 (mt) REVERT: F 375 GLN cc_start: 0.8998 (mt0) cc_final: 0.8592 (mm-40) REVERT: F 463 ILE cc_start: 0.7901 (tp) cc_final: 0.7622 (tp) REVERT: F 464 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8141 (mt-10) REVERT: G 4 LYS cc_start: 0.8236 (tptt) cc_final: 0.7904 (tppp) REVERT: G 24 LYS cc_start: 0.4991 (tmtt) cc_final: 0.4563 (mtpt) REVERT: G 247 MET cc_start: 0.7265 (tpt) cc_final: 0.6805 (tpt) outliers start: 78 outliers final: 54 residues processed: 772 average time/residue: 0.3173 time to fit residues: 380.6495 Evaluate side-chains 769 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 713 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 283 LEU Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 474 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 450 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 185 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 145 optimal weight: 0.9990 chunk 263 optimal weight: 0.0870 chunk 79 optimal weight: 4.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN B 115 ASN C 381 GLN D 52 GLN ** D 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS E 195 ASN E 223 ASN ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 21978 Z= 0.395 Angle : 0.661 7.830 29983 Z= 0.344 Chirality : 0.046 0.154 3681 Planarity : 0.005 0.054 3859 Dihedral : 7.420 101.618 3423 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 6.32 % Allowed : 19.12 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3044 helix: 0.59 (0.15), residues: 1201 sheet: -0.09 (0.23), residues: 492 loop : -0.06 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 191 HIS 0.005 0.001 HIS C 145 PHE 0.032 0.002 PHE A 470 TYR 0.030 0.002 TYR E 242 ARG 0.005 0.001 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 852 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 727 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8099 (mm-30) REVERT: A 83 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7974 (mt) REVERT: A 98 ASP cc_start: 0.8586 (p0) cc_final: 0.8293 (p0) REVERT: A 129 SER cc_start: 0.8580 (m) cc_final: 0.7998 (t) REVERT: A 159 VAL cc_start: 0.9120 (t) cc_final: 0.8697 (m) REVERT: A 199 LYS cc_start: 0.8459 (mttt) cc_final: 0.8230 (mttt) REVERT: A 309 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7359 (mm-30) REVERT: A 399 TYR cc_start: 0.7926 (t80) cc_final: 0.7491 (t80) REVERT: B 84 VAL cc_start: 0.8949 (t) cc_final: 0.8678 (p) REVERT: B 91 LYS cc_start: 0.8468 (mttt) cc_final: 0.8179 (mtpp) REVERT: B 192 ASN cc_start: 0.8987 (m-40) cc_final: 0.8611 (t0) REVERT: B 228 MET cc_start: 0.9003 (tpt) cc_final: 0.8583 (tpp) REVERT: B 309 GLU cc_start: 0.8502 (mm-30) cc_final: 0.6965 (mm-30) REVERT: B 448 TYR cc_start: 0.8025 (t80) cc_final: 0.7291 (t80) REVERT: B 480 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8619 (tm-30) REVERT: B 486 ARG cc_start: 0.8711 (ttt180) cc_final: 0.8425 (mtp85) REVERT: C 43 VAL cc_start: 0.9029 (m) cc_final: 0.8770 (p) REVERT: C 106 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8823 (mp) REVERT: C 223 GLU cc_start: 0.9130 (mm-30) cc_final: 0.8821 (mm-30) REVERT: C 282 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8391 (tt0) REVERT: C 345 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8735 (mp) REVERT: C 364 ARG cc_start: 0.8947 (mtt180) cc_final: 0.8523 (mtt180) REVERT: C 398 GLN cc_start: 0.8779 (mt0) cc_final: 0.8489 (mt0) REVERT: C 425 ARG cc_start: 0.8907 (mtt90) cc_final: 0.8204 (mtt90) REVERT: C 440 THR cc_start: 0.8904 (p) cc_final: 0.8676 (t) REVERT: C 478 HIS cc_start: 0.8100 (m-70) cc_final: 0.7874 (m90) REVERT: D 12 LYS cc_start: 0.8552 (mptt) cc_final: 0.8026 (mtpp) REVERT: D 60 ARG cc_start: 0.7066 (ttm170) cc_final: 0.6797 (ttt180) REVERT: D 89 ARG cc_start: 0.8177 (mmt-90) cc_final: 0.7055 (ttp80) REVERT: D 90 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7257 (mm-30) REVERT: D 110 LYS cc_start: 0.8230 (mttt) cc_final: 0.7894 (mttp) REVERT: D 144 LEU cc_start: 0.8071 (mt) cc_final: 0.7831 (mt) REVERT: D 267 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7961 (mt-10) REVERT: D 282 GLN cc_start: 0.9200 (pm20) cc_final: 0.8658 (pm20) REVERT: D 356 ARG cc_start: 0.7845 (ttt90) cc_final: 0.7540 (ttm-80) REVERT: D 375 GLN cc_start: 0.8264 (mt0) cc_final: 0.7801 (tm-30) REVERT: D 412 ARG cc_start: 0.7929 (mtt90) cc_final: 0.7591 (mtt-85) REVERT: E 9 ILE cc_start: 0.8507 (mt) cc_final: 0.8171 (mt) REVERT: E 128 SER cc_start: 0.9036 (t) cc_final: 0.8766 (p) REVERT: E 352 ASP cc_start: 0.7712 (m-30) cc_final: 0.6013 (t70) REVERT: E 354 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7702 (tttm) REVERT: F 35 ASN cc_start: 0.9152 (m-40) cc_final: 0.8752 (m-40) REVERT: F 201 MET cc_start: 0.8741 (mmt) cc_final: 0.8266 (mmt) REVERT: F 281 TYR cc_start: 0.9225 (m-80) cc_final: 0.8960 (m-80) REVERT: F 282 GLN cc_start: 0.9447 (pm20) cc_final: 0.8466 (pm20) REVERT: F 288 ASP cc_start: 0.7964 (m-30) cc_final: 0.7402 (m-30) REVERT: F 349 ASP cc_start: 0.8654 (t0) cc_final: 0.8292 (t0) REVERT: F 375 GLN cc_start: 0.9112 (mt0) cc_final: 0.8726 (mm-40) REVERT: F 449 TYR cc_start: 0.8737 (m-80) cc_final: 0.8523 (m-10) REVERT: F 464 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8229 (mt-10) REVERT: G 4 LYS cc_start: 0.8284 (tptt) cc_final: 0.8056 (tppp) REVERT: G 24 LYS cc_start: 0.4758 (tmtt) cc_final: 0.4241 (mtpt) REVERT: G 247 MET cc_start: 0.7184 (tpt) cc_final: 0.6825 (tpt) outliers start: 125 outliers final: 100 residues processed: 768 average time/residue: 0.3158 time to fit residues: 376.1102 Evaluate side-chains 800 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 696 time to evaluate : 2.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 282 GLN Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 99 ILE Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 251 VAL Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 336 SER Chi-restraints excluded: chain F residue 369 ASP Chi-restraints excluded: chain F residue 376 GLU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain G residue 29 THR Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 252 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 218 optimal weight: 0.0770 chunk 121 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 203 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 150 optimal weight: 0.6980 chunk 263 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN D 52 GLN D 168 GLN E 24 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN F 249 GLN F 293 GLN F 328 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 21978 Z= 0.170 Angle : 0.546 8.198 29983 Z= 0.282 Chirality : 0.043 0.162 3681 Planarity : 0.004 0.054 3859 Dihedral : 6.826 94.515 3423 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.69 % Allowed : 22.66 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.16), residues: 3044 helix: 0.80 (0.15), residues: 1212 sheet: 0.01 (0.23), residues: 477 loop : 0.06 (0.18), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 191 HIS 0.006 0.001 HIS E 24 PHE 0.039 0.002 PHE A 470 TYR 0.023 0.001 TYR E 242 ARG 0.007 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 737 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7847 (tp30) REVERT: A 83 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7988 (mt) REVERT: A 98 ASP cc_start: 0.8575 (p0) cc_final: 0.8298 (p0) REVERT: A 129 SER cc_start: 0.8450 (m) cc_final: 0.7761 (t) REVERT: A 159 VAL cc_start: 0.9152 (t) cc_final: 0.8784 (m) REVERT: A 196 ASP cc_start: 0.7251 (p0) cc_final: 0.7004 (p0) REVERT: A 199 LYS cc_start: 0.8388 (mttt) cc_final: 0.8017 (mttm) REVERT: A 283 LEU cc_start: 0.9223 (tp) cc_final: 0.8809 (tt) REVERT: A 302 TYR cc_start: 0.8532 (t80) cc_final: 0.8179 (t80) REVERT: A 309 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7593 (mm-30) REVERT: A 399 TYR cc_start: 0.7920 (t80) cc_final: 0.7393 (t80) REVERT: A 473 TYR cc_start: 0.7289 (t80) cc_final: 0.6998 (t80) REVERT: B 91 LYS cc_start: 0.8431 (mttt) cc_final: 0.8150 (mtpp) REVERT: B 192 ASN cc_start: 0.8915 (m-40) cc_final: 0.8508 (t0) REVERT: B 228 MET cc_start: 0.8874 (tpt) cc_final: 0.8356 (tpp) REVERT: B 309 GLU cc_start: 0.8384 (mm-30) cc_final: 0.6900 (mm-30) REVERT: B 349 ASP cc_start: 0.8075 (m-30) cc_final: 0.7183 (m-30) REVERT: B 448 TYR cc_start: 0.7889 (t80) cc_final: 0.7261 (t80) REVERT: B 480 GLU cc_start: 0.8927 (tm-30) cc_final: 0.8584 (tm-30) REVERT: B 486 ARG cc_start: 0.8671 (ttt180) cc_final: 0.8378 (mtp85) REVERT: C 43 VAL cc_start: 0.9049 (m) cc_final: 0.8800 (p) REVERT: C 106 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8705 (mp) REVERT: C 198 SER cc_start: 0.8814 (p) cc_final: 0.8494 (t) REVERT: C 220 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8151 (tp40) REVERT: C 223 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8678 (mm-30) REVERT: C 345 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8405 (mp) REVERT: C 425 ARG cc_start: 0.8839 (mtt90) cc_final: 0.7967 (mtt90) REVERT: D 12 LYS cc_start: 0.8599 (mptt) cc_final: 0.8048 (mtpp) REVERT: D 60 ARG cc_start: 0.6887 (ttm170) cc_final: 0.6598 (ttt180) REVERT: D 89 ARG cc_start: 0.8144 (mmt-90) cc_final: 0.6717 (ttp80) REVERT: D 90 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7273 (mm-30) REVERT: D 110 LYS cc_start: 0.8096 (mttt) cc_final: 0.7801 (mttp) REVERT: D 282 GLN cc_start: 0.9132 (pm20) cc_final: 0.8712 (pm20) REVERT: D 356 ARG cc_start: 0.7802 (ttt90) cc_final: 0.7494 (ttm-80) REVERT: D 368 TYR cc_start: 0.8506 (t80) cc_final: 0.7964 (t80) REVERT: D 373 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7723 (tppt) REVERT: D 375 GLN cc_start: 0.8106 (mt0) cc_final: 0.7511 (tm-30) REVERT: D 464 GLU cc_start: 0.7420 (pm20) cc_final: 0.7182 (pm20) REVERT: E 9 ILE cc_start: 0.8568 (mt) cc_final: 0.8211 (mt) REVERT: E 128 SER cc_start: 0.9010 (t) cc_final: 0.8802 (p) REVERT: E 352 ASP cc_start: 0.7624 (m-30) cc_final: 0.5917 (t70) REVERT: F 35 ASN cc_start: 0.9116 (m-40) cc_final: 0.8722 (m110) REVERT: F 201 MET cc_start: 0.8625 (mmt) cc_final: 0.8138 (mmt) REVERT: F 237 LEU cc_start: 0.8878 (mp) cc_final: 0.8604 (mp) REVERT: F 252 LEU cc_start: 0.8511 (tp) cc_final: 0.8281 (mp) REVERT: F 281 TYR cc_start: 0.9143 (m-80) cc_final: 0.8790 (m-80) REVERT: F 282 GLN cc_start: 0.9354 (pm20) cc_final: 0.8367 (pm20) REVERT: F 288 ASP cc_start: 0.7940 (m-30) cc_final: 0.7356 (m-30) REVERT: F 349 ASP cc_start: 0.8614 (t0) cc_final: 0.8290 (t0) REVERT: F 375 GLN cc_start: 0.8978 (mt0) cc_final: 0.8658 (mm-40) REVERT: F 464 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8086 (mt-10) REVERT: G 24 LYS cc_start: 0.4775 (tmtt) cc_final: 0.4260 (ttpt) REVERT: G 247 MET cc_start: 0.7195 (tpt) cc_final: 0.6587 (tpp) outliers start: 73 outliers final: 49 residues processed: 768 average time/residue: 0.3224 time to fit residues: 384.1247 Evaluate side-chains 761 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 706 time to evaluate : 2.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 447 ILE Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain G residue 257 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 5.9990 chunk 264 optimal weight: 6.9990 chunk 58 optimal weight: 0.0470 chunk 172 optimal weight: 0.0670 chunk 72 optimal weight: 0.9980 chunk 294 optimal weight: 30.0000 chunk 244 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN D 52 GLN E 24 HIS E 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21978 Z= 0.203 Angle : 0.561 8.306 29983 Z= 0.286 Chirality : 0.044 0.173 3681 Planarity : 0.004 0.054 3859 Dihedral : 6.737 97.867 3423 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.96 % Allowed : 22.81 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 3044 helix: 0.86 (0.15), residues: 1208 sheet: 0.06 (0.24), residues: 472 loop : 0.06 (0.18), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 191 HIS 0.004 0.001 HIS E 24 PHE 0.027 0.001 PHE A 466 TYR 0.034 0.002 TYR E 242 ARG 0.010 0.000 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 724 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7755 (mm-30) REVERT: A 98 ASP cc_start: 0.8615 (p0) cc_final: 0.8337 (p0) REVERT: A 129 SER cc_start: 0.8497 (m) cc_final: 0.7831 (t) REVERT: A 159 VAL cc_start: 0.9211 (t) cc_final: 0.8848 (m) REVERT: A 240 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7549 (mm-30) REVERT: A 302 TYR cc_start: 0.8531 (t80) cc_final: 0.8182 (t80) REVERT: A 309 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7642 (mm-30) REVERT: A 399 TYR cc_start: 0.7978 (t80) cc_final: 0.7500 (t80) REVERT: B 91 LYS cc_start: 0.8429 (mttt) cc_final: 0.8147 (mtpp) REVERT: B 192 ASN cc_start: 0.8940 (m-40) cc_final: 0.8548 (t0) REVERT: B 228 MET cc_start: 0.8886 (tpt) cc_final: 0.8444 (tpp) REVERT: B 309 GLU cc_start: 0.8501 (mm-30) cc_final: 0.6968 (mm-30) REVERT: B 349 ASP cc_start: 0.7854 (m-30) cc_final: 0.7042 (m-30) REVERT: B 448 TYR cc_start: 0.7897 (t80) cc_final: 0.7285 (t80) REVERT: B 480 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8604 (tm-30) REVERT: B 486 ARG cc_start: 0.8674 (ttt180) cc_final: 0.8384 (mtp85) REVERT: C 43 VAL cc_start: 0.9050 (m) cc_final: 0.8799 (p) REVERT: C 106 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8760 (mp) REVERT: C 220 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8227 (tp40) REVERT: C 223 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8734 (mm-30) REVERT: C 387 GLN cc_start: 0.7984 (mt0) cc_final: 0.7767 (mt0) REVERT: C 398 GLN cc_start: 0.8855 (mt0) cc_final: 0.8540 (mm-40) REVERT: C 425 ARG cc_start: 0.8871 (mtt90) cc_final: 0.7902 (mtt90) REVERT: C 478 HIS cc_start: 0.7934 (m-70) cc_final: 0.7667 (m-70) REVERT: D 12 LYS cc_start: 0.8590 (mptt) cc_final: 0.8009 (mtpp) REVERT: D 60 ARG cc_start: 0.6858 (ttm170) cc_final: 0.6619 (ttt180) REVERT: D 89 ARG cc_start: 0.8257 (mmt-90) cc_final: 0.6799 (ttp80) REVERT: D 90 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7285 (mm-30) REVERT: D 110 LYS cc_start: 0.8080 (mttt) cc_final: 0.7782 (mttp) REVERT: D 168 GLN cc_start: 0.8913 (mt0) cc_final: 0.8695 (tt0) REVERT: D 282 GLN cc_start: 0.9163 (pm20) cc_final: 0.8686 (pm20) REVERT: D 356 ARG cc_start: 0.7861 (ttt90) cc_final: 0.7575 (ttm-80) REVERT: D 368 TYR cc_start: 0.8518 (t80) cc_final: 0.7946 (t80) REVERT: D 373 LYS cc_start: 0.8049 (OUTLIER) cc_final: 0.7664 (tppt) REVERT: D 375 GLN cc_start: 0.8144 (mt0) cc_final: 0.7660 (tm-30) REVERT: D 458 TYR cc_start: 0.6053 (OUTLIER) cc_final: 0.4571 (t80) REVERT: E 9 ILE cc_start: 0.8594 (mt) cc_final: 0.8261 (mt) REVERT: E 128 SER cc_start: 0.9011 (t) cc_final: 0.8788 (p) REVERT: E 224 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8238 (mt-10) REVERT: E 293 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8216 (mm110) REVERT: E 352 ASP cc_start: 0.7633 (m-30) cc_final: 0.5919 (t70) REVERT: E 354 LYS cc_start: 0.7968 (mtpt) cc_final: 0.7674 (tttm) REVERT: F 35 ASN cc_start: 0.9115 (m-40) cc_final: 0.8721 (m110) REVERT: F 201 MET cc_start: 0.8669 (mmt) cc_final: 0.8160 (mmt) REVERT: F 263 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: F 281 TYR cc_start: 0.9168 (m-80) cc_final: 0.8806 (m-80) REVERT: F 282 GLN cc_start: 0.9354 (pm20) cc_final: 0.8380 (pm20) REVERT: F 288 ASP cc_start: 0.7914 (m-30) cc_final: 0.7281 (m-30) REVERT: F 349 ASP cc_start: 0.8644 (t0) cc_final: 0.8378 (t0) REVERT: F 375 GLN cc_start: 0.9025 (mt0) cc_final: 0.8705 (mm-40) REVERT: F 464 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8142 (mt-10) REVERT: G 24 LYS cc_start: 0.4633 (tmtt) cc_final: 0.4059 (ttpt) REVERT: G 247 MET cc_start: 0.7103 (tpt) cc_final: 0.6458 (tpp) outliers start: 98 outliers final: 78 residues processed: 763 average time/residue: 0.3279 time to fit residues: 391.4594 Evaluate side-chains 784 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 701 time to evaluate : 2.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 115 ASN Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 62 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 222 MET Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 193 GLU Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 388 ILE Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 257 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 8.9990 chunk 33 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 293 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 135 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN B 479 ASN E 24 HIS ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 21978 Z= 0.337 Angle : 0.627 7.263 29983 Z= 0.324 Chirality : 0.045 0.213 3681 Planarity : 0.005 0.054 3859 Dihedral : 7.065 105.176 3423 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.02 % Allowed : 22.71 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3044 helix: 0.71 (0.15), residues: 1195 sheet: -0.12 (0.24), residues: 478 loop : -0.12 (0.17), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 258 HIS 0.004 0.001 HIS E 24 PHE 0.027 0.002 PHE A 466 TYR 0.029 0.002 TYR E 242 ARG 0.006 0.001 ARG B 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 706 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7796 (mt) REVERT: A 98 ASP cc_start: 0.8647 (p0) cc_final: 0.8394 (p0) REVERT: A 159 VAL cc_start: 0.9200 (t) cc_final: 0.8771 (m) REVERT: A 199 LYS cc_start: 0.8400 (mttt) cc_final: 0.8015 (mttm) REVERT: A 284 SER cc_start: 0.9205 (m) cc_final: 0.9002 (m) REVERT: A 309 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 399 TYR cc_start: 0.7879 (t80) cc_final: 0.7356 (t80) REVERT: A 473 TYR cc_start: 0.7373 (t80) cc_final: 0.7025 (t80) REVERT: B 84 VAL cc_start: 0.8890 (t) cc_final: 0.8625 (p) REVERT: B 91 LYS cc_start: 0.8445 (mttt) cc_final: 0.8131 (mtpp) REVERT: B 228 MET cc_start: 0.8943 (tpt) cc_final: 0.8567 (tpp) REVERT: B 349 ASP cc_start: 0.7814 (m-30) cc_final: 0.7019 (m-30) REVERT: B 448 TYR cc_start: 0.7929 (t80) cc_final: 0.7230 (t80) REVERT: B 480 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8599 (tm-30) REVERT: B 486 ARG cc_start: 0.8732 (ttt180) cc_final: 0.8426 (mtp85) REVERT: C 43 VAL cc_start: 0.8939 (m) cc_final: 0.8699 (p) REVERT: C 106 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8800 (mp) REVERT: C 142 ARG cc_start: 0.8756 (tmm-80) cc_final: 0.8277 (tmm-80) REVERT: C 153 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8293 (mtpp) REVERT: C 220 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8205 (tp40) REVERT: C 223 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8827 (mm-30) REVERT: C 398 GLN cc_start: 0.8951 (mt0) cc_final: 0.8704 (mm-40) REVERT: C 425 ARG cc_start: 0.8904 (mtt90) cc_final: 0.7941 (mtt90) REVERT: D 12 LYS cc_start: 0.8489 (mptt) cc_final: 0.7969 (mtpp) REVERT: D 60 ARG cc_start: 0.6884 (ttm170) cc_final: 0.6610 (ttt180) REVERT: D 89 ARG cc_start: 0.8338 (mmt-90) cc_final: 0.6916 (ttp80) REVERT: D 90 GLU cc_start: 0.7579 (mm-30) cc_final: 0.7257 (mm-30) REVERT: D 110 LYS cc_start: 0.8143 (mttt) cc_final: 0.7759 (mttp) REVERT: D 134 LEU cc_start: 0.8215 (tp) cc_final: 0.7903 (tp) REVERT: D 282 GLN cc_start: 0.9237 (pm20) cc_final: 0.8677 (pm20) REVERT: D 356 ARG cc_start: 0.7951 (ttt90) cc_final: 0.7602 (ttm-80) REVERT: D 373 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7762 (tppt) REVERT: D 375 GLN cc_start: 0.8271 (mt0) cc_final: 0.7585 (tm-30) REVERT: D 458 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.4873 (t80) REVERT: E 9 ILE cc_start: 0.8603 (mt) cc_final: 0.8277 (mt) REVERT: E 128 SER cc_start: 0.9038 (t) cc_final: 0.8772 (p) REVERT: E 224 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8445 (mt-10) REVERT: E 352 ASP cc_start: 0.7747 (m-30) cc_final: 0.6080 (t70) REVERT: E 354 LYS cc_start: 0.7967 (mtpt) cc_final: 0.7692 (tttm) REVERT: F 35 ASN cc_start: 0.9101 (m-40) cc_final: 0.8770 (m-40) REVERT: F 156 PHE cc_start: 0.8606 (m-80) cc_final: 0.8341 (m-80) REVERT: F 201 MET cc_start: 0.8695 (mmt) cc_final: 0.8249 (mmt) REVERT: F 263 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8630 (tt0) REVERT: F 281 TYR cc_start: 0.9231 (m-80) cc_final: 0.9021 (m-80) REVERT: F 282 GLN cc_start: 0.9411 (pm20) cc_final: 0.8442 (pm20) REVERT: F 288 ASP cc_start: 0.7984 (m-30) cc_final: 0.7397 (m-30) REVERT: F 349 ASP cc_start: 0.8718 (t0) cc_final: 0.8451 (t0) REVERT: F 356 ARG cc_start: 0.8735 (tpt90) cc_final: 0.8409 (tpp-160) REVERT: F 375 GLN cc_start: 0.9099 (mt0) cc_final: 0.8746 (mm-40) REVERT: F 464 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8141 (mt-10) REVERT: G 247 MET cc_start: 0.6964 (tpt) cc_final: 0.6300 (tpp) outliers start: 119 outliers final: 98 residues processed: 759 average time/residue: 0.3248 time to fit residues: 383.9353 Evaluate side-chains 803 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 698 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 479 ASN Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 296 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain G residue 45 ASP Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 257 ARG Chi-restraints excluded: chain G residue 263 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 144 optimal weight: 0.0370 chunk 27 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 overall best weight: 2.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 433 ASN B 479 ASN C 225 HIS E 24 HIS E 223 ASN ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 21978 Z= 0.414 Angle : 0.682 9.223 29983 Z= 0.352 Chirality : 0.047 0.214 3681 Planarity : 0.005 0.055 3859 Dihedral : 7.291 103.708 3423 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 7.08 % Allowed : 22.21 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.15), residues: 3044 helix: 0.43 (0.15), residues: 1188 sheet: -0.23 (0.24), residues: 474 loop : -0.31 (0.17), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 258 HIS 0.006 0.001 HIS F 328 PHE 0.031 0.002 PHE A 466 TYR 0.028 0.002 TYR E 242 ARG 0.007 0.001 ARG F 433 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 851 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 711 time to evaluate : 3.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7900 (mt) REVERT: A 98 ASP cc_start: 0.8641 (p0) cc_final: 0.8401 (p0) REVERT: A 159 VAL cc_start: 0.9180 (t) cc_final: 0.8695 (m) REVERT: A 160 PRO cc_start: 0.9409 (Cg_exo) cc_final: 0.9171 (Cg_endo) REVERT: A 177 LYS cc_start: 0.9005 (mtmm) cc_final: 0.8742 (mtmm) REVERT: A 199 LYS cc_start: 0.8358 (mttt) cc_final: 0.7967 (mttm) REVERT: A 230 TYR cc_start: 0.8980 (p90) cc_final: 0.8749 (p90) REVERT: A 309 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7500 (mm-30) REVERT: A 399 TYR cc_start: 0.7630 (t80) cc_final: 0.7186 (t80) REVERT: B 84 VAL cc_start: 0.8931 (t) cc_final: 0.8610 (p) REVERT: B 91 LYS cc_start: 0.8409 (mttt) cc_final: 0.8093 (mtpp) REVERT: B 228 MET cc_start: 0.8996 (tpt) cc_final: 0.8657 (tpp) REVERT: B 448 TYR cc_start: 0.7946 (t80) cc_final: 0.7167 (t80) REVERT: B 480 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8654 (tm-30) REVERT: B 486 ARG cc_start: 0.8815 (ttt180) cc_final: 0.8472 (mtp85) REVERT: C 43 VAL cc_start: 0.8941 (m) cc_final: 0.8708 (p) REVERT: C 106 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8825 (mp) REVERT: C 153 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8433 (mtpp) REVERT: C 198 SER cc_start: 0.8798 (p) cc_final: 0.8461 (t) REVERT: C 220 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8177 (tp40) REVERT: C 223 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8839 (mm-30) REVERT: C 425 ARG cc_start: 0.8923 (mtt90) cc_final: 0.7970 (mtt90) REVERT: D 12 LYS cc_start: 0.8503 (mptt) cc_final: 0.7953 (mtpp) REVERT: D 60 ARG cc_start: 0.6883 (ttm170) cc_final: 0.6605 (ttt180) REVERT: D 89 ARG cc_start: 0.8386 (mmt-90) cc_final: 0.7001 (ttp80) REVERT: D 90 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7289 (mm-30) REVERT: D 110 LYS cc_start: 0.8187 (mttt) cc_final: 0.7819 (mttt) REVERT: D 134 LEU cc_start: 0.8309 (tp) cc_final: 0.8011 (tp) REVERT: D 176 LYS cc_start: 0.8604 (tttt) cc_final: 0.8200 (ttpt) REVERT: D 282 GLN cc_start: 0.9293 (pm20) cc_final: 0.8765 (pm20) REVERT: D 356 ARG cc_start: 0.8009 (ttt90) cc_final: 0.7624 (ttm-80) REVERT: D 373 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7745 (tppt) REVERT: D 375 GLN cc_start: 0.8283 (mt0) cc_final: 0.7595 (tm-30) REVERT: D 412 ARG cc_start: 0.7873 (mtt90) cc_final: 0.7289 (mtt-85) REVERT: D 458 TYR cc_start: 0.6641 (OUTLIER) cc_final: 0.5157 (t80) REVERT: E 9 ILE cc_start: 0.8677 (mt) cc_final: 0.8319 (mt) REVERT: E 128 SER cc_start: 0.9046 (t) cc_final: 0.8775 (p) REVERT: E 352 ASP cc_start: 0.7742 (m-30) cc_final: 0.7383 (m-30) REVERT: E 354 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7703 (tttm) REVERT: F 35 ASN cc_start: 0.9108 (m-40) cc_final: 0.8805 (m110) REVERT: F 156 PHE cc_start: 0.8694 (m-80) cc_final: 0.8429 (m-80) REVERT: F 191 THR cc_start: 0.9064 (m) cc_final: 0.8729 (p) REVERT: F 201 MET cc_start: 0.8690 (mmt) cc_final: 0.8267 (mmt) REVERT: F 263 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: F 281 TYR cc_start: 0.9237 (m-80) cc_final: 0.8943 (m-80) REVERT: F 282 GLN cc_start: 0.9411 (pm20) cc_final: 0.8384 (pm20) REVERT: F 288 ASP cc_start: 0.8003 (m-30) cc_final: 0.7444 (m-30) REVERT: F 349 ASP cc_start: 0.8770 (t0) cc_final: 0.8436 (t0) REVERT: F 356 ARG cc_start: 0.8720 (tpt90) cc_final: 0.8433 (tpp-160) REVERT: F 464 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8141 (mt-10) REVERT: G 247 MET cc_start: 0.6940 (tpt) cc_final: 0.6365 (tpp) outliers start: 140 outliers final: 114 residues processed: 768 average time/residue: 0.3147 time to fit residues: 374.5404 Evaluate side-chains 825 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 704 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 251 THR Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 433 ASN Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 28 ASN Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 27 LEU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 ILE Chi-restraints excluded: chain C residue 177 LYS Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 440 THR Chi-restraints excluded: chain C residue 444 VAL Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 481 LEU Chi-restraints excluded: chain C residue 485 ILE Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 258 ILE Chi-restraints excluded: chain D residue 266 SER Chi-restraints excluded: chain D residue 287 THR Chi-restraints excluded: chain D residue 299 THR Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 440 SER Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 223 ASN Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 46 LEU Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 91 THR Chi-restraints excluded: chain F residue 133 ILE Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 208 ASN Chi-restraints excluded: chain F residue 239 ILE Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 266 SER Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 296 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 336 SER Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 437 THR Chi-restraints excluded: chain F residue 450 ASP Chi-restraints excluded: chain G residue 230 ILE Chi-restraints excluded: chain G residue 241 SER Chi-restraints excluded: chain G residue 252 SER Chi-restraints excluded: chain G residue 257 ARG Chi-restraints excluded: chain G residue 263 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 0.0470 chunk 280 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 273 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 246 optimal weight: 0.9990 chunk 258 optimal weight: 0.0870 chunk 272 optimal weight: 0.8980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 GLN A 433 ASN D 57 ASN E 24 HIS ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 127 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21978 Z= 0.175 Angle : 0.578 9.043 29983 Z= 0.296 Chirality : 0.044 0.175 3681 Planarity : 0.004 0.052 3859 Dihedral : 6.695 97.379 3423 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.95 % Allowed : 26.30 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.16), residues: 3044 helix: 0.68 (0.15), residues: 1205 sheet: -0.13 (0.24), residues: 475 loop : -0.02 (0.18), residues: 1364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 191 HIS 0.006 0.001 HIS E 24 PHE 0.031 0.001 PHE A 44 TYR 0.026 0.002 TYR E 242 ARG 0.007 0.000 ARG F 433 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 715 time to evaluate : 2.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 ASP cc_start: 0.8654 (p0) cc_final: 0.8453 (p0) REVERT: A 159 VAL cc_start: 0.9184 (t) cc_final: 0.8749 (m) REVERT: A 177 LYS cc_start: 0.9105 (mtmm) cc_final: 0.8831 (mtmm) REVERT: A 199 LYS cc_start: 0.8384 (mttt) cc_final: 0.7951 (mttm) REVERT: A 247 LEU cc_start: 0.9345 (mt) cc_final: 0.8889 (tp) REVERT: A 309 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7557 (mm-30) REVERT: A 399 TYR cc_start: 0.7897 (t80) cc_final: 0.7455 (t80) REVERT: A 473 TYR cc_start: 0.7405 (t80) cc_final: 0.7046 (t80) REVERT: A 506 PHE cc_start: 0.7057 (t80) cc_final: 0.6754 (m-80) REVERT: B 84 VAL cc_start: 0.8852 (t) cc_final: 0.8593 (p) REVERT: B 91 LYS cc_start: 0.8416 (mttt) cc_final: 0.8115 (mtpp) REVERT: B 192 ASN cc_start: 0.8847 (m-40) cc_final: 0.8606 (t0) REVERT: B 228 MET cc_start: 0.8873 (tpt) cc_final: 0.8490 (tpp) REVERT: B 349 ASP cc_start: 0.7794 (m-30) cc_final: 0.6974 (m-30) REVERT: B 448 TYR cc_start: 0.7838 (t80) cc_final: 0.7242 (t80) REVERT: B 480 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8581 (tm-30) REVERT: B 486 ARG cc_start: 0.8712 (ttt180) cc_final: 0.8402 (mtp85) REVERT: C 43 VAL cc_start: 0.9011 (m) cc_final: 0.8808 (p) REVERT: C 106 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8626 (mp) REVERT: C 142 ARG cc_start: 0.8474 (tmm-80) cc_final: 0.8220 (tmm-80) REVERT: C 153 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8314 (mtpp) REVERT: C 198 SER cc_start: 0.8734 (p) cc_final: 0.8414 (t) REVERT: C 220 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8178 (tp40) REVERT: C 223 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8833 (mm-30) REVERT: C 224 GLN cc_start: 0.8698 (tp40) cc_final: 0.8357 (tp40) REVERT: C 398 GLN cc_start: 0.8952 (mt0) cc_final: 0.8717 (mm-40) REVERT: C 425 ARG cc_start: 0.8864 (mtt90) cc_final: 0.7869 (mtt90) REVERT: D 12 LYS cc_start: 0.8530 (mptt) cc_final: 0.8019 (mtpp) REVERT: D 60 ARG cc_start: 0.6794 (ttm170) cc_final: 0.6543 (ttt180) REVERT: D 89 ARG cc_start: 0.8242 (mmt-90) cc_final: 0.6861 (ttp80) REVERT: D 90 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7302 (mm-30) REVERT: D 110 LYS cc_start: 0.8009 (mttt) cc_final: 0.7656 (mttp) REVERT: D 144 LEU cc_start: 0.8024 (mt) cc_final: 0.7732 (mt) REVERT: D 282 GLN cc_start: 0.9266 (pm20) cc_final: 0.8855 (pm20) REVERT: D 356 ARG cc_start: 0.7929 (ttt90) cc_final: 0.7578 (ttm-80) REVERT: D 368 TYR cc_start: 0.8452 (t80) cc_final: 0.8004 (t80) REVERT: D 373 LYS cc_start: 0.7865 (OUTLIER) cc_final: 0.7608 (tppt) REVERT: D 375 GLN cc_start: 0.8013 (mt0) cc_final: 0.7594 (tm-30) REVERT: D 458 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.4663 (t80) REVERT: E 9 ILE cc_start: 0.8620 (mt) cc_final: 0.8261 (mt) REVERT: E 128 SER cc_start: 0.9013 (t) cc_final: 0.8807 (p) REVERT: E 224 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8369 (mt-10) REVERT: E 352 ASP cc_start: 0.7701 (m-30) cc_final: 0.6002 (t70) REVERT: E 354 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7762 (tttm) REVERT: F 35 ASN cc_start: 0.8918 (m-40) cc_final: 0.8519 (m110) REVERT: F 56 GLU cc_start: 0.8304 (pm20) cc_final: 0.8043 (pm20) REVERT: F 191 THR cc_start: 0.9105 (m) cc_final: 0.8841 (p) REVERT: F 201 MET cc_start: 0.8652 (mmt) cc_final: 0.8153 (mmt) REVERT: F 263 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: F 282 GLN cc_start: 0.9330 (pm20) cc_final: 0.8295 (pm20) REVERT: F 288 ASP cc_start: 0.7891 (m-30) cc_final: 0.7301 (m-30) REVERT: F 356 ARG cc_start: 0.8630 (tpt90) cc_final: 0.8415 (tpp-160) REVERT: F 464 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8097 (mt-10) REVERT: G 247 MET cc_start: 0.7032 (tpt) cc_final: 0.6321 (tpp) outliers start: 78 outliers final: 58 residues processed: 757 average time/residue: 0.3210 time to fit residues: 374.0165 Evaluate side-chains 759 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 695 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 143 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 373 LYS Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain F residue 450 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 5.9990 chunk 288 optimal weight: 20.0000 chunk 176 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 302 optimal weight: 0.5980 chunk 278 optimal weight: 4.9990 chunk 241 optimal weight: 0.0770 chunk 25 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 ASN A 304 HIS B 479 ASN ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21978 Z= 0.186 Angle : 0.579 10.511 29983 Z= 0.293 Chirality : 0.043 0.177 3681 Planarity : 0.005 0.051 3859 Dihedral : 6.520 98.166 3423 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.34 % Allowed : 26.71 % Favored : 69.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 3044 helix: 0.82 (0.16), residues: 1200 sheet: -0.05 (0.24), residues: 475 loop : 0.01 (0.18), residues: 1369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 191 HIS 0.004 0.001 HIS E 24 PHE 0.029 0.001 PHE A 466 TYR 0.026 0.001 TYR E 242 ARG 0.008 0.000 ARG B 32 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 702 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.8690 (mtt-85) cc_final: 0.8155 (mpt-90) REVERT: A 159 VAL cc_start: 0.9122 (t) cc_final: 0.8608 (m) REVERT: A 199 LYS cc_start: 0.8434 (mttt) cc_final: 0.7998 (mttm) REVERT: A 247 LEU cc_start: 0.9378 (mt) cc_final: 0.8861 (tp) REVERT: A 302 TYR cc_start: 0.8469 (t80) cc_final: 0.8032 (t80) REVERT: A 309 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7556 (mm-30) REVERT: A 399 TYR cc_start: 0.7925 (t80) cc_final: 0.7464 (t80) REVERT: B 84 VAL cc_start: 0.8826 (t) cc_final: 0.8607 (p) REVERT: B 91 LYS cc_start: 0.8402 (mttt) cc_final: 0.8093 (mtpp) REVERT: B 228 MET cc_start: 0.8829 (tpt) cc_final: 0.8474 (tpp) REVERT: B 349 ASP cc_start: 0.7683 (m-30) cc_final: 0.6938 (m-30) REVERT: B 448 TYR cc_start: 0.7827 (t80) cc_final: 0.7229 (t80) REVERT: B 480 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8474 (tm-30) REVERT: B 486 ARG cc_start: 0.8733 (ttt180) cc_final: 0.8474 (mtp85) REVERT: C 43 VAL cc_start: 0.9013 (m) cc_final: 0.8802 (p) REVERT: C 142 ARG cc_start: 0.8501 (tmm-80) cc_final: 0.8226 (tmm-80) REVERT: C 153 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8355 (mtpp) REVERT: C 198 SER cc_start: 0.8628 (p) cc_final: 0.8389 (t) REVERT: C 220 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7968 (tp40) REVERT: C 223 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8789 (mm-30) REVERT: C 224 GLN cc_start: 0.8710 (tp40) cc_final: 0.8353 (tp40) REVERT: C 398 GLN cc_start: 0.8951 (mt0) cc_final: 0.8724 (mm-40) REVERT: C 425 ARG cc_start: 0.8812 (mtt90) cc_final: 0.7924 (mtt90) REVERT: D 12 LYS cc_start: 0.8470 (mptt) cc_final: 0.8008 (mtpp) REVERT: D 89 ARG cc_start: 0.8300 (mmt-90) cc_final: 0.6899 (ttp80) REVERT: D 90 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7169 (mm-30) REVERT: D 110 LYS cc_start: 0.7939 (mttt) cc_final: 0.7575 (mttp) REVERT: D 144 LEU cc_start: 0.8024 (mt) cc_final: 0.7716 (mt) REVERT: D 168 GLN cc_start: 0.8916 (mt0) cc_final: 0.8706 (tt0) REVERT: D 282 GLN cc_start: 0.9251 (pm20) cc_final: 0.8805 (pm20) REVERT: D 356 ARG cc_start: 0.7935 (ttt90) cc_final: 0.7575 (ttm-80) REVERT: D 368 TYR cc_start: 0.8520 (t80) cc_final: 0.8029 (t80) REVERT: D 375 GLN cc_start: 0.8092 (mt0) cc_final: 0.7650 (tm-30) REVERT: D 458 TYR cc_start: 0.6084 (OUTLIER) cc_final: 0.4721 (t80) REVERT: E 9 ILE cc_start: 0.8632 (mt) cc_final: 0.8260 (mt) REVERT: E 128 SER cc_start: 0.9012 (t) cc_final: 0.8794 (p) REVERT: E 224 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8386 (mt-10) REVERT: E 352 ASP cc_start: 0.7665 (m-30) cc_final: 0.5919 (t70) REVERT: E 354 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7797 (tttm) REVERT: F 35 ASN cc_start: 0.8910 (m-40) cc_final: 0.8382 (m-40) REVERT: F 56 GLU cc_start: 0.8452 (pm20) cc_final: 0.8189 (pm20) REVERT: F 191 THR cc_start: 0.9107 (m) cc_final: 0.8850 (p) REVERT: F 201 MET cc_start: 0.8649 (mmt) cc_final: 0.8167 (mmt) REVERT: F 263 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8642 (tt0) REVERT: F 281 TYR cc_start: 0.9050 (m-80) cc_final: 0.8749 (m-80) REVERT: F 282 GLN cc_start: 0.9339 (pm20) cc_final: 0.8365 (pm20) REVERT: F 288 ASP cc_start: 0.7864 (m-30) cc_final: 0.7292 (m-30) REVERT: F 356 ARG cc_start: 0.8602 (tpt90) cc_final: 0.8337 (tpp-160) REVERT: F 464 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8176 (mt-10) REVERT: G 11 LYS cc_start: 0.8155 (mttt) cc_final: 0.7834 (mttm) REVERT: G 247 MET cc_start: 0.7060 (tpt) cc_final: 0.6387 (tpp) outliers start: 66 outliers final: 56 residues processed: 733 average time/residue: 0.3162 time to fit residues: 357.6632 Evaluate side-chains 747 residues out of total 2492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 687 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 40 ILE Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 360 TYR Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 132 GLN Chi-restraints excluded: chain C residue 145 HIS Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 153 LYS Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 220 GLN Chi-restraints excluded: chain C residue 251 THR Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 367 ILE Chi-restraints excluded: chain C residue 452 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 136 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 326 PHE Chi-restraints excluded: chain D residue 329 LEU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 458 TYR Chi-restraints excluded: chain E residue 17 ILE Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 174 ILE Chi-restraints excluded: chain E residue 232 VAL Chi-restraints excluded: chain E residue 251 VAL Chi-restraints excluded: chain E residue 266 SER Chi-restraints excluded: chain E residue 299 THR Chi-restraints excluded: chain E residue 358 LEU Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 155 LEU Chi-restraints excluded: chain F residue 262 THR Chi-restraints excluded: chain F residue 263 GLN Chi-restraints excluded: chain F residue 269 SER Chi-restraints excluded: chain F residue 310 VAL Chi-restraints excluded: chain F residue 387 ILE Chi-restraints excluded: chain F residue 415 SER Chi-restraints excluded: chain G residue 252 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 5.9990 chunk 256 optimal weight: 5.9990 chunk 73 optimal weight: 0.0370 chunk 222 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 241 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.0062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 HIS ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.136827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.119424 restraints weight = 35870.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.122774 restraints weight = 19119.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.125015 restraints weight = 11662.968| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.3735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21978 Z= 0.207 Angle : 0.583 8.458 29983 Z= 0.298 Chirality : 0.044 0.181 3681 Planarity : 0.005 0.061 3859 Dihedral : 6.568 99.585 3423 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.44 % Allowed : 27.06 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.58 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.16), residues: 3044 helix: 0.79 (0.15), residues: 1205 sheet: -0.03 (0.24), residues: 473 loop : 0.01 (0.18), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 258 HIS 0.003 0.001 HIS F 328 PHE 0.017 0.001 PHE C 470 TYR 0.033 0.002 TYR E 242 ARG 0.015 0.000 ARG B 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6159.02 seconds wall clock time: 110 minutes 3.32 seconds (6603.32 seconds total)