Starting phenix.real_space_refine on Sun Aug 24 00:17:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bc7_44426/08_2025/9bc7_44426.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bc7_44426/08_2025/9bc7_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/cci-nas-00/data/ceres_data/9bc7_44426/08_2025/9bc7_44426.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bc7_44426/08_2025/9bc7_44426.map" model { file = "/net/cci-nas-00/data/ceres_data/9bc7_44426/08_2025/9bc7_44426.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bc7_44426/08_2025/9bc7_44426.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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, 'ARG:plan': 6, 'PHE:plan': 2, 'GLU:plan': 14, 'ASP:plan': 15, 'ASN:plan1': 2} 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: B, C, D Time building chain proxies: 2.79, per 1000 atoms: 0.18 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: 0.89 Conformation dependent library (CDL) restraints added in 576.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.35 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: 2.33 Time building geometry restraints manager: 1.18 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: 0.05 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: 0.000 Normalize map: mean=0, sd=1: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.490 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.560 ------------------------------------------------------------------------------- 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= 0.924 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG B 549 TYR 0.100 0.018 TYR C 347 PHE 0.037 0.009 PHE D 141 TRP 0.056 0.014 TRP B 311 HIS 0.010 0.004 HIS B 421 Details of bonding type rmsd covalent geometry : bond 0.01492 (16008) covalent geometry : angle 1.83194 (21712) hydrogen bonds : bond 0.23508 ( 972) hydrogen bonds : angle 7.44036 ( 2856) *********************** 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 to be fit. rotamer outliers: 8 poor density : 461 time to evaluate : 0.542 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: 0.1254 time to fit residues: 83.6668 Evaluate side-chains 354 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 350 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.168541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.138911 restraints weight = 17135.761| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 1.87 r_work: 0.3256 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16008 Z= 0.155 Angle : 0.676 12.110 21712 Z= 0.356 Chirality : 0.044 0.132 2440 Planarity : 0.004 0.034 2716 Dihedral : 14.164 146.882 2412 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.19 % Allowed : 6.51 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.18), residues: 2008 helix: 0.68 (0.14), residues: 1352 sheet: 2.10 (0.38), residues: 112 loop : -0.61 (0.25), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 404 TYR 0.015 0.002 TYR C 576 PHE 0.015 0.002 PHE D 236 TRP 0.035 0.002 TRP A 281 HIS 0.009 0.002 HIS D 286 Details of bonding type rmsd covalent geometry : bond 0.00314 (16008) covalent geometry : angle 0.67631 (21712) hydrogen bonds : bond 0.05619 ( 972) hydrogen bonds : angle 4.50798 ( 2856) *********************** 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 397 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 351 time to evaluate : 0.568 Fit side-chains REVERT: A 117 GLN cc_start: 0.6157 (mt0) cc_final: 0.4946 (tp-100) REVERT: A 123 GLU cc_start: 0.6270 (tp30) cc_final: 0.5838 (tp30) REVERT: A 144 TYR cc_start: 0.6996 (m-10) cc_final: 0.6551 (m-10) REVERT: A 304 MET cc_start: 0.7601 (mmm) cc_final: 0.7361 (tpt) REVERT: A 343 LYS cc_start: 0.7914 (tppp) cc_final: 0.7580 (tptp) REVERT: A 347 TYR cc_start: 0.7675 (t80) cc_final: 0.7428 (t80) REVERT: A 404 ARG cc_start: 0.7674 (tpp80) cc_final: 0.7454 (tpp80) REVERT: A 502 ILE cc_start: 0.8394 (mt) cc_final: 0.8180 (mt) REVERT: A 517 HIS cc_start: 0.7354 (t-170) cc_final: 0.6900 (t-90) REVERT: A 576 TYR cc_start: 0.7397 (m-80) cc_final: 0.7088 (m-80) REVERT: A 588 ILE cc_start: 0.7976 (tp) cc_final: 0.7684 (pt) REVERT: B 117 GLN cc_start: 0.6129 (mt0) cc_final: 0.4910 (tp-100) REVERT: B 123 GLU cc_start: 0.6296 (tp30) cc_final: 0.5916 (tp30) REVERT: B 144 TYR cc_start: 0.7028 (m-10) cc_final: 0.6600 (m-10) REVERT: B 304 MET cc_start: 0.7598 (mmm) cc_final: 0.7351 (tpt) REVERT: B 343 LYS cc_start: 0.7928 (tppp) cc_final: 0.7591 (tptp) REVERT: B 347 TYR cc_start: 0.7711 (t80) cc_final: 0.7419 (t80) REVERT: B 473 MET cc_start: 0.7460 (ttm) cc_final: 0.7214 (ttm) REVERT: B 502 ILE cc_start: 0.8387 (mt) cc_final: 0.8174 (mt) REVERT: B 517 HIS cc_start: 0.7348 (t-170) cc_final: 0.6877 (t-90) REVERT: B 576 TYR cc_start: 0.7284 (m-80) cc_final: 0.6963 (m-80) REVERT: B 588 ILE cc_start: 0.8024 (tp) cc_final: 0.7706 (pt) REVERT: C 117 GLN cc_start: 0.6085 (mt0) cc_final: 0.4891 (tp-100) REVERT: C 123 GLU cc_start: 0.6235 (tp30) cc_final: 0.5856 (tp30) REVERT: C 144 TYR cc_start: 0.7006 (m-10) cc_final: 0.6575 (m-10) REVERT: C 304 MET cc_start: 0.7591 (mmm) cc_final: 0.7347 (tpt) REVERT: C 343 LYS cc_start: 0.7927 (tppp) cc_final: 0.7587 (tptp) REVERT: C 347 TYR cc_start: 0.7741 (t80) cc_final: 0.7503 (t80) REVERT: C 473 MET cc_start: 0.7465 (ttm) cc_final: 0.7230 (ttm) REVERT: C 502 ILE cc_start: 0.8375 (mt) cc_final: 0.8155 (mt) REVERT: C 517 HIS cc_start: 0.7211 (t70) cc_final: 0.6776 (t-90) REVERT: C 530 MET cc_start: 0.6461 (OUTLIER) cc_final: 0.6003 (mtm) REVERT: C 588 ILE cc_start: 0.7994 (tp) cc_final: 0.7678 (pt) REVERT: D 117 GLN cc_start: 0.6120 (mt0) cc_final: 0.4944 (tp-100) REVERT: D 123 GLU cc_start: 0.6017 (tp30) cc_final: 0.5639 (tp30) REVERT: D 144 TYR cc_start: 0.6823 (m-10) cc_final: 0.6355 (m-10) REVERT: D 304 MET cc_start: 0.7600 (mmm) cc_final: 0.7360 (tpt) REVERT: D 343 LYS cc_start: 0.7925 (tppp) cc_final: 0.7570 (tptp) REVERT: D 347 TYR cc_start: 0.7684 (t80) cc_final: 0.7430 (t80) REVERT: D 404 ARG cc_start: 0.7606 (tpp80) cc_final: 0.7403 (tpp80) REVERT: D 502 ILE cc_start: 0.8400 (mt) cc_final: 0.8187 (mt) REVERT: D 517 HIS cc_start: 0.7370 (t-170) cc_final: 0.6900 (t-90) REVERT: D 530 MET cc_start: 0.6486 (OUTLIER) cc_final: 0.6001 (mtm) REVERT: D 576 TYR cc_start: 0.7307 (m-80) cc_final: 0.6980 (m-80) REVERT: D 588 ILE cc_start: 0.8024 (tp) cc_final: 0.7720 (pt) outliers start: 46 outliers final: 16 residues processed: 371 average time/residue: 0.1071 time to fit residues: 59.2417 Evaluate side-chains 312 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 294 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 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 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 530 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 530 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 74 optimal weight: 1.9990 chunk 73 optimal weight: 0.4980 chunk 133 optimal weight: 3.9990 chunk 97 optimal weight: 0.0570 chunk 118 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 overall best weight: 1.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 GLN A 437 HIS A 440 GLN A 463 ASN A 482 ASN B 136 HIS B 398 GLN B 437 HIS B 440 GLN B 463 ASN B 482 ASN B 517 HIS C 136 HIS C 398 GLN C 437 HIS C 440 GLN C 482 ASN D 136 HIS D 398 GLN D 437 HIS D 440 GLN D 463 ASN D 482 ASN D 517 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.164869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134711 restraints weight = 17655.435| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.82 r_work: 0.3193 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16008 Z= 0.150 Angle : 0.599 8.559 21712 Z= 0.309 Chirality : 0.042 0.150 2440 Planarity : 0.004 0.036 2716 Dihedral : 14.024 150.731 2412 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.12 % Allowed : 10.32 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.19), residues: 2008 helix: 1.08 (0.14), residues: 1384 sheet: 1.96 (0.38), residues: 112 loop : -0.83 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 404 TYR 0.013 0.002 TYR D 411 PHE 0.017 0.002 PHE A 236 TRP 0.016 0.002 TRP A 373 HIS 0.006 0.002 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00338 (16008) covalent geometry : angle 0.59948 (21712) hydrogen bonds : bond 0.04781 ( 972) hydrogen bonds : angle 4.06111 ( 2856) *********************** 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 352 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 307 time to evaluate : 0.433 Fit side-chains REVERT: A 117 GLN cc_start: 0.6072 (mt0) cc_final: 0.4760 (tp-100) REVERT: A 123 GLU cc_start: 0.5958 (tp30) cc_final: 0.5558 (tp30) REVERT: A 144 TYR cc_start: 0.7046 (m-10) cc_final: 0.6799 (m-10) REVERT: A 259 PHE cc_start: 0.6942 (t80) cc_final: 0.6675 (t80) REVERT: A 304 MET cc_start: 0.7829 (mmm) cc_final: 0.7498 (tpt) REVERT: A 343 LYS cc_start: 0.8073 (tppp) cc_final: 0.7618 (tptp) REVERT: A 361 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7817 (m-80) REVERT: A 433 ASP cc_start: 0.8541 (t70) cc_final: 0.8340 (t0) REVERT: A 463 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7938 (m-40) REVERT: A 487 MET cc_start: 0.8010 (ttm) cc_final: 0.7661 (ttm) REVERT: A 502 ILE cc_start: 0.8406 (mt) cc_final: 0.8188 (mt) REVERT: A 517 HIS cc_start: 0.7541 (t-170) cc_final: 0.6981 (t-90) REVERT: A 588 ILE cc_start: 0.7992 (tp) cc_final: 0.7657 (mt) REVERT: B 117 GLN cc_start: 0.6169 (mt0) cc_final: 0.4795 (tp-100) REVERT: B 144 TYR cc_start: 0.7044 (m-10) cc_final: 0.6778 (m-10) REVERT: B 259 PHE cc_start: 0.6917 (t80) cc_final: 0.6686 (t80) REVERT: B 304 MET cc_start: 0.7815 (mmm) cc_final: 0.7488 (tpt) REVERT: B 343 LYS cc_start: 0.8095 (tppp) cc_final: 0.7610 (tptp) REVERT: B 361 TYR cc_start: 0.8431 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: B 433 ASP cc_start: 0.8507 (t70) cc_final: 0.8301 (t0) REVERT: B 463 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7930 (m-40) REVERT: B 487 MET cc_start: 0.8019 (ttm) cc_final: 0.7645 (ttm) REVERT: B 502 ILE cc_start: 0.8414 (mt) cc_final: 0.8202 (mt) REVERT: B 517 HIS cc_start: 0.7544 (t70) cc_final: 0.7150 (t-90) REVERT: B 576 TYR cc_start: 0.7101 (m-80) cc_final: 0.6823 (m-80) REVERT: B 588 ILE cc_start: 0.7976 (tp) cc_final: 0.7645 (mt) REVERT: C 117 GLN cc_start: 0.6125 (mt0) cc_final: 0.4763 (tp-100) REVERT: C 144 TYR cc_start: 0.7038 (m-10) cc_final: 0.6765 (m-10) REVERT: C 259 PHE cc_start: 0.6886 (t80) cc_final: 0.6650 (t80) REVERT: C 304 MET cc_start: 0.7813 (mmm) cc_final: 0.7495 (tpt) REVERT: C 343 LYS cc_start: 0.8070 (tppp) cc_final: 0.7619 (tptp) REVERT: C 361 TYR cc_start: 0.8378 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: C 369 MET cc_start: 0.7978 (mmm) cc_final: 0.7610 (mmp) REVERT: C 487 MET cc_start: 0.8038 (ttm) cc_final: 0.7689 (ttm) REVERT: C 502 ILE cc_start: 0.8423 (mt) cc_final: 0.8204 (mt) REVERT: C 517 HIS cc_start: 0.7498 (t70) cc_final: 0.7270 (t-90) REVERT: C 530 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6310 (mtm) REVERT: C 541 ILE cc_start: 0.7599 (mm) cc_final: 0.7332 (mt) REVERT: C 588 ILE cc_start: 0.7968 (tp) cc_final: 0.7626 (mt) REVERT: D 117 GLN cc_start: 0.6064 (mt0) cc_final: 0.4720 (tp-100) REVERT: D 144 TYR cc_start: 0.7014 (m-10) cc_final: 0.6744 (m-10) REVERT: D 259 PHE cc_start: 0.6888 (t80) cc_final: 0.6672 (t80) REVERT: D 304 MET cc_start: 0.7833 (mmm) cc_final: 0.7500 (tpt) REVERT: D 343 LYS cc_start: 0.8086 (tppp) cc_final: 0.7632 (tptp) REVERT: D 361 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: D 463 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7946 (m-40) REVERT: D 487 MET cc_start: 0.8024 (ttm) cc_final: 0.7652 (ttm) REVERT: D 502 ILE cc_start: 0.8432 (mt) cc_final: 0.8222 (mt) REVERT: D 517 HIS cc_start: 0.7537 (t70) cc_final: 0.7143 (t-90) REVERT: D 530 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6341 (mtm) REVERT: D 588 ILE cc_start: 0.8001 (tp) cc_final: 0.7663 (mt) outliers start: 45 outliers final: 20 residues processed: 330 average time/residue: 0.0968 time to fit residues: 48.0252 Evaluate side-chains 291 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 262 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 281 TRP Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 367 VAL 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 151 ILE Chi-restraints excluded: chain B residue 281 TRP Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 367 VAL 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 151 ILE Chi-restraints excluded: chain C residue 281 TRP Chi-restraints excluded: chain C residue 361 TYR Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 418 MET Chi-restraints excluded: chain C residue 445 ASP Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 281 TRP Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 463 ASN Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 69 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 152 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 chunk 169 optimal weight: 0.8980 chunk 166 optimal weight: 0.1980 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 463 ASN A 517 HIS B 156 ASN B 432 HIS B 463 ASN C 156 ASN C 432 HIS C 463 ASN D 156 ASN D 432 HIS D 463 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.166656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137091 restraints weight = 17467.515| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.75 r_work: 0.3217 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 16008 Z= 0.114 Angle : 0.534 8.350 21712 Z= 0.274 Chirality : 0.039 0.123 2440 Planarity : 0.003 0.039 2716 Dihedral : 13.696 149.151 2412 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.77 % Allowed : 10.87 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.19), residues: 2008 helix: 1.39 (0.14), residues: 1392 sheet: 2.10 (0.39), residues: 112 loop : -0.87 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 554 TYR 0.016 0.001 TYR C 411 PHE 0.013 0.001 PHE D 236 TRP 0.013 0.001 TRP A 281 HIS 0.005 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00236 (16008) covalent geometry : angle 0.53428 (21712) hydrogen bonds : bond 0.04014 ( 972) hydrogen bonds : angle 3.80807 ( 2856) *********************** 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 315 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 275 time to evaluate : 0.537 Fit side-chains REVERT: A 117 GLN cc_start: 0.6040 (mt0) cc_final: 0.4724 (tp-100) REVERT: A 123 GLU cc_start: 0.5935 (tp30) cc_final: 0.5583 (tp30) REVERT: A 149 MET cc_start: 0.7671 (mmp) cc_final: 0.7338 (mmp) REVERT: A 153 MET cc_start: 0.7581 (ttm) cc_final: 0.7337 (mtt) REVERT: A 233 ASP cc_start: 0.7202 (p0) cc_final: 0.6970 (p0) REVERT: A 259 PHE cc_start: 0.6875 (t80) cc_final: 0.6650 (t80) REVERT: A 304 MET cc_start: 0.7838 (mmm) cc_final: 0.7491 (tpt) REVERT: A 361 TYR cc_start: 0.8286 (OUTLIER) cc_final: 0.7722 (m-80) REVERT: A 473 MET cc_start: 0.6678 (ttp) cc_final: 0.6059 (ttm) REVERT: A 487 MET cc_start: 0.8034 (ttm) cc_final: 0.7643 (ttm) REVERT: A 502 ILE cc_start: 0.8411 (mt) cc_final: 0.8209 (mt) REVERT: A 517 HIS cc_start: 0.7552 (t70) cc_final: 0.7193 (t-90) REVERT: A 541 ILE cc_start: 0.7657 (mm) cc_final: 0.7348 (mt) REVERT: A 588 ILE cc_start: 0.7934 (tp) cc_final: 0.7590 (mt) REVERT: B 117 GLN cc_start: 0.6157 (mt0) cc_final: 0.4779 (tp-100) REVERT: B 125 GLU cc_start: 0.6640 (tp30) cc_final: 0.6369 (tp30) REVERT: B 149 MET cc_start: 0.7669 (mmp) cc_final: 0.7330 (mmp) REVERT: B 153 MET cc_start: 0.7585 (ttm) cc_final: 0.7340 (mtt) REVERT: B 233 ASP cc_start: 0.7189 (p0) cc_final: 0.6962 (p0) REVERT: B 259 PHE cc_start: 0.6879 (t80) cc_final: 0.6667 (t80) REVERT: B 304 MET cc_start: 0.7853 (mmm) cc_final: 0.7510 (tpt) REVERT: B 361 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7718 (m-80) REVERT: B 473 MET cc_start: 0.7115 (ttp) cc_final: 0.6523 (ttm) REVERT: B 487 MET cc_start: 0.8047 (ttm) cc_final: 0.7646 (ttm) REVERT: B 502 ILE cc_start: 0.8424 (mt) cc_final: 0.8214 (mt) REVERT: B 517 HIS cc_start: 0.7591 (t70) cc_final: 0.7223 (t-90) REVERT: B 541 ILE cc_start: 0.7680 (mm) cc_final: 0.7368 (mt) REVERT: B 588 ILE cc_start: 0.8003 (tp) cc_final: 0.7651 (mt) REVERT: C 117 GLN cc_start: 0.6115 (mt0) cc_final: 0.4755 (tp-100) REVERT: C 125 GLU cc_start: 0.6641 (tp30) cc_final: 0.6368 (tp30) REVERT: C 144 TYR cc_start: 0.7009 (m-10) cc_final: 0.6784 (m-10) REVERT: C 149 MET cc_start: 0.7664 (mmp) cc_final: 0.7338 (mmp) REVERT: C 153 MET cc_start: 0.7595 (ttm) cc_final: 0.7365 (mtt) REVERT: C 233 ASP cc_start: 0.7128 (p0) cc_final: 0.6910 (p0) REVERT: C 259 PHE cc_start: 0.6868 (t80) cc_final: 0.6651 (t80) REVERT: C 304 MET cc_start: 0.7836 (mmm) cc_final: 0.7488 (tpt) REVERT: C 361 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: C 463 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.8004 (m-40) REVERT: C 473 MET cc_start: 0.7175 (ttp) cc_final: 0.6540 (ttm) REVERT: C 487 MET cc_start: 0.8048 (ttm) cc_final: 0.7657 (ttm) REVERT: C 502 ILE cc_start: 0.8428 (mt) cc_final: 0.8211 (mt) REVERT: C 517 HIS cc_start: 0.7489 (t70) cc_final: 0.7287 (t-90) REVERT: C 530 MET cc_start: 0.6751 (OUTLIER) cc_final: 0.6420 (mtm) REVERT: C 541 ILE cc_start: 0.7640 (mm) cc_final: 0.7377 (mt) REVERT: C 588 ILE cc_start: 0.8032 (tp) cc_final: 0.7673 (mt) REVERT: D 117 GLN cc_start: 0.6109 (mt0) cc_final: 0.4767 (tp-100) REVERT: D 125 GLU cc_start: 0.6601 (tp30) cc_final: 0.6319 (tp30) REVERT: D 144 TYR cc_start: 0.6986 (m-10) cc_final: 0.6767 (m-10) REVERT: D 149 MET cc_start: 0.7668 (mmp) cc_final: 0.7338 (mmp) REVERT: D 153 MET cc_start: 0.7580 (ttm) cc_final: 0.7345 (mtt) REVERT: D 233 ASP cc_start: 0.7146 (p0) cc_final: 0.6922 (p0) REVERT: D 304 MET cc_start: 0.7843 (mmm) cc_final: 0.7501 (tpt) REVERT: D 361 TYR cc_start: 0.8296 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: D 473 MET cc_start: 0.6697 (ttp) cc_final: 0.6083 (ttm) REVERT: D 487 MET cc_start: 0.8046 (ttm) cc_final: 0.7653 (ttm) REVERT: D 502 ILE cc_start: 0.8418 (mt) cc_final: 0.8205 (mt) REVERT: D 517 HIS cc_start: 0.7560 (t70) cc_final: 0.7195 (t-90) REVERT: D 530 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6400 (mtm) REVERT: D 541 ILE cc_start: 0.7674 (mm) cc_final: 0.7362 (mt) REVERT: D 588 ILE cc_start: 0.7938 (tp) cc_final: 0.7589 (mt) outliers start: 40 outliers final: 17 residues processed: 300 average time/residue: 0.1087 time to fit residues: 49.0331 Evaluate side-chains 278 residues out of total 1828 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 192 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 361 TYR Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 418 MET Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 361 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 418 MET Chi-restraints excluded: chain B residue 445 ASP Chi-restraints excluded: chain C residue 134 ILE 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 C residue 445 ASP Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 530 MET Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 361 TYR Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain D residue 418 MET Chi-restraints excluded: chain D residue 445 ASP Chi-restraints excluded: chain D residue 530 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.347 > 50: distance: 14 - 21: 16.320 distance: 21 - 22: 21.890 distance: 21 - 147: 17.698 distance: 22 - 23: 14.429 distance: 22 - 25: 11.468 distance: 23 - 24: 20.634 distance: 23 - 29: 18.398 distance: 25 - 26: 10.280 distance: 25 - 27: 9.055 distance: 26 - 28: 12.534 distance: 29 - 30: 29.467 distance: 30 - 31: 48.092 distance: 30 - 33: 24.525 distance: 31 - 32: 23.055 distance: 31 - 37: 51.997 distance: 33 - 34: 29.062 distance: 33 - 35: 31.016 distance: 34 - 36: 31.629 distance: 37 - 38: 50.151 distance: 38 - 39: 21.403 distance: 38 - 41: 14.594 distance: 39 - 40: 19.752 distance: 39 - 48: 16.230 distance: 41 - 42: 10.417 distance: 42 - 43: 14.006 distance: 43 - 44: 4.919 distance: 44 - 45: 8.026 distance: 45 - 46: 3.424 distance: 45 - 47: 4.347 distance: 48 - 49: 25.449 distance: 49 - 50: 16.151 distance: 49 - 52: 32.102 distance: 50 - 51: 19.896 distance: 50 - 53: 22.163 distance: 53 - 54: 27.024 distance: 54 - 55: 51.812 distance: 55 - 56: 44.698 distance: 55 - 57: 31.084 distance: 57 - 58: 31.109 distance: 58 - 59: 44.521 distance: 58 - 61: 39.217 distance: 59 - 60: 32.433 distance: 59 - 62: 14.223 distance: 62 - 63: 16.984 distance: 63 - 64: 6.598 distance: 63 - 66: 18.231 distance: 64 - 65: 20.382 distance: 64 - 67: 31.332 distance: 67 - 68: 31.249 distance: 68 - 69: 23.991 distance: 69 - 70: 18.440 distance: 69 - 71: 29.110 distance: 71 - 72: 14.424 distance: 72 - 73: 13.481 distance: 72 - 75: 33.898 distance: 73 - 74: 14.763 distance: 73 - 76: 36.018 distance: 76 - 77: 33.846 distance: 77 - 78: 7.530 distance: 77 - 80: 18.629 distance: 78 - 79: 28.294 distance: 78 - 85: 14.132 distance: 80 - 81: 13.585 distance: 81 - 82: 7.212 distance: 82 - 83: 20.622 distance: 83 - 84: 9.191