Starting phenix.real_space_refine on Fri Sep 27 10:19:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bc7_44426/09_2024/9bc7_44426.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bc7_44426/09_2024/9bc7_44426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bc7_44426/09_2024/9bc7_44426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bc7_44426/09_2024/9bc7_44426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bc7_44426/09_2024/9bc7_44426.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bc7_44426/09_2024/9bc7_44426.cif" } resolution = 3.3 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 112 5.16 5 C 10248 2.51 5 N 2624 2.21 5 O 2640 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15628 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 3828 Classifications: {'peptide': 506} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 16, 'TRANS': 489} Chain breaks: 1 Unresolved non-hydrogen bonds: 321 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 2, 'ASP:plan': 15, 'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 173 Chain: "A" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 79 Unusual residues: {'PCW': 3} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PCW:plan-1': 2, 'PCW:plan-3': 2, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 22 Restraints were copied for chains: C, B, D Time building chain proxies: 8.40, per 1000 atoms: 0.54 Number of scatterers: 15628 At special positions: 0 Unit cell: (115.838, 115.838, 127.747, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 112 16.00 P 4 15.00 O 2640 8.00 N 2624 7.00 C 10248 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 - 3.00 Amino acid : True - 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: 3.67 Conformation dependent library (CDL) restraints added in 2.1 seconds 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3856 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 8 sheets defined 72.0% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.964A pdb=" N PHE A 98 " --> pdb=" O MET A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 removed outlier: 3.557A pdb=" N LEU A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.705A pdb=" N LYS A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 166 removed outlier: 3.712A pdb=" N GLY A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Proline residue: A 161 - end of helix Processing helix chain 'A' and resid 172 through 194 removed outlier: 3.636A pdb=" N VAL A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE A 186 " --> pdb=" O SER A 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 219 removed outlier: 3.574A pdb=" N MET A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 219 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 241 through 242 No H-bonds generated for 'chain 'A' and resid 241 through 242' Processing helix chain 'A' and resid 252 through 252 No H-bonds generated for 'chain 'A' and resid 252 through 252' Processing helix chain 'A' and resid 253 through 265 removed outlier: 4.163A pdb=" N VAL A 257 " --> pdb=" O ALA A 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 265 " --> pdb=" O LYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 290 removed outlier: 3.922A pdb=" N GLU A 283 " --> pdb=" O HIS A 279 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 323 removed outlier: 3.738A pdb=" N GLY A 303 " --> pdb=" O PHE A 299 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE A 317 " --> pdb=" O GLY A 313 " (cutoff:3.500A) Proline residue: A 320 - end of helix Processing helix chain 'A' and resid 329 through 334 Processing helix chain 'A' and resid 340 through 357 Processing helix chain 'A' and resid 368 through 401 removed outlier: 3.589A pdb=" N MET A 388 " --> pdb=" O THR A 384 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP A 401 " --> pdb=" O ILE A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 421 removed outlier: 3.701A pdb=" N GLN A 413 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 415 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 440 Processing helix chain 'A' and resid 445 through 453 removed outlier: 4.032A pdb=" N ASN A 451 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 452 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 480 through 489 removed outlier: 3.504A pdb=" N ALA A 486 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 546 removed outlier: 4.239A pdb=" N LEU A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 576 removed outlier: 3.942A pdb=" N GLU A 575 " --> pdb=" O GLU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 594 removed outlier: 4.057A pdb=" N ARG A 580 " --> pdb=" O TYR A 576 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 581 " --> pdb=" O PRO A 577 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP A 589 " --> pdb=" O THR A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 606 removed outlier: 3.516A pdb=" N LEU A 602 " --> pdb=" O ASN A 598 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN A 606 " --> pdb=" O LEU A 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 107 through 115 removed outlier: 3.557A pdb=" N LEU B 111 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.705A pdb=" N LYS B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 166 removed outlier: 3.712A pdb=" N GLY B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Proline residue: B 161 - end of helix Processing helix chain 'B' and resid 172 through 194 removed outlier: 3.635A pdb=" N VAL B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 219 removed outlier: 3.574A pdb=" N MET B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 219 " --> pdb=" O MET B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 228 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 241 through 242 No H-bonds generated for 'chain 'B' and resid 241 through 242' Processing helix chain 'B' and resid 252 through 252 No H-bonds generated for 'chain 'B' and resid 252 through 252' Processing helix chain 'B' and resid 253 through 265 removed outlier: 4.163A pdb=" N VAL B 257 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 269 Processing helix chain 'B' and resid 270 through 290 removed outlier: 3.922A pdb=" N GLU B 283 " --> pdb=" O HIS B 279 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 284 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP B 290 " --> pdb=" O HIS B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 323 removed outlier: 3.737A pdb=" N GLY B 303 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) Proline residue: B 320 - end of helix Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 357 Processing helix chain 'B' and resid 368 through 401 removed outlier: 3.588A pdb=" N MET B 388 " --> pdb=" O THR B 384 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 421 removed outlier: 3.701A pdb=" N GLN B 413 " --> pdb=" O GLU B 409 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU B 415 " --> pdb=" O TYR B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 440 Processing helix chain 'B' and resid 445 through 453 removed outlier: 4.031A pdb=" N ASN B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 452 " --> pdb=" O ASN B 448 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 453 " --> pdb=" O ILE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 465 Processing helix chain 'B' and resid 466 through 473 Processing helix chain 'B' and resid 480 through 489 removed outlier: 3.503A pdb=" N ALA B 486 " --> pdb=" O ASN B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 546 removed outlier: 4.239A pdb=" N LEU B 543 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 576 removed outlier: 3.942A pdb=" N GLU B 575 " --> pdb=" O GLU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 594 removed outlier: 4.057A pdb=" N ARG B 580 " --> pdb=" O TYR B 576 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASP B 589 " --> pdb=" O THR B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 606 removed outlier: 3.516A pdb=" N LEU B 602 " --> pdb=" O ASN B 598 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN B 606 " --> pdb=" O LEU B 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 100 Processing helix chain 'C' and resid 107 through 115 removed outlier: 3.557A pdb=" N LEU C 111 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.706A pdb=" N LYS C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 166 removed outlier: 3.712A pdb=" N GLY C 155 " --> pdb=" O ILE C 151 " (cutoff:3.500A) Proline residue: C 161 - end of helix Processing helix chain 'C' and resid 172 through 194 removed outlier: 3.637A pdb=" N VAL C 185 " --> pdb=" O ALA C 181 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE C 186 " --> pdb=" O SER C 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 219 removed outlier: 3.574A pdb=" N MET C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 218 " --> pdb=" O LYS C 214 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS C 219 " --> pdb=" O MET C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 228 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 241 through 242 No H-bonds generated for 'chain 'C' and resid 241 through 242' Processing helix chain 'C' and resid 252 through 252 No H-bonds generated for 'chain 'C' and resid 252 through 252' Processing helix chain 'C' and resid 253 through 265 removed outlier: 4.163A pdb=" N VAL C 257 " --> pdb=" O ALA C 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG C 258 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 269 Processing helix chain 'C' and resid 270 through 290 removed outlier: 3.922A pdb=" N GLU C 283 " --> pdb=" O HIS C 279 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 284 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP C 290 " --> pdb=" O HIS C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 323 removed outlier: 3.738A pdb=" N GLY C 303 " --> pdb=" O PHE C 299 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE C 317 " --> pdb=" O GLY C 313 " (cutoff:3.500A) Proline residue: C 320 - end of helix Processing helix chain 'C' and resid 329 through 334 Processing helix chain 'C' and resid 340 through 357 Processing helix chain 'C' and resid 368 through 401 removed outlier: 3.589A pdb=" N MET C 388 " --> pdb=" O THR C 384 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP C 401 " --> pdb=" O ILE C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 421 removed outlier: 3.701A pdb=" N GLN C 413 " --> pdb=" O GLU C 409 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU C 415 " --> pdb=" O TYR C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 440 Processing helix chain 'C' and resid 445 through 453 removed outlier: 4.032A pdb=" N ASN C 451 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 452 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 465 Processing helix chain 'C' and resid 466 through 473 Processing helix chain 'C' and resid 480 through 489 removed outlier: 3.504A pdb=" N ALA C 486 " --> pdb=" O ASN C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 546 removed outlier: 4.239A pdb=" N LEU C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 576 removed outlier: 3.942A pdb=" N GLU C 575 " --> pdb=" O GLU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 594 removed outlier: 4.057A pdb=" N ARG C 580 " --> pdb=" O TYR C 576 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG C 581 " --> pdb=" O PRO C 577 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP C 589 " --> pdb=" O THR C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 606 removed outlier: 3.515A pdb=" N LEU C 602 " --> pdb=" O ASN C 598 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLN C 606 " --> pdb=" O LEU C 602 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 107 through 115 removed outlier: 3.557A pdb=" N LEU D 111 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.706A pdb=" N LYS D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 166 removed outlier: 3.712A pdb=" N GLY D 155 " --> pdb=" O ILE D 151 " (cutoff:3.500A) Proline residue: D 161 - end of helix Processing helix chain 'D' and resid 172 through 194 removed outlier: 3.636A pdb=" N VAL D 185 " --> pdb=" O ALA D 181 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N PHE D 186 " --> pdb=" O SER D 182 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N PHE D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 219 removed outlier: 3.573A pdb=" N MET D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS D 219 " --> pdb=" O MET D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 228 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 241 through 242 No H-bonds generated for 'chain 'D' and resid 241 through 242' Processing helix chain 'D' and resid 252 through 252 No H-bonds generated for 'chain 'D' and resid 252 through 252' Processing helix chain 'D' and resid 253 through 265 removed outlier: 4.162A pdb=" N VAL D 257 " --> pdb=" O ALA D 253 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 258 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU D 265 " --> pdb=" O LYS D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 269 Processing helix chain 'D' and resid 270 through 290 removed outlier: 3.922A pdb=" N GLU D 283 " --> pdb=" O HIS D 279 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE D 284 " --> pdb=" O GLN D 280 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 323 removed outlier: 3.738A pdb=" N GLY D 303 " --> pdb=" O PHE D 299 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE D 317 " --> pdb=" O GLY D 313 " (cutoff:3.500A) Proline residue: D 320 - end of helix Processing helix chain 'D' and resid 329 through 334 Processing helix chain 'D' and resid 340 through 357 Processing helix chain 'D' and resid 368 through 401 removed outlier: 3.588A pdb=" N MET D 388 " --> pdb=" O THR D 384 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP D 401 " --> pdb=" O ILE D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 421 removed outlier: 3.700A pdb=" N GLN D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 415 " --> pdb=" O TYR D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 440 Processing helix chain 'D' and resid 445 through 453 removed outlier: 4.032A pdb=" N ASN D 451 " --> pdb=" O GLU D 447 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU D 452 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU D 453 " --> pdb=" O ILE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 465 Processing helix chain 'D' and resid 466 through 473 Processing helix chain 'D' and resid 480 through 489 removed outlier: 3.504A pdb=" N ALA D 486 " --> pdb=" O ASN D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 546 removed outlier: 4.239A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 576 removed outlier: 3.942A pdb=" N GLU D 575 " --> pdb=" O GLU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 594 removed outlier: 4.057A pdb=" N ARG D 580 " --> pdb=" O TYR D 576 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG D 581 " --> pdb=" O PRO D 577 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP D 589 " --> pdb=" O THR D 585 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 606 removed outlier: 3.516A pdb=" N LEU D 602 " --> pdb=" O ASN D 598 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN D 606 " --> pdb=" O LEU D 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 492 through 496 removed outlier: 6.668A pdb=" N ARG A 560 " --> pdb=" O GLN A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 501 through 503 removed outlier: 6.520A pdb=" N VAL A 553 " --> pdb=" O ILE A 502 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A 530 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 492 through 496 removed outlier: 6.668A pdb=" N ARG B 560 " --> pdb=" O GLN B 516 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 501 through 503 removed outlier: 6.521A pdb=" N VAL B 553 " --> pdb=" O ILE B 502 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET B 530 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 492 through 496 removed outlier: 6.668A pdb=" N ARG C 560 " --> pdb=" O GLN C 516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 501 through 503 removed outlier: 6.520A pdb=" N VAL C 553 " --> pdb=" O ILE C 502 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET C 530 " --> pdb=" O VAL C 522 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 492 through 496 removed outlier: 6.668A pdb=" N ARG D 560 " --> pdb=" O GLN D 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 501 through 503 removed outlier: 6.520A pdb=" N VAL D 553 " --> pdb=" O ILE D 502 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET D 530 " --> pdb=" O VAL D 522 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2856 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: 4.57 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2376 1.29 - 1.42: 4488 1.42 - 1.55: 8931 1.55 - 1.68: 17 1.68 - 1.82: 196 Bond restraints: 16008 Sorted by residual: bond pdb=" C4 CMP D 704 " pdb=" C5 CMP D 704 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" C4 CMP B 704 " pdb=" C5 CMP B 704 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" C4 CMP A 704 " pdb=" C5 CMP A 704 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" C4 CMP C 704 " pdb=" C5 CMP C 704 " ideal model delta sigma weight residual 1.490 1.342 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" CA ARG A 405 " pdb=" C ARG A 405 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.26e-02 6.30e+03 4.54e+01 ... (remaining 16003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 17404 2.27 - 4.54: 3907 4.54 - 6.80: 337 6.80 - 9.07: 48 9.07 - 11.34: 16 Bond angle restraints: 21712 Sorted by residual: angle pdb=" N PHE D 143 " pdb=" CA PHE D 143 " pdb=" C PHE D 143 " ideal model delta sigma weight residual 111.36 117.74 -6.38 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N PHE C 143 " pdb=" CA PHE C 143 " pdb=" C PHE C 143 " ideal model delta sigma weight residual 111.36 117.73 -6.37 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N PHE A 143 " pdb=" CA PHE A 143 " pdb=" C PHE A 143 " ideal model delta sigma weight residual 111.36 117.73 -6.37 1.09e+00 8.42e-01 3.42e+01 angle pdb=" N PHE B 143 " pdb=" CA PHE B 143 " pdb=" C PHE B 143 " ideal model delta sigma weight residual 111.36 117.72 -6.36 1.09e+00 8.42e-01 3.41e+01 angle pdb=" N VAL C 508 " pdb=" CA VAL C 508 " pdb=" C VAL C 508 " ideal model delta sigma weight residual 108.27 116.06 -7.79 1.37e+00 5.33e-01 3.23e+01 ... (remaining 21707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.27: 9160 30.27 - 60.55: 204 60.55 - 90.82: 16 90.82 - 121.09: 4 121.09 - 151.37: 12 Dihedral angle restraints: 9396 sinusoidal: 3436 harmonic: 5960 Sorted by residual: dihedral pdb=" C5' CMP D 704 " pdb=" O5' CMP D 704 " pdb=" P CMP D 704 " pdb=" O1P CMP D 704 " ideal model delta sinusoidal sigma weight residual 60.00 -173.53 -126.47 1 2.00e+01 2.50e-03 3.83e+01 dihedral pdb=" C5' CMP A 704 " pdb=" O5' CMP A 704 " pdb=" P CMP A 704 " pdb=" O1P CMP A 704 " ideal model delta sinusoidal sigma weight residual 60.00 -173.56 -126.44 1 2.00e+01 2.50e-03 3.83e+01 dihedral pdb=" C5' CMP B 704 " pdb=" O5' CMP B 704 " pdb=" P CMP B 704 " pdb=" O1P CMP B 704 " ideal model delta sinusoidal sigma weight residual 60.00 -173.59 -126.41 1 2.00e+01 2.50e-03 3.82e+01 ... (remaining 9393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1764 0.095 - 0.191: 535 0.191 - 0.286: 105 0.286 - 0.381: 24 0.381 - 0.476: 12 Chirality restraints: 2440 Sorted by residual: chirality pdb=" CA ARG B 438 " pdb=" N ARG B 438 " pdb=" C ARG B 438 " pdb=" CB ARG B 438 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CA ARG D 438 " pdb=" N ARG D 438 " pdb=" C ARG D 438 " pdb=" CB ARG D 438 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CA ARG A 438 " pdb=" N ARG A 438 " pdb=" C ARG A 438 " pdb=" CB ARG A 438 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 2437 not shown) Planarity restraints: 2716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 347 " 0.100 2.00e-02 2.50e+03 5.34e-02 5.71e+01 pdb=" CG TYR C 347 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR C 347 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR C 347 " -0.045 2.00e-02 2.50e+03 pdb=" CE1 TYR C 347 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR C 347 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR C 347 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 347 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 347 " 0.100 2.00e-02 2.50e+03 5.33e-02 5.68e+01 pdb=" CG TYR A 347 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 347 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR A 347 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR A 347 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 347 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR A 347 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 347 " 0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 347 " 0.100 2.00e-02 2.50e+03 5.33e-02 5.67e+01 pdb=" CG TYR D 347 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR D 347 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR D 347 " -0.044 2.00e-02 2.50e+03 pdb=" CE1 TYR D 347 " -0.025 2.00e-02 2.50e+03 pdb=" CE2 TYR D 347 " -0.029 2.00e-02 2.50e+03 pdb=" CZ TYR D 347 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 347 " 0.077 2.00e-02 2.50e+03 ... (remaining 2713 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 652 2.75 - 3.29: 15715 3.29 - 3.82: 22632 3.82 - 4.36: 28903 4.36 - 4.90: 48617 Nonbonded interactions: 116519 Sorted by model distance: nonbonded pdb=" OD2 ASP B 401 " pdb=" CD ARG C 297 " model vdw 2.210 3.440 nonbonded pdb=" OD2 ASP A 401 " pdb=" CD ARG B 297 " model vdw 2.215 3.440 nonbonded pdb=" CD ARG A 297 " pdb=" OD2 ASP D 401 " model vdw 2.218 3.440 nonbonded pdb=" OD2 ASP C 401 " pdb=" CD ARG D 297 " model vdw 2.225 3.440 nonbonded pdb=" O ALA D 507 " pdb=" CD ARG D 548 " model vdw 2.459 3.440 ... (remaining 116514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 34.730 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 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 : 0.015 0.148 16008 Z= 0.973 Angle : 1.832 11.341 21712 Z= 1.222 Chirality : 0.098 0.476 2440 Planarity : 0.013 0.100 2716 Dihedral : 14.652 151.368 5540 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.55 % Allowed : 1.59 % Favored : 97.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.16), residues: 2008 helix: -1.31 (0.12), residues: 1360 sheet: 2.25 (0.39), residues: 112 loop : -0.72 (0.24), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.014 TRP B 311 HIS 0.010 0.004 HIS B 421 PHE 0.037 0.009 PHE D 141 TYR 0.100 0.018 TYR C 347 ARG 0.008 0.001 ARG B 549 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 461 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 GLN cc_start: 0.5760 (mt0) cc_final: 0.5377 (tt0) REVERT: A 140 ASP cc_start: 0.7275 (m-30) cc_final: 0.6849 (m-30) REVERT: A 144 TYR cc_start: 0.6543 (m-10) cc_final: 0.6300 (m-80) REVERT: A 281 TRP cc_start: 0.5863 (t60) cc_final: 0.5267 (t60) REVERT: A 343 LYS cc_start: 0.7183 (tppp) cc_final: 0.6462 (tptt) REVERT: A 347 TYR cc_start: 0.6922 (t80) cc_final: 0.5660 (t80) REVERT: A 351 LYS cc_start: 0.7230 (ttmm) cc_final: 0.6930 (tttm) REVERT: A 361 TYR cc_start: 0.6992 (OUTLIER) cc_final: 0.5454 (m-80) REVERT: A 367 VAL cc_start: 0.8659 (t) cc_final: 0.8366 (m) REVERT: A 426 ASP cc_start: 0.7430 (p0) cc_final: 0.7147 (t0) REVERT: A 430 LYS cc_start: 0.7146 (mtpt) cc_final: 0.6832 (mtpp) REVERT: A 433 ASP cc_start: 0.7663 (t70) cc_final: 0.7430 (t0) REVERT: A 451 ASN cc_start: 0.7767 (t0) cc_final: 0.7293 (m110) REVERT: A 494 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7231 (mt-10) REVERT: A 501 TYR cc_start: 0.8367 (m-80) cc_final: 0.8133 (m-80) REVERT: A 511 LYS cc_start: 0.7876 (mttt) cc_final: 0.7256 (mtmt) REVERT: A 554 ARG cc_start: 0.7700 (ttp-170) cc_final: 0.7409 (ttp-110) REVERT: B 117 GLN cc_start: 0.5683 (mt0) cc_final: 0.5282 (tt0) REVERT: B 123 GLU cc_start: 0.5935 (tp30) cc_final: 0.5557 (tp30) REVERT: B 140 ASP cc_start: 0.7183 (m-30) cc_final: 0.6771 (m-30) REVERT: B 144 TYR cc_start: 0.6603 (m-10) cc_final: 0.6365 (m-80) REVERT: B 281 TRP cc_start: 0.5878 (t60) cc_final: 0.5258 (t60) REVERT: B 343 LYS cc_start: 0.7188 (tppp) cc_final: 0.6465 (tptt) REVERT: B 347 TYR cc_start: 0.6864 (t80) cc_final: 0.5659 (t80) REVERT: B 361 TYR cc_start: 0.6993 (OUTLIER) cc_final: 0.5452 (m-80) REVERT: B 367 VAL cc_start: 0.8653 (t) cc_final: 0.8353 (m) REVERT: B 426 ASP cc_start: 0.7435 (p0) cc_final: 0.7141 (t0) REVERT: B 430 LYS cc_start: 0.7097 (mtpt) cc_final: 0.6791 (mtpp) REVERT: B 432 HIS cc_start: 0.7058 (t70) cc_final: 0.6855 (t70) REVERT: B 433 ASP cc_start: 0.7651 (t70) cc_final: 0.7404 (t0) REVERT: B 436 GLU cc_start: 0.7393 (mt-10) cc_final: 0.7078 (mm-30) REVERT: B 451 ASN cc_start: 0.7761 (t0) cc_final: 0.7304 (m110) REVERT: B 494 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7102 (mt-10) REVERT: B 501 TYR cc_start: 0.8384 (m-80) cc_final: 0.8139 (m-80) REVERT: B 511 LYS cc_start: 0.7925 (mttt) cc_final: 0.7393 (mtmt) REVERT: B 554 ARG cc_start: 0.7722 (ttp-170) cc_final: 0.7425 (ttp-110) REVERT: C 117 GLN cc_start: 0.5694 (mt0) cc_final: 0.5287 (tt0) REVERT: C 123 GLU cc_start: 0.5951 (tp30) cc_final: 0.5574 (tp30) REVERT: C 140 ASP cc_start: 0.7199 (m-30) cc_final: 0.6770 (m-30) REVERT: C 144 TYR cc_start: 0.6574 (m-10) cc_final: 0.6330 (m-80) REVERT: C 281 TRP cc_start: 0.5887 (t60) cc_final: 0.5289 (t60) REVERT: C 343 LYS cc_start: 0.7180 (tppp) cc_final: 0.6462 (tptt) REVERT: C 347 TYR cc_start: 0.6866 (t80) cc_final: 0.5671 (t80) REVERT: C 361 TYR cc_start: 0.7048 (OUTLIER) cc_final: 0.5464 (m-80) REVERT: C 367 VAL cc_start: 0.8660 (t) cc_final: 0.8352 (m) REVERT: C 426 ASP cc_start: 0.7426 (p0) cc_final: 0.7149 (t0) REVERT: C 430 LYS cc_start: 0.7154 (mtpt) cc_final: 0.6809 (mtpp) REVERT: C 432 HIS cc_start: 0.6982 (t70) cc_final: 0.6728 (t70) REVERT: C 433 ASP cc_start: 0.7658 (t70) cc_final: 0.7405 (t0) REVERT: C 436 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7093 (mm-30) REVERT: C 451 ASN cc_start: 0.7753 (t0) cc_final: 0.7296 (m110) REVERT: C 494 GLU cc_start: 0.7747 (mt-10) cc_final: 0.6933 (mt-10) REVERT: C 501 TYR cc_start: 0.8388 (m-80) cc_final: 0.8142 (m-80) REVERT: C 511 LYS cc_start: 0.7903 (mttt) cc_final: 0.7379 (mtmt) REVERT: C 517 HIS cc_start: 0.6444 (t70) cc_final: 0.6219 (t70) REVERT: C 554 ARG cc_start: 0.7709 (ttp-170) cc_final: 0.7419 (ttp-110) REVERT: D 117 GLN cc_start: 0.5745 (mt0) cc_final: 0.5361 (tt0) REVERT: D 123 GLU cc_start: 0.5588 (tp30) cc_final: 0.5215 (tp30) REVERT: D 140 ASP cc_start: 0.7286 (m-30) cc_final: 0.6896 (m-30) REVERT: D 144 TYR cc_start: 0.6445 (m-10) cc_final: 0.6219 (m-80) REVERT: D 281 TRP cc_start: 0.5881 (t60) cc_final: 0.5258 (t60) REVERT: D 297 ARG cc_start: 0.4764 (mtp85) cc_final: 0.4461 (mtp85) REVERT: D 343 LYS cc_start: 0.7180 (tppp) cc_final: 0.6459 (tptt) REVERT: D 347 TYR cc_start: 0.6866 (t80) cc_final: 0.5664 (t80) REVERT: D 351 LYS cc_start: 0.7237 (ttmm) cc_final: 0.6943 (tttm) REVERT: D 353 MET cc_start: 0.7961 (ptp) cc_final: 0.7759 (ptm) REVERT: D 361 TYR cc_start: 0.7075 (OUTLIER) cc_final: 0.5583 (m-80) REVERT: D 367 VAL cc_start: 0.8644 (t) cc_final: 0.8339 (m) REVERT: D 426 ASP cc_start: 0.7391 (p0) cc_final: 0.7113 (t0) REVERT: D 430 LYS cc_start: 0.7155 (mtpt) cc_final: 0.6802 (mtpp) REVERT: D 432 HIS cc_start: 0.7107 (t70) cc_final: 0.6893 (t70) REVERT: D 433 ASP cc_start: 0.7669 (t70) cc_final: 0.7419 (t0) REVERT: D 436 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7097 (mm-30) REVERT: D 451 ASN cc_start: 0.7757 (t0) cc_final: 0.7290 (m110) REVERT: D 494 GLU cc_start: 0.7741 (mt-10) cc_final: 0.6934 (mt-10) REVERT: D 501 TYR cc_start: 0.8374 (m-80) cc_final: 0.8151 (m-80) REVERT: D 511 LYS cc_start: 0.7922 (mttt) cc_final: 0.7379 (mtmt) REVERT: D 554 ARG cc_start: 0.7715 (ttp-170) cc_final: 0.7416 (ttp-110) outliers start: 8 outliers final: 0 residues processed: 469 average time/residue: 0.2946 time to fit residues: 195.6207 Evaluate side-chains 354 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 350 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain D residue 361 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 95 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 HIS A 355 HIS A 440 GLN A 482 ASN B 286 HIS B 355 HIS B 440 GLN B 482 ASN C 286 HIS C 355 HIS C 440 GLN C 482 ASN D 286 HIS D 355 HIS D 440 GLN D 482 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6267 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16008 Z= 0.264 Angle : 0.694 11.363 21712 Z= 0.363 Chirality : 0.044 0.140 2440 Planarity : 0.004 0.033 2716 Dihedral : 14.198 148.306 2412 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.12 % Allowed : 7.06 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2008 helix: 0.57 (0.14), residues: 1352 sheet: 2.04 (0.39), residues: 112 loop : -0.62 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 281 HIS 0.009 0.002 HIS D 355 PHE 0.015 0.002 PHE D 236 TYR 0.014 0.002 TYR C 576 ARG 0.005 0.001 ARG C 404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 348 time to evaluate : 1.719 Fit side-chains REVERT: A 113 MET cc_start: 0.6376 (mmp) cc_final: 0.6170 (mmm) REVERT: A 117 GLN cc_start: 0.5653 (mt0) cc_final: 0.4324 (tp-100) REVERT: A 123 GLU cc_start: 0.5837 (tp30) cc_final: 0.5414 (tp30) REVERT: A 144 TYR cc_start: 0.6216 (m-10) cc_final: 0.5774 (m-10) REVERT: A 343 LYS cc_start: 0.6544 (tppp) cc_final: 0.5989 (tptp) REVERT: A 367 VAL cc_start: 0.8720 (t) cc_final: 0.8510 (m) REVERT: A 404 ARG cc_start: 0.7296 (tpp80) cc_final: 0.7004 (tpp80) REVERT: A 409 GLU cc_start: 0.6826 (tt0) cc_final: 0.6564 (mt-10) REVERT: A 451 ASN cc_start: 0.7455 (t0) cc_final: 0.7132 (m-40) REVERT: A 473 MET cc_start: 0.7619 (ttm) cc_final: 0.7200 (ttm) REVERT: A 494 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7463 (mt-10) REVERT: A 517 HIS cc_start: 0.6722 (t-170) cc_final: 0.6122 (t-90) REVERT: A 588 ILE cc_start: 0.7882 (tp) cc_final: 0.7545 (pt) REVERT: B 113 MET cc_start: 0.6405 (mmp) cc_final: 0.6191 (mmm) REVERT: B 117 GLN cc_start: 0.5646 (mt0) cc_final: 0.4308 (tp-100) REVERT: B 123 GLU cc_start: 0.5837 (tp30) cc_final: 0.5436 (tp30) REVERT: B 144 TYR cc_start: 0.6207 (m-10) cc_final: 0.5746 (m-10) REVERT: B 343 LYS cc_start: 0.6554 (tppp) cc_final: 0.5997 (tptp) REVERT: B 367 VAL cc_start: 0.8716 (t) cc_final: 0.8497 (m) REVERT: B 404 ARG cc_start: 0.7303 (tpp80) cc_final: 0.7018 (tpp80) REVERT: B 409 GLU cc_start: 0.6806 (tt0) cc_final: 0.6548 (mt-10) REVERT: B 433 ASP cc_start: 0.7339 (t70) cc_final: 0.7130 (t0) REVERT: B 451 ASN cc_start: 0.7441 (t0) cc_final: 0.7168 (m-40) REVERT: B 473 MET cc_start: 0.7611 (ttm) cc_final: 0.7189 (ttm) REVERT: B 494 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7551 (mt-10) REVERT: B 517 HIS cc_start: 0.6727 (t-170) cc_final: 0.6125 (t-90) REVERT: B 588 ILE cc_start: 0.7867 (tp) cc_final: 0.7519 (pt) REVERT: C 113 MET cc_start: 0.6414 (mmp) cc_final: 0.6207 (mmm) REVERT: C 117 GLN cc_start: 0.5631 (mt0) cc_final: 0.4301 (tp-100) REVERT: C 123 GLU cc_start: 0.5826 (tp30) cc_final: 0.5424 (tp30) REVERT: C 144 TYR cc_start: 0.6211 (m-10) cc_final: 0.5679 (m-10) REVERT: C 343 LYS cc_start: 0.6538 (tppp) cc_final: 0.5987 (tptp) REVERT: C 367 VAL cc_start: 0.8713 (t) cc_final: 0.8492 (m) REVERT: C 409 GLU cc_start: 0.6822 (tt0) cc_final: 0.6563 (mt-10) REVERT: C 433 ASP cc_start: 0.7334 (t70) cc_final: 0.7122 (t0) REVERT: C 451 ASN cc_start: 0.7553 (t0) cc_final: 0.7256 (m-40) REVERT: C 473 MET cc_start: 0.7611 (ttm) cc_final: 0.7203 (ttm) REVERT: C 494 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7506 (mt-10) REVERT: C 517 HIS cc_start: 0.6644 (t70) cc_final: 0.6106 (t-90) REVERT: C 588 ILE cc_start: 0.7873 (tp) cc_final: 0.7534 (pt) REVERT: D 113 MET cc_start: 0.6409 (mmp) cc_final: 0.6194 (mmm) REVERT: D 117 GLN cc_start: 0.5682 (mt0) cc_final: 0.4340 (tp-100) REVERT: D 123 GLU cc_start: 0.5835 (tp30) cc_final: 0.5461 (tp30) REVERT: D 144 TYR cc_start: 0.6206 (m-10) cc_final: 0.5747 (m-10) REVERT: D 343 LYS cc_start: 0.6548 (tppp) cc_final: 0.5989 (tptp) REVERT: D 367 VAL cc_start: 0.8733 (t) cc_final: 0.8515 (m) REVERT: D 404 ARG cc_start: 0.7301 (tpp80) cc_final: 0.7002 (tpp80) REVERT: D 409 GLU cc_start: 0.6815 (tt0) cc_final: 0.6549 (mt-10) REVERT: D 433 ASP cc_start: 0.7346 (t70) cc_final: 0.7134 (t0) REVERT: D 451 ASN cc_start: 0.7435 (t0) cc_final: 0.7160 (m-40) REVERT: D 473 MET cc_start: 0.7615 (ttm) cc_final: 0.7184 (ttm) REVERT: D 494 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7557 (mt-10) REVERT: D 517 HIS cc_start: 0.6719 (t-170) cc_final: 0.6111 (t-90) REVERT: D 588 ILE cc_start: 0.7884 (tp) cc_final: 0.7548 (pt) outliers start: 45 outliers final: 20 residues processed: 368 average time/residue: 0.2758 time to fit residues: 149.7351 Evaluate side-chains 312 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 292 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 179 ASN Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 179 ASN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 179 ASN Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 418 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 123 optimal weight: 0.0980 chunk 50 optimal weight: 20.0000 chunk 181 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 180 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 398 GLN A 437 HIS A 440 GLN A 463 ASN A 482 ASN B 156 ASN B 398 GLN B 440 GLN B 463 ASN B 482 ASN C 156 ASN C 398 GLN C 440 GLN C 463 ASN C 482 ASN D 156 ASN D 398 GLN D 440 GLN D 463 ASN D 482 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16008 Z= 0.173 Angle : 0.558 8.051 21712 Z= 0.291 Chirality : 0.041 0.129 2440 Planarity : 0.004 0.037 2716 Dihedral : 13.951 149.638 2412 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.22 % Allowed : 10.80 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.19), residues: 2008 helix: 1.04 (0.14), residues: 1376 sheet: 2.26 (0.40), residues: 112 loop : -0.54 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 281 HIS 0.005 0.001 HIS A 432 PHE 0.016 0.001 PHE A 236 TYR 0.013 0.001 TYR A 411 ARG 0.003 0.000 ARG C 554 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 305 time to evaluate : 1.634 Fit side-chains REVERT: A 117 GLN cc_start: 0.5523 (mt0) cc_final: 0.4233 (tp-100) REVERT: A 123 GLU cc_start: 0.5879 (tp30) cc_final: 0.5502 (tp30) REVERT: A 144 TYR cc_start: 0.6063 (m-10) cc_final: 0.5765 (m-10) REVERT: A 343 LYS cc_start: 0.6472 (tppp) cc_final: 0.5895 (tptp) REVERT: A 409 GLU cc_start: 0.6642 (tt0) cc_final: 0.6354 (mt-10) REVERT: A 451 ASN cc_start: 0.7426 (t0) cc_final: 0.7183 (m-40) REVERT: A 463 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.6992 (m-40) REVERT: A 494 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7505 (mt-10) REVERT: A 502 ILE cc_start: 0.7447 (mt) cc_final: 0.7242 (mt) REVERT: A 517 HIS cc_start: 0.6636 (t-170) cc_final: 0.6011 (t-90) REVERT: A 588 ILE cc_start: 0.7887 (tp) cc_final: 0.7568 (mt) REVERT: B 117 GLN cc_start: 0.5512 (mt0) cc_final: 0.4210 (tp-100) REVERT: B 123 GLU cc_start: 0.5446 (tp30) cc_final: 0.5073 (tp30) REVERT: B 144 TYR cc_start: 0.6064 (m-10) cc_final: 0.5734 (m-10) REVERT: B 259 PHE cc_start: 0.5909 (t80) cc_final: 0.5701 (t80) REVERT: B 343 LYS cc_start: 0.6507 (tppp) cc_final: 0.5909 (tptp) REVERT: B 409 GLU cc_start: 0.6655 (tt0) cc_final: 0.6360 (mt-10) REVERT: B 433 ASP cc_start: 0.7410 (t70) cc_final: 0.7162 (t0) REVERT: B 451 ASN cc_start: 0.7480 (t0) cc_final: 0.7211 (m-40) REVERT: B 463 ASN cc_start: 0.7295 (OUTLIER) cc_final: 0.6988 (m-40) REVERT: B 494 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7492 (mt-10) REVERT: B 517 HIS cc_start: 0.6633 (t-170) cc_final: 0.6007 (t-90) REVERT: B 588 ILE cc_start: 0.7875 (tp) cc_final: 0.7555 (mt) REVERT: C 117 GLN cc_start: 0.5513 (mt0) cc_final: 0.4165 (tp-100) REVERT: C 123 GLU cc_start: 0.5463 (tp30) cc_final: 0.5113 (tp30) REVERT: C 144 TYR cc_start: 0.6066 (m-10) cc_final: 0.5731 (m-10) REVERT: C 343 LYS cc_start: 0.6490 (tppp) cc_final: 0.5898 (tptp) REVERT: C 409 GLU cc_start: 0.6651 (tt0) cc_final: 0.6364 (mt-10) REVERT: C 433 ASP cc_start: 0.7407 (t70) cc_final: 0.7152 (t0) REVERT: C 451 ASN cc_start: 0.7470 (t0) cc_final: 0.7204 (m-40) REVERT: C 463 ASN cc_start: 0.7291 (OUTLIER) cc_final: 0.6989 (m-40) REVERT: C 494 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7506 (mt-10) REVERT: C 517 HIS cc_start: 0.6638 (t70) cc_final: 0.6130 (t-90) REVERT: C 541 ILE cc_start: 0.7292 (mm) cc_final: 0.7006 (mt) REVERT: C 588 ILE cc_start: 0.7844 (tp) cc_final: 0.7500 (mt) REVERT: D 117 GLN cc_start: 0.5518 (mt0) cc_final: 0.4184 (tp-100) REVERT: D 144 TYR cc_start: 0.6063 (m-10) cc_final: 0.5734 (m-10) REVERT: D 343 LYS cc_start: 0.6499 (tppp) cc_final: 0.5906 (tptp) REVERT: D 433 ASP cc_start: 0.7414 (t70) cc_final: 0.7165 (t0) REVERT: D 451 ASN cc_start: 0.7476 (t0) cc_final: 0.7204 (m-40) REVERT: D 463 ASN cc_start: 0.7300 (OUTLIER) cc_final: 0.6995 (m-40) REVERT: D 494 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7506 (mt-10) REVERT: D 517 HIS cc_start: 0.6635 (t-170) cc_final: 0.6012 (t-90) REVERT: D 588 ILE cc_start: 0.7876 (tp) cc_final: 0.7557 (mt) outliers start: 32 outliers final: 8 residues processed: 325 average time/residue: 0.2578 time to fit residues: 124.8392 Evaluate side-chains 285 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 273 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 463 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 193 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 173 optimal weight: 3.9990 chunk 52 optimal weight: 9.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** B 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 463 ASN ** C 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN ** D 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 16008 Z= 0.344 Angle : 0.646 9.162 21712 Z= 0.331 Chirality : 0.043 0.139 2440 Planarity : 0.004 0.040 2716 Dihedral : 14.157 152.267 2412 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.67 % Allowed : 9.63 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.19), residues: 2008 helix: 0.92 (0.14), residues: 1396 sheet: 2.11 (0.40), residues: 112 loop : -0.96 (0.27), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 373 HIS 0.004 0.002 HIS A 432 PHE 0.013 0.002 PHE C 514 TYR 0.015 0.002 TYR B 411 ARG 0.005 0.001 ARG A 554 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 286 time to evaluate : 1.538 Fit side-chains REVERT: A 117 GLN cc_start: 0.5652 (mt0) cc_final: 0.4231 (tp-100) REVERT: A 123 GLU cc_start: 0.5498 (tp30) cc_final: 0.5101 (tp30) REVERT: A 144 TYR cc_start: 0.6041 (m-10) cc_final: 0.5693 (m-10) REVERT: A 343 LYS cc_start: 0.6630 (tppp) cc_final: 0.6038 (tptt) REVERT: A 361 TYR cc_start: 0.7352 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: A 409 GLU cc_start: 0.6704 (tt0) cc_final: 0.6393 (mt-10) REVERT: A 451 ASN cc_start: 0.7437 (t0) cc_final: 0.7182 (m-40) REVERT: A 463 ASN cc_start: 0.7180 (OUTLIER) cc_final: 0.6964 (m-40) REVERT: A 494 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7452 (mt-10) REVERT: A 502 ILE cc_start: 0.7465 (mt) cc_final: 0.7231 (mt) REVERT: A 517 HIS cc_start: 0.6659 (t-170) cc_final: 0.6192 (t-90) REVERT: A 576 TYR cc_start: 0.7253 (m-80) cc_final: 0.6959 (m-80) REVERT: A 588 ILE cc_start: 0.7803 (tp) cc_final: 0.7489 (mt) REVERT: B 117 GLN cc_start: 0.5763 (mt0) cc_final: 0.4323 (tp-100) REVERT: B 123 GLU cc_start: 0.5366 (tp30) cc_final: 0.5031 (tp30) REVERT: B 144 TYR cc_start: 0.6009 (m-10) cc_final: 0.5619 (m-10) REVERT: B 343 LYS cc_start: 0.6598 (tppp) cc_final: 0.6014 (tptt) REVERT: B 361 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6705 (m-80) REVERT: B 409 GLU cc_start: 0.6673 (tt0) cc_final: 0.6356 (mt-10) REVERT: B 451 ASN cc_start: 0.7436 (t0) cc_final: 0.7181 (m-40) REVERT: B 463 ASN cc_start: 0.7178 (OUTLIER) cc_final: 0.6960 (m-40) REVERT: B 494 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7417 (mt-10) REVERT: B 517 HIS cc_start: 0.6657 (t-170) cc_final: 0.6191 (t-90) REVERT: B 576 TYR cc_start: 0.7261 (m-80) cc_final: 0.6962 (m-80) REVERT: B 588 ILE cc_start: 0.7791 (tp) cc_final: 0.7470 (mt) REVERT: C 117 GLN cc_start: 0.5680 (mt0) cc_final: 0.4272 (tp-100) REVERT: C 123 GLU cc_start: 0.5354 (tp30) cc_final: 0.5023 (tp30) REVERT: C 144 TYR cc_start: 0.6009 (m-10) cc_final: 0.5617 (m-10) REVERT: C 343 LYS cc_start: 0.6585 (tppp) cc_final: 0.6004 (tptt) REVERT: C 361 TYR cc_start: 0.7313 (OUTLIER) cc_final: 0.6734 (m-80) REVERT: C 409 GLU cc_start: 0.6702 (tt0) cc_final: 0.6389 (mt-10) REVERT: C 451 ASN cc_start: 0.7426 (t0) cc_final: 0.7187 (m-40) REVERT: C 463 ASN cc_start: 0.7182 (OUTLIER) cc_final: 0.6964 (m-40) REVERT: C 494 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7423 (mt-10) REVERT: C 517 HIS cc_start: 0.6610 (t70) cc_final: 0.6382 (t-90) REVERT: C 576 TYR cc_start: 0.7239 (m-80) cc_final: 0.6972 (m-80) REVERT: C 588 ILE cc_start: 0.7825 (tp) cc_final: 0.7494 (mt) REVERT: D 117 GLN cc_start: 0.5786 (mt0) cc_final: 0.4333 (tp-100) REVERT: D 123 GLU cc_start: 0.5435 (tp30) cc_final: 0.5111 (tp30) REVERT: D 125 GLU cc_start: 0.6181 (tp30) cc_final: 0.5964 (tp30) REVERT: D 144 TYR cc_start: 0.6004 (m-10) cc_final: 0.5618 (m-10) REVERT: D 343 LYS cc_start: 0.6593 (tppp) cc_final: 0.6007 (tptt) REVERT: D 361 TYR cc_start: 0.7345 (OUTLIER) cc_final: 0.6693 (m-80) REVERT: D 409 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6320 (mt-10) REVERT: D 451 ASN cc_start: 0.7432 (t0) cc_final: 0.7183 (m-40) REVERT: D 463 ASN cc_start: 0.7181 (OUTLIER) cc_final: 0.6965 (m-40) REVERT: D 494 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7421 (mt-10) REVERT: D 517 HIS cc_start: 0.6668 (t-170) cc_final: 0.6194 (t-90) REVERT: D 576 TYR cc_start: 0.7267 (m-80) cc_final: 0.6961 (m-80) REVERT: D 588 ILE cc_start: 0.7805 (tp) cc_final: 0.7487 (mt) outliers start: 53 outliers final: 26 residues processed: 317 average time/residue: 0.2468 time to fit residues: 117.9045 Evaluate side-chains 309 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 275 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 463 ASN Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 463 ASN Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 427 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 463 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 2 optimal weight: 0.0570 chunk 143 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 98 optimal weight: 0.8980 chunk 173 optimal weight: 0.0060 chunk 48 optimal weight: 0.7980 overall best weight: 1.1516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 HIS A 440 GLN A 463 ASN B 432 HIS B 437 HIS B 440 GLN B 463 ASN C 432 HIS C 437 HIS C 440 GLN C 463 ASN D 432 HIS D 437 HIS D 440 GLN D 463 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16008 Z= 0.209 Angle : 0.556 8.095 21712 Z= 0.286 Chirality : 0.040 0.128 2440 Planarity : 0.004 0.041 2716 Dihedral : 13.960 151.015 2412 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.49 % Allowed : 10.94 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.19), residues: 2008 helix: 1.22 (0.14), residues: 1400 sheet: 2.11 (0.41), residues: 112 loop : -0.95 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 373 HIS 0.003 0.001 HIS D 432 PHE 0.011 0.001 PHE C 569 TYR 0.012 0.001 TYR B 411 ARG 0.005 0.000 ARG B 554 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 287 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.6272 (mmp) cc_final: 0.5805 (mmm) REVERT: A 117 GLN cc_start: 0.5731 (mt0) cc_final: 0.4356 (tp-100) REVERT: A 123 GLU cc_start: 0.5423 (tp30) cc_final: 0.5086 (tp30) REVERT: A 125 GLU cc_start: 0.6088 (tp30) cc_final: 0.5881 (tp30) REVERT: A 144 TYR cc_start: 0.6003 (m-10) cc_final: 0.5689 (m-10) REVERT: A 343 LYS cc_start: 0.6514 (tppp) cc_final: 0.5953 (tptt) REVERT: A 361 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6738 (m-80) REVERT: A 409 GLU cc_start: 0.6630 (tt0) cc_final: 0.6345 (mt-10) REVERT: A 451 ASN cc_start: 0.7445 (t0) cc_final: 0.7227 (m-40) REVERT: A 494 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7472 (mt-10) REVERT: A 502 ILE cc_start: 0.7445 (mt) cc_final: 0.7213 (mt) REVERT: A 517 HIS cc_start: 0.6668 (t-170) cc_final: 0.5977 (t-90) REVERT: A 588 ILE cc_start: 0.7798 (tp) cc_final: 0.7504 (mt) REVERT: A 593 ARG cc_start: 0.7488 (ttm110) cc_final: 0.7236 (ttp-110) REVERT: B 113 MET cc_start: 0.6272 (mmp) cc_final: 0.5803 (mmm) REVERT: B 117 GLN cc_start: 0.5709 (mt0) cc_final: 0.4325 (tp-100) REVERT: B 123 GLU cc_start: 0.5366 (tp30) cc_final: 0.5032 (tp30) REVERT: B 125 GLU cc_start: 0.6142 (tp30) cc_final: 0.5883 (tp30) REVERT: B 144 TYR cc_start: 0.5997 (m-10) cc_final: 0.5656 (m-10) REVERT: B 149 MET cc_start: 0.6824 (mmp) cc_final: 0.6502 (mmp) REVERT: B 343 LYS cc_start: 0.6515 (tppp) cc_final: 0.5926 (tptt) REVERT: B 361 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6720 (m-80) REVERT: B 409 GLU cc_start: 0.6653 (tt0) cc_final: 0.6380 (mt-10) REVERT: B 451 ASN cc_start: 0.7443 (t0) cc_final: 0.7218 (m-40) REVERT: B 494 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7452 (mt-10) REVERT: B 517 HIS cc_start: 0.6671 (t-170) cc_final: 0.6037 (t-90) REVERT: B 588 ILE cc_start: 0.7807 (tp) cc_final: 0.7474 (mt) REVERT: B 593 ARG cc_start: 0.7407 (ttm110) cc_final: 0.7158 (ttp-110) REVERT: C 113 MET cc_start: 0.6267 (mmp) cc_final: 0.5782 (mmm) REVERT: C 123 GLU cc_start: 0.5392 (tp30) cc_final: 0.5062 (tp30) REVERT: C 125 GLU cc_start: 0.6140 (tp30) cc_final: 0.5886 (tp30) REVERT: C 144 TYR cc_start: 0.6044 (m-10) cc_final: 0.5694 (m-10) REVERT: C 149 MET cc_start: 0.6826 (mmp) cc_final: 0.6507 (mmp) REVERT: C 361 TYR cc_start: 0.7265 (OUTLIER) cc_final: 0.6739 (m-80) REVERT: C 409 GLU cc_start: 0.6653 (tt0) cc_final: 0.6381 (mt-10) REVERT: C 451 ASN cc_start: 0.7436 (t0) cc_final: 0.7221 (m-40) REVERT: C 494 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7469 (mt-10) REVERT: C 517 HIS cc_start: 0.6633 (t70) cc_final: 0.6393 (t-90) REVERT: C 588 ILE cc_start: 0.7808 (tp) cc_final: 0.7461 (mt) REVERT: C 593 ARG cc_start: 0.7403 (ttm110) cc_final: 0.7153 (ttp-110) REVERT: D 125 GLU cc_start: 0.6154 (tp30) cc_final: 0.5926 (tp30) REVERT: D 144 TYR cc_start: 0.6034 (m-10) cc_final: 0.5685 (m-10) REVERT: D 343 LYS cc_start: 0.6509 (tppp) cc_final: 0.5923 (tptt) REVERT: D 409 GLU cc_start: 0.6616 (mt-10) cc_final: 0.6296 (mt-10) REVERT: D 451 ASN cc_start: 0.7439 (t0) cc_final: 0.7217 (m-40) REVERT: D 494 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7464 (mt-10) REVERT: D 517 HIS cc_start: 0.6657 (t-170) cc_final: 0.6190 (t-90) REVERT: D 588 ILE cc_start: 0.7798 (tp) cc_final: 0.7502 (mt) REVERT: D 593 ARG cc_start: 0.7480 (ttm110) cc_final: 0.7228 (ttp-110) outliers start: 36 outliers final: 27 residues processed: 299 average time/residue: 0.2619 time to fit residues: 115.8144 Evaluate side-chains 316 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 286 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 427 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 427 MET Chi-restraints excluded: chain D residue 445 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 8.9990 chunk 193 optimal weight: 0.0870 chunk 160 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 101 optimal weight: 4.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN B 463 ASN B 517 HIS C 117 GLN C 463 ASN D 117 GLN D 463 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16008 Z= 0.158 Angle : 0.522 8.359 21712 Z= 0.268 Chirality : 0.039 0.142 2440 Planarity : 0.003 0.042 2716 Dihedral : 13.598 148.926 2410 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.08 % Allowed : 13.16 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 2008 helix: 1.45 (0.14), residues: 1400 sheet: 2.19 (0.42), residues: 112 loop : -0.90 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 373 HIS 0.005 0.001 HIS A 432 PHE 0.012 0.001 PHE D 143 TYR 0.012 0.001 TYR A 411 ARG 0.005 0.000 ARG C 554 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 275 time to evaluate : 1.650 Fit side-chains REVERT: A 113 MET cc_start: 0.6350 (mmp) cc_final: 0.5887 (mmm) REVERT: A 262 ILE cc_start: 0.6970 (mp) cc_final: 0.6627 (tt) REVERT: A 451 ASN cc_start: 0.7474 (t0) cc_final: 0.7243 (m-40) REVERT: A 473 MET cc_start: 0.6947 (OUTLIER) cc_final: 0.6393 (ttm) REVERT: A 487 MET cc_start: 0.7655 (ttm) cc_final: 0.7256 (ttm) REVERT: A 494 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 502 ILE cc_start: 0.7466 (mt) cc_final: 0.7224 (mt) REVERT: A 517 HIS cc_start: 0.6646 (t-170) cc_final: 0.6022 (t-90) REVERT: A 588 ILE cc_start: 0.7835 (tp) cc_final: 0.7515 (pt) REVERT: B 113 MET cc_start: 0.6348 (mmp) cc_final: 0.5882 (mmm) REVERT: B 123 GLU cc_start: 0.5509 (tp30) cc_final: 0.5206 (tp30) REVERT: B 125 GLU cc_start: 0.6215 (tp30) cc_final: 0.5985 (tp30) REVERT: B 259 PHE cc_start: 0.5826 (t80) cc_final: 0.5316 (t80) REVERT: B 262 ILE cc_start: 0.6964 (mp) cc_final: 0.6653 (tt) REVERT: B 451 ASN cc_start: 0.7472 (t0) cc_final: 0.7247 (m-40) REVERT: B 473 MET cc_start: 0.6942 (OUTLIER) cc_final: 0.6397 (ttm) REVERT: B 487 MET cc_start: 0.7590 (ttm) cc_final: 0.7204 (ttm) REVERT: B 494 GLU cc_start: 0.7720 (mt-10) cc_final: 0.7471 (mt-10) REVERT: B 517 HIS cc_start: 0.6494 (t70) cc_final: 0.6084 (t-90) REVERT: B 588 ILE cc_start: 0.7835 (tp) cc_final: 0.7512 (pt) REVERT: C 113 MET cc_start: 0.6350 (mmp) cc_final: 0.5865 (mmm) REVERT: C 123 GLU cc_start: 0.5499 (tp30) cc_final: 0.5185 (tp30) REVERT: C 125 GLU cc_start: 0.6199 (tp30) cc_final: 0.5973 (tp30) REVERT: C 262 ILE cc_start: 0.6962 (mp) cc_final: 0.6619 (tt) REVERT: C 451 ASN cc_start: 0.7460 (t0) cc_final: 0.7242 (m-40) REVERT: C 473 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6391 (ttm) REVERT: C 487 MET cc_start: 0.7592 (ttm) cc_final: 0.7208 (ttm) REVERT: C 494 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7480 (mt-10) REVERT: C 517 HIS cc_start: 0.6646 (t70) cc_final: 0.6435 (t-90) REVERT: C 588 ILE cc_start: 0.7837 (tp) cc_final: 0.7515 (pt) REVERT: C 593 ARG cc_start: 0.7403 (ttm110) cc_final: 0.7201 (ttp-110) REVERT: D 113 MET cc_start: 0.6253 (mmp) cc_final: 0.5740 (mmm) REVERT: D 262 ILE cc_start: 0.6924 (mp) cc_final: 0.6568 (tt) REVERT: D 361 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.6605 (m-80) REVERT: D 409 GLU cc_start: 0.6582 (mt-10) cc_final: 0.6277 (mt-10) REVERT: D 451 ASN cc_start: 0.7464 (t0) cc_final: 0.7236 (m-40) REVERT: D 473 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6398 (ttm) REVERT: D 487 MET cc_start: 0.7658 (ttm) cc_final: 0.7260 (ttm) REVERT: D 494 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7480 (mt-10) REVERT: D 517 HIS cc_start: 0.6652 (t-170) cc_final: 0.6028 (t-90) REVERT: D 588 ILE cc_start: 0.7837 (tp) cc_final: 0.7516 (pt) outliers start: 30 outliers final: 23 residues processed: 285 average time/residue: 0.2718 time to fit residues: 116.4823 Evaluate side-chains 296 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 268 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 473 MET Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 473 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 0.1980 chunk 141 optimal weight: 0.0020 chunk 109 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 432 HIS B 117 GLN C 117 GLN D 117 GLN D 517 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6233 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16008 Z= 0.142 Angle : 0.500 8.486 21712 Z= 0.255 Chirality : 0.038 0.119 2440 Planarity : 0.003 0.042 2716 Dihedral : 13.229 148.305 2404 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.80 % Allowed : 13.37 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.19), residues: 2008 helix: 1.67 (0.14), residues: 1400 sheet: 2.34 (0.43), residues: 112 loop : -0.83 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 373 HIS 0.004 0.001 HIS D 432 PHE 0.012 0.001 PHE B 143 TYR 0.012 0.001 TYR A 411 ARG 0.005 0.000 ARG C 554 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 281 time to evaluate : 1.601 Fit side-chains REVERT: A 113 MET cc_start: 0.6394 (mmp) cc_final: 0.5892 (mmm) REVERT: A 262 ILE cc_start: 0.6946 (mp) cc_final: 0.6589 (tt) REVERT: A 361 TYR cc_start: 0.7174 (OUTLIER) cc_final: 0.6669 (m-80) REVERT: A 364 GLN cc_start: 0.5943 (pm20) cc_final: 0.5734 (pm20) REVERT: A 404 ARG cc_start: 0.7028 (tpp80) cc_final: 0.6675 (tpp80) REVERT: A 409 GLU cc_start: 0.6540 (mt-10) cc_final: 0.6261 (mt-10) REVERT: A 473 MET cc_start: 0.6935 (ttp) cc_final: 0.6523 (ttm) REVERT: A 487 MET cc_start: 0.7567 (ttm) cc_final: 0.7149 (ttm) REVERT: A 494 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7491 (mt-10) REVERT: A 502 ILE cc_start: 0.7463 (mt) cc_final: 0.7208 (mt) REVERT: A 517 HIS cc_start: 0.6612 (t-170) cc_final: 0.6003 (t-90) REVERT: A 588 ILE cc_start: 0.7834 (tp) cc_final: 0.7521 (pt) REVERT: B 113 MET cc_start: 0.6433 (mmp) cc_final: 0.5944 (mmm) REVERT: B 123 GLU cc_start: 0.5548 (tp30) cc_final: 0.5281 (tp30) REVERT: B 259 PHE cc_start: 0.5810 (t80) cc_final: 0.5270 (t80) REVERT: B 262 ILE cc_start: 0.6827 (mp) cc_final: 0.6521 (tt) REVERT: B 361 TYR cc_start: 0.7158 (OUTLIER) cc_final: 0.6636 (m-80) REVERT: B 409 GLU cc_start: 0.6568 (mt-10) cc_final: 0.6293 (mt-10) REVERT: B 451 ASN cc_start: 0.7450 (t0) cc_final: 0.7232 (m-40) REVERT: B 473 MET cc_start: 0.6933 (ttp) cc_final: 0.6524 (ttm) REVERT: B 487 MET cc_start: 0.7575 (ttm) cc_final: 0.7160 (ttm) REVERT: B 494 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7449 (mt-10) REVERT: B 517 HIS cc_start: 0.6522 (t70) cc_final: 0.6076 (t-90) REVERT: B 588 ILE cc_start: 0.7834 (tp) cc_final: 0.7519 (pt) REVERT: C 113 MET cc_start: 0.6368 (mmp) cc_final: 0.5883 (mmm) REVERT: C 123 GLU cc_start: 0.5493 (tp30) cc_final: 0.5223 (tp30) REVERT: C 125 GLU cc_start: 0.6217 (tp30) cc_final: 0.5995 (tp30) REVERT: C 262 ILE cc_start: 0.6938 (mp) cc_final: 0.6580 (tt) REVERT: C 361 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: C 409 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6270 (mt-10) REVERT: C 451 ASN cc_start: 0.7444 (t0) cc_final: 0.7230 (m-40) REVERT: C 473 MET cc_start: 0.6930 (ttp) cc_final: 0.6567 (ttm) REVERT: C 487 MET cc_start: 0.7573 (ttm) cc_final: 0.7155 (ttm) REVERT: C 494 GLU cc_start: 0.7712 (mt-10) cc_final: 0.7463 (mt-10) REVERT: C 588 ILE cc_start: 0.7870 (tp) cc_final: 0.7516 (pt) REVERT: C 593 ARG cc_start: 0.7321 (ttm110) cc_final: 0.7121 (ttp-110) REVERT: D 113 MET cc_start: 0.6293 (mmp) cc_final: 0.5780 (mmm) REVERT: D 262 ILE cc_start: 0.6933 (mp) cc_final: 0.6575 (tt) REVERT: D 312 ASP cc_start: 0.6716 (t0) cc_final: 0.6486 (t0) REVERT: D 361 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6616 (m-80) REVERT: D 369 MET cc_start: 0.6967 (mmm) cc_final: 0.6740 (mmp) REVERT: D 404 ARG cc_start: 0.7121 (tpp80) cc_final: 0.6778 (tpp80) REVERT: D 409 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6258 (mt-10) REVERT: D 451 ASN cc_start: 0.7441 (t0) cc_final: 0.7231 (m-40) REVERT: D 473 MET cc_start: 0.6940 (ttp) cc_final: 0.6527 (ttm) REVERT: D 487 MET cc_start: 0.7569 (ttm) cc_final: 0.7150 (ttm) REVERT: D 494 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7460 (mt-10) REVERT: D 517 HIS cc_start: 0.6479 (t70) cc_final: 0.6088 (t-90) REVERT: D 588 ILE cc_start: 0.7834 (tp) cc_final: 0.7520 (pt) outliers start: 26 outliers final: 18 residues processed: 290 average time/residue: 0.2519 time to fit residues: 110.2122 Evaluate side-chains 294 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 272 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 152 MET Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 445 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 37 optimal weight: 0.0470 chunk 122 optimal weight: 0.0570 chunk 131 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 151 optimal weight: 0.5980 chunk 175 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 432 HIS B 117 GLN C 117 GLN D 117 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16008 Z= 0.144 Angle : 0.509 8.538 21712 Z= 0.260 Chirality : 0.039 0.155 2440 Planarity : 0.003 0.042 2716 Dihedral : 12.982 148.085 2404 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.80 % Allowed : 14.40 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.19), residues: 2008 helix: 1.74 (0.14), residues: 1404 sheet: 2.47 (0.43), residues: 112 loop : -0.78 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 373 HIS 0.004 0.001 HIS B 432 PHE 0.012 0.001 PHE A 143 TYR 0.012 0.001 TYR A 411 ARG 0.008 0.000 ARG D 554 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 284 time to evaluate : 1.849 Fit side-chains REVERT: A 113 MET cc_start: 0.6453 (mmp) cc_final: 0.5958 (mmm) REVERT: A 262 ILE cc_start: 0.7024 (mp) cc_final: 0.6675 (tt) REVERT: A 364 GLN cc_start: 0.5947 (pm20) cc_final: 0.5716 (pm20) REVERT: A 404 ARG cc_start: 0.7133 (tpp80) cc_final: 0.6783 (tpp80) REVERT: A 409 GLU cc_start: 0.6556 (mt-10) cc_final: 0.6283 (mt-10) REVERT: A 487 MET cc_start: 0.7584 (ttm) cc_final: 0.7148 (ttm) REVERT: A 517 HIS cc_start: 0.6620 (t-170) cc_final: 0.6027 (t-90) REVERT: A 573 LEU cc_start: 0.7037 (mm) cc_final: 0.6757 (mt) REVERT: A 588 ILE cc_start: 0.7847 (tp) cc_final: 0.7514 (pt) REVERT: B 113 MET cc_start: 0.6432 (mmp) cc_final: 0.5958 (mmm) REVERT: B 123 GLU cc_start: 0.5587 (tp30) cc_final: 0.5321 (tp30) REVERT: B 259 PHE cc_start: 0.5657 (t80) cc_final: 0.5185 (t80) REVERT: B 262 ILE cc_start: 0.7005 (mp) cc_final: 0.6683 (tt) REVERT: B 361 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6682 (m-80) REVERT: B 364 GLN cc_start: 0.5938 (pm20) cc_final: 0.5717 (pm20) REVERT: B 404 ARG cc_start: 0.7118 (tpp80) cc_final: 0.6791 (tpp80) REVERT: B 409 GLU cc_start: 0.6571 (mt-10) cc_final: 0.6257 (mt-10) REVERT: B 448 ASN cc_start: 0.7445 (t0) cc_final: 0.7043 (m-40) REVERT: B 451 ASN cc_start: 0.7206 (t0) cc_final: 0.6850 (m-40) REVERT: B 487 MET cc_start: 0.7593 (ttm) cc_final: 0.7157 (ttm) REVERT: B 494 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7422 (mt-10) REVERT: B 517 HIS cc_start: 0.6516 (t70) cc_final: 0.6074 (t-90) REVERT: B 573 LEU cc_start: 0.7034 (mm) cc_final: 0.6759 (mt) REVERT: B 588 ILE cc_start: 0.7892 (tp) cc_final: 0.7541 (pt) REVERT: C 113 MET cc_start: 0.6441 (mmp) cc_final: 0.5951 (mmm) REVERT: C 123 GLU cc_start: 0.5512 (tp30) cc_final: 0.5255 (tp30) REVERT: C 262 ILE cc_start: 0.7019 (mp) cc_final: 0.6667 (tt) REVERT: C 361 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.6731 (m-80) REVERT: C 409 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6224 (mt-10) REVERT: C 451 ASN cc_start: 0.7197 (t0) cc_final: 0.6846 (m-40) REVERT: C 487 MET cc_start: 0.7590 (ttm) cc_final: 0.7153 (ttm) REVERT: C 494 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7451 (mt-10) REVERT: C 573 LEU cc_start: 0.7022 (mm) cc_final: 0.6754 (mt) REVERT: C 588 ILE cc_start: 0.7880 (tp) cc_final: 0.7521 (pt) REVERT: D 113 MET cc_start: 0.6317 (mmp) cc_final: 0.5789 (mmm) REVERT: D 262 ILE cc_start: 0.7016 (mt) cc_final: 0.6663 (tt) REVERT: D 361 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6635 (m-80) REVERT: D 404 ARG cc_start: 0.7135 (tpp80) cc_final: 0.6788 (tpp80) REVERT: D 409 GLU cc_start: 0.6452 (mt-10) cc_final: 0.6177 (mt-10) REVERT: D 487 MET cc_start: 0.7590 (ttm) cc_final: 0.7151 (ttm) REVERT: D 494 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7449 (mt-10) REVERT: D 517 HIS cc_start: 0.6497 (t70) cc_final: 0.6051 (t-90) REVERT: D 573 LEU cc_start: 0.7031 (mm) cc_final: 0.6754 (mt) REVERT: D 588 ILE cc_start: 0.7877 (tp) cc_final: 0.7540 (pt) outliers start: 26 outliers final: 18 residues processed: 292 average time/residue: 0.2659 time to fit residues: 115.6918 Evaluate side-chains 303 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 282 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 445 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 0.0470 chunk 168 optimal weight: 0.0070 chunk 179 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 78 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 162 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 279 HIS B 117 GLN C 117 GLN D 117 GLN D 279 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 16008 Z= 0.140 Angle : 0.501 8.543 21712 Z= 0.256 Chirality : 0.039 0.146 2440 Planarity : 0.003 0.042 2716 Dihedral : 12.794 148.198 2404 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.39 % Allowed : 14.34 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 2008 helix: 1.88 (0.14), residues: 1396 sheet: 2.39 (0.47), residues: 88 loop : -0.70 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 373 HIS 0.005 0.001 HIS A 432 PHE 0.011 0.001 PHE A 143 TYR 0.011 0.001 TYR D 411 ARG 0.008 0.000 ARG D 554 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 294 time to evaluate : 1.668 Fit side-chains REVERT: A 113 MET cc_start: 0.6397 (mmp) cc_final: 0.5913 (mmm) REVERT: A 262 ILE cc_start: 0.7034 (mp) cc_final: 0.6702 (tt) REVERT: A 361 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.6779 (m-80) REVERT: A 364 GLN cc_start: 0.5944 (pm20) cc_final: 0.5718 (pm20) REVERT: A 404 ARG cc_start: 0.7146 (tpp80) cc_final: 0.6792 (tpp80) REVERT: A 409 GLU cc_start: 0.6568 (mt-10) cc_final: 0.6253 (mt-10) REVERT: A 487 MET cc_start: 0.7581 (ttm) cc_final: 0.7107 (ttm) REVERT: A 517 HIS cc_start: 0.6410 (t-170) cc_final: 0.6016 (t-90) REVERT: A 588 ILE cc_start: 0.7891 (tp) cc_final: 0.7544 (pt) REVERT: B 113 MET cc_start: 0.6457 (mmp) cc_final: 0.5987 (mmm) REVERT: B 123 GLU cc_start: 0.5548 (tp30) cc_final: 0.5319 (tp30) REVERT: B 259 PHE cc_start: 0.5693 (t80) cc_final: 0.5203 (t80) REVERT: B 262 ILE cc_start: 0.6844 (mt) cc_final: 0.6544 (tt) REVERT: B 404 ARG cc_start: 0.7145 (tpp80) cc_final: 0.6816 (tpp80) REVERT: B 409 GLU cc_start: 0.6567 (mt-10) cc_final: 0.6284 (mt-10) REVERT: B 448 ASN cc_start: 0.7446 (t0) cc_final: 0.7028 (m-40) REVERT: B 451 ASN cc_start: 0.7169 (t0) cc_final: 0.6831 (m-40) REVERT: B 487 MET cc_start: 0.7588 (ttm) cc_final: 0.7118 (ttm) REVERT: B 494 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7499 (mt-10) REVERT: B 517 HIS cc_start: 0.6459 (t70) cc_final: 0.6029 (t-90) REVERT: B 588 ILE cc_start: 0.7937 (tp) cc_final: 0.7598 (pt) REVERT: C 113 MET cc_start: 0.6461 (mmp) cc_final: 0.5974 (mmm) REVERT: C 123 GLU cc_start: 0.5505 (tp30) cc_final: 0.5251 (tp30) REVERT: C 258 ARG cc_start: 0.5912 (mtm180) cc_final: 0.4776 (ptm160) REVERT: C 262 ILE cc_start: 0.7012 (mt) cc_final: 0.6761 (tt) REVERT: C 361 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.6772 (m-80) REVERT: C 404 ARG cc_start: 0.7131 (tpp80) cc_final: 0.6813 (tpp80) REVERT: C 409 GLU cc_start: 0.6561 (mt-10) cc_final: 0.6274 (mt-10) REVERT: C 451 ASN cc_start: 0.7157 (t0) cc_final: 0.6820 (m-40) REVERT: C 487 MET cc_start: 0.7585 (ttm) cc_final: 0.7116 (ttm) REVERT: C 494 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7507 (mt-10) REVERT: C 588 ILE cc_start: 0.7933 (tp) cc_final: 0.7591 (pt) REVERT: D 113 MET cc_start: 0.6329 (mmp) cc_final: 0.5803 (mmm) REVERT: D 262 ILE cc_start: 0.7018 (mt) cc_final: 0.6662 (tt) REVERT: D 361 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: D 404 ARG cc_start: 0.7161 (tpp80) cc_final: 0.6827 (tpp80) REVERT: D 409 GLU cc_start: 0.6451 (mt-10) cc_final: 0.6174 (mt-10) REVERT: D 487 MET cc_start: 0.7585 (ttm) cc_final: 0.7112 (ttm) REVERT: D 494 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7502 (mt-10) REVERT: D 517 HIS cc_start: 0.6474 (t70) cc_final: 0.6043 (t-90) REVERT: D 588 ILE cc_start: 0.7936 (tp) cc_final: 0.7596 (pt) outliers start: 20 outliers final: 16 residues processed: 301 average time/residue: 0.2557 time to fit residues: 115.2962 Evaluate side-chains 294 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 275 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 156 ASN Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 418 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 199 optimal weight: 40.0000 chunk 183 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 122 optimal weight: 0.0270 chunk 97 optimal weight: 0.8980 chunk 126 optimal weight: 7.9990 chunk 169 optimal weight: 1.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 117 GLN C 117 GLN D 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6234 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16008 Z= 0.176 Angle : 0.526 8.408 21712 Z= 0.269 Chirality : 0.040 0.141 2440 Planarity : 0.004 0.042 2716 Dihedral : 12.801 149.149 2404 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.39 % Allowed : 14.75 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.19), residues: 2008 helix: 1.85 (0.14), residues: 1396 sheet: 2.27 (0.46), residues: 88 loop : -0.74 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 373 HIS 0.005 0.001 HIS A 432 PHE 0.010 0.001 PHE B 143 TYR 0.012 0.001 TYR A 411 ARG 0.009 0.000 ARG C 554 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4016 Ramachandran restraints generated. 2008 Oldfield, 0 Emsley, 2008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 272 time to evaluate : 1.850 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.6410 (mmp) cc_final: 0.5931 (mmm) REVERT: A 262 ILE cc_start: 0.7041 (mp) cc_final: 0.6719 (tt) REVERT: A 361 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.6770 (m-80) REVERT: A 364 GLN cc_start: 0.6012 (pm20) cc_final: 0.5765 (pm20) REVERT: A 404 ARG cc_start: 0.7185 (tpp80) cc_final: 0.6832 (tpp80) REVERT: A 409 GLU cc_start: 0.6573 (mt-10) cc_final: 0.6266 (mt-10) REVERT: A 487 MET cc_start: 0.7593 (ttm) cc_final: 0.7141 (ttm) REVERT: A 517 HIS cc_start: 0.6445 (t-170) cc_final: 0.6031 (t-90) REVERT: A 588 ILE cc_start: 0.7940 (tp) cc_final: 0.7600 (pt) REVERT: B 113 MET cc_start: 0.6393 (mmp) cc_final: 0.5924 (mmm) REVERT: B 123 GLU cc_start: 0.5549 (tp30) cc_final: 0.5321 (tp30) REVERT: B 259 PHE cc_start: 0.5705 (t80) cc_final: 0.5222 (t80) REVERT: B 262 ILE cc_start: 0.7021 (mt) cc_final: 0.6703 (tt) REVERT: B 361 TYR cc_start: 0.7252 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: B 404 ARG cc_start: 0.7187 (tpp80) cc_final: 0.6848 (tpp80) REVERT: B 409 GLU cc_start: 0.6550 (mt-10) cc_final: 0.6266 (mt-10) REVERT: B 448 ASN cc_start: 0.7517 (t0) cc_final: 0.7076 (m-40) REVERT: B 451 ASN cc_start: 0.7105 (t0) cc_final: 0.6773 (m-40) REVERT: B 487 MET cc_start: 0.7599 (ttm) cc_final: 0.7149 (ttm) REVERT: B 494 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7489 (mt-10) REVERT: B 517 HIS cc_start: 0.6468 (t70) cc_final: 0.6033 (t-90) REVERT: B 588 ILE cc_start: 0.7942 (tp) cc_final: 0.7602 (pt) REVERT: C 113 MET cc_start: 0.6393 (mmp) cc_final: 0.5892 (mmm) REVERT: C 123 GLU cc_start: 0.5498 (tp30) cc_final: 0.5260 (tp30) REVERT: C 262 ILE cc_start: 0.7032 (mt) cc_final: 0.6702 (tt) REVERT: C 404 ARG cc_start: 0.7197 (tpp80) cc_final: 0.6838 (tpp80) REVERT: C 409 GLU cc_start: 0.6555 (mt-10) cc_final: 0.6283 (mt-10) REVERT: C 451 ASN cc_start: 0.7094 (t0) cc_final: 0.6859 (m-40) REVERT: C 487 MET cc_start: 0.7590 (ttm) cc_final: 0.7138 (ttm) REVERT: C 494 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7497 (mt-10) REVERT: C 588 ILE cc_start: 0.7940 (tp) cc_final: 0.7600 (pt) REVERT: D 113 MET cc_start: 0.6335 (mmp) cc_final: 0.5749 (mmm) REVERT: D 123 GLU cc_start: 0.5583 (tp30) cc_final: 0.5383 (tp30) REVERT: D 262 ILE cc_start: 0.7033 (mt) cc_final: 0.6696 (tt) REVERT: D 361 TYR cc_start: 0.7223 (OUTLIER) cc_final: 0.6733 (m-80) REVERT: D 409 GLU cc_start: 0.6487 (mt-10) cc_final: 0.6222 (mt-10) REVERT: D 487 MET cc_start: 0.7598 (ttm) cc_final: 0.7141 (ttm) REVERT: D 494 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7491 (mt-10) REVERT: D 517 HIS cc_start: 0.6476 (t70) cc_final: 0.6046 (t-90) REVERT: D 588 ILE cc_start: 0.7941 (tp) cc_final: 0.7601 (pt) outliers start: 20 outliers final: 14 residues processed: 280 average time/residue: 0.2624 time to fit residues: 110.0078 Evaluate side-chains 290 residues out of total 1828 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 273 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain A residue 445 ASP Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 418 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 158 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 163 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN B 117 GLN C 117 GLN D 117 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.165896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.132159 restraints weight = 17628.440| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.96 r_work: 0.3209 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16008 Z= 0.170 Angle : 0.518 8.322 21712 Z= 0.266 Chirality : 0.039 0.139 2440 Planarity : 0.003 0.043 2716 Dihedral : 12.637 149.918 2404 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.52 % Allowed : 14.75 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.19), residues: 2008 helix: 1.88 (0.14), residues: 1400 sheet: 2.18 (0.46), residues: 88 loop : -0.67 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 373 HIS 0.005 0.001 HIS D 432 PHE 0.011 0.001 PHE B 143 TYR 0.011 0.001 TYR A 411 ARG 0.009 0.000 ARG D 554 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3377.86 seconds wall clock time: 60 minutes 37.87 seconds (3637.87 seconds total)