Starting phenix.real_space_refine on Mon Aug 25 12:16:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sku_40567/08_2025/8sku_40567_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sku_40567/08_2025/8sku_40567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sku_40567/08_2025/8sku_40567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sku_40567/08_2025/8sku_40567.map" model { file = "/net/cci-nas-00/data/ceres_data/8sku_40567/08_2025/8sku_40567_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sku_40567/08_2025/8sku_40567_trim.cif" } resolution = 3.2 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= 0.017 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 S 76 5.16 5 C 9176 2.51 5 N 2466 2.21 5 O 2758 1.98 5 H 13425 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 27901 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 2997 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 17, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 7, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 3104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 3104 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 17, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 112 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 73 Chain: "E" Number of atoms: 8097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 8097 Classifications: {'peptide': 534} Link IDs: {'PTRANS': 25, 'TRANS': 508} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "R" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2714 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 12, 'TRANS': 177} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'ASP:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "C" Number of atoms: 3144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3144 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 18, 'TRANS': 212} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 7, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 80 Chain: "S" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2714 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 12, 'TRANS': 177} Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 4, 'ASP:plan': 4, 'TYR:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 72 Chain: "D" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 2978 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 18, 'TRANS': 204} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 7, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 87 Chain: "J" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1985 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.75, per 1000 atoms: 0.21 Number of scatterers: 27901 At special positions: 0 Unit cell: (115.902, 162.756, 184.95, 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 76 16.00 O 2758 8.00 N 2466 7.00 C 9176 6.00 H 13425 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=29, symmetry=0 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 369 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 323 " distance=2.04 Simple disulfide: pdb=" SG CYS B 369 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 471 " - pdb=" SG CYS J 69 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS E 38 " - pdb=" SG CYS E 46 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 202 " distance=2.03 Simple disulfide: pdb=" SG CYS E 239 " - pdb=" SG CYS E 307 " distance=2.04 Simple disulfide: pdb=" SG CYS E 253 " - pdb=" SG CYS E 261 " distance=2.04 Simple disulfide: pdb=" SG CYS E 464 " - pdb=" SG CYS E 526 " distance=2.04 Simple disulfide: pdb=" SG CYS E 468 " - pdb=" SG CYS C 311 " distance=2.03 Simple disulfide: pdb=" SG CYS E 478 " - pdb=" SG CYS E 485 " distance=2.03 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 79 " distance=2.03 Simple disulfide: pdb=" SG CYS R 125 " - pdb=" SG CYS R 172 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS D 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 323 " distance=2.03 Simple disulfide: pdb=" SG CYS C 299 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 369 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 471 " - pdb=" SG CYS J 15 " distance=2.02 Simple disulfide: pdb=" SG CYS S 28 " - pdb=" SG CYS S 79 " distance=2.03 Simple disulfide: pdb=" SG CYS S 125 " - pdb=" SG CYS S 172 " distance=2.03 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 323 " distance=2.03 Simple disulfide: pdb=" SG CYS D 369 " - pdb=" SG CYS D 432 " distance=2.03 Simple disulfide: pdb=" SG CYS J 13 " - pdb=" SG CYS J 101 " distance=2.03 Simple disulfide: pdb=" SG CYS J 72 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 109 " - pdb=" SG CYS J 134 " distance=2.03 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 Links applied BETA1-4 " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 501 " - " ASN A 263 " " NAG B 501 " - " ASN B 263 " " NAG E 601 " - " ASN E 65 " " NAG E 602 " - " ASN E 403 " " NAG H 1 " - " ASN E 451 " " NAG I 1 " - " ASN C 263 " " NAG K 1 " - " ASN J 49 " " NAG L 1 " - " ASN E 72 " Time building additional restraints: 2.57 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3618 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 40 sheets defined 7.4% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 252 through 258 Processing helix chain 'A' and resid 311 through 318 Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.733A pdb=" N GLY A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 258 Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 355 through 360 removed outlier: 3.528A pdb=" N LEU B 359 " --> pdb=" O PRO B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 427 removed outlier: 3.778A pdb=" N GLY B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 33 removed outlier: 3.525A pdb=" N HIS E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'E' and resid 166 through 170 removed outlier: 3.901A pdb=" N THR E 170 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 242 through 246 Processing helix chain 'E' and resid 356 through 360 removed outlier: 3.698A pdb=" N SER E 360 " --> pdb=" O ARG E 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 471 Processing helix chain 'C' and resid 253 through 258 Processing helix chain 'C' and resid 311 through 317 removed outlier: 3.935A pdb=" N TRP C 315 " --> pdb=" O CYS C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 362 removed outlier: 4.103A pdb=" N LEU C 361 " --> pdb=" O GLU C 357 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN C 362 " --> pdb=" O GLU C 358 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 357 through 362' Processing helix chain 'C' and resid 420 through 427 Processing helix chain 'C' and resid 451 through 453 No H-bonds generated for 'chain 'C' and resid 451 through 453' Processing helix chain 'S' and resid 163 through 167 Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 355 through 361 Processing helix chain 'D' and resid 421 through 427 removed outlier: 3.609A pdb=" N GLY D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'J' and resid 64 through 69 removed outlier: 3.649A pdb=" N CYS J 69 " --> pdb=" O LEU J 65 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 245 through 249 removed outlier: 3.629A pdb=" N THR A 265 " --> pdb=" O HIS A 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 280 through 281 removed outlier: 3.539A pdb=" N THR A 280 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 365 through 374 current: chain 'A' and resid 411 through 419 Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 389 removed outlier: 3.773A pdb=" N GLN A 388 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 459 through 461 removed outlier: 6.025A pdb=" N ASN A 459 " --> pdb=" O VAL B 460 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL B 462 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N SER A 461 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N PHE J 61 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N SER B 461 " --> pdb=" O PHE J 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 246 through 249 removed outlier: 3.590A pdb=" N THR B 265 " --> pdb=" O HIS B 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 278 through 281 Processing sheet with id=AA8, first strand: chain 'B' and resid 295 through 296 Processing sheet with id=AA9, first strand: chain 'B' and resid 348 through 352 removed outlier: 3.772A pdb=" N ARG B 372 " --> pdb=" O GLU B 348 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 368 " --> pdb=" O LEU B 352 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 364 through 374 current: chain 'B' and resid 410 through 420 Processing sheet with id=AB1, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.148A pdb=" N VAL E 10 " --> pdb=" O GLU E 108 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N SER E 110 " --> pdb=" O VAL E 10 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N SER E 12 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E 50 " --> pdb=" O TRP E 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 18 through 23 removed outlier: 3.613A pdb=" N ILE E 20 " --> pdb=" O VAL E 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 119 through 120 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 119 through 120 current: chain 'E' and resid 154 through 160 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 154 through 160 current: chain 'E' and resid 214 through 220 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 130 through 135 Processing sheet with id=AB6, first strand: chain 'E' and resid 225 through 229 removed outlier: 3.679A pdb=" N GLN E 325 " --> pdb=" O GLU E 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 234 through 239 Processing sheet with id=AB8, first strand: chain 'E' and resid 265 through 266 removed outlier: 3.780A pdb=" N VAL E 265 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 340 through 344 removed outlier: 6.137A pdb=" N VAL E 341 " --> pdb=" O LYS E 438 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE E 440 " --> pdb=" O VAL E 341 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N GLY E 343 " --> pdb=" O ILE E 440 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LYS E 364 " --> pdb=" O ASP E 382 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ASP E 382 " --> pdb=" O LYS E 364 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP E 366 " --> pdb=" O LEU E 380 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TRP E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 348 through 354 removed outlier: 3.664A pdb=" N LEU E 410 " --> pdb=" O VAL E 349 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 452 through 455 removed outlier: 3.615A pdb=" N PHE E 533 " --> pdb=" O GLN E 530 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL E 528 " --> pdb=" O GLY E 535 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N THR E 537 " --> pdb=" O CYS E 526 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N CYS E 526 " --> pdb=" O THR E 537 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ALA E 539 " --> pdb=" O TYR E 524 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR E 524 " --> pdb=" O ALA E 539 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR E 541 " --> pdb=" O GLY E 522 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY E 522 " --> pdb=" O TYR E 541 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 460 through 464 Processing sheet with id=AC4, first strand: chain 'R' and resid 11 through 12 Processing sheet with id=AC5, first strand: chain 'R' and resid 34 through 39 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 51 through 53 current: chain 'R' and resid 87 through 89 Processing sheet with id=AC6, first strand: chain 'R' and resid 106 through 109 Processing sheet with id=AC7, first strand: chain 'R' and resid 148 through 150 removed outlier: 4.419A pdb=" N HIS R 148 " --> pdb=" O LEU R 137 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE R 135 " --> pdb=" O SER R 150 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 245 through 249 removed outlier: 3.708A pdb=" N THR C 265 " --> pdb=" O HIS C 249 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS C 301 " --> pdb=" O ASP C 297 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 324 through 325 Processing sheet with id=AD1, first strand: chain 'C' and resid 350 through 352 removed outlier: 3.546A pdb=" N THR C 368 " --> pdb=" O LEU C 352 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 388 through 389 removed outlier: 3.521A pdb=" N GLN C 388 " --> pdb=" O GLN C 385 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 459 through 463 removed outlier: 3.985A pdb=" N MET C 464 " --> pdb=" O VAL D 463 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS C 457 " --> pdb=" O ARG J 36 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE J 38 " --> pdb=" O HIS C 457 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN C 459 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE J 40 " --> pdb=" O ASN C 459 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N SER C 461 " --> pdb=" O ILE J 40 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N VAL J 42 " --> pdb=" O SER C 461 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL C 463 " --> pdb=" O VAL J 42 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N SER J 20 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL J 7 " --> pdb=" O SER J 20 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 10 through 12 Processing sheet with id=AD5, first strand: chain 'S' and resid 17 through 19 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 17 through 19 current: chain 'S' and resid 49 through 54 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 49 through 54 current: chain 'S' and resid 87 through 89 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 87 through 89 current: chain 'S' and resid 148 through 150 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 148 through 150 current: chain 'S' and resid 179 through 183 No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'S' and resid 106 through 109 Processing sheet with id=AD7, first strand: chain 'D' and resid 245 through 248 Processing sheet with id=AD8, first strand: chain 'D' and resid 280 through 281 Processing sheet with id=AD9, first strand: chain 'D' and resid 295 through 297 removed outlier: 3.547A pdb=" N GLU D 295 " --> pdb=" O SER D 303 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 348 through 352 removed outlier: 3.603A pdb=" N THR D 368 " --> pdb=" O LEU D 352 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 364 through 372 current: chain 'D' and resid 411 through 420 Processing sheet with id=AE2, first strand: chain 'D' and resid 388 through 389 Processing sheet with id=AE3, first strand: chain 'J' and resid 75 through 78 Processing sheet with id=AE4, first strand: chain 'J' and resid 111 through 118 removed outlier: 3.718A pdb=" N ALA J 112 " --> pdb=" O THR J 127 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 789 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: 8.04 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 13420 1.03 - 1.23: 295 1.23 - 1.43: 5846 1.43 - 1.63: 8596 1.63 - 1.82: 89 Bond restraints: 28246 Sorted by residual: bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" CG PRO J 29 " pdb=" CD PRO J 29 " ideal model delta sigma weight residual 1.503 1.558 -0.055 3.40e-02 8.65e+02 2.60e+00 bond pdb=" CB PRO E 449 " pdb=" CG PRO E 449 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.42e+00 bond pdb=" C1 NAG H 1 " pdb=" C2 NAG H 1 " ideal model delta sigma weight residual 1.532 1.503 0.029 2.00e-02 2.50e+03 2.15e+00 ... (remaining 28241 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 50555 2.15 - 4.29: 326 4.29 - 6.44: 13 6.44 - 8.59: 1 8.59 - 10.73: 1 Bond angle restraints: 50896 Sorted by residual: angle pdb=" CA PRO E 449 " pdb=" N PRO E 449 " pdb=" CD PRO E 449 " ideal model delta sigma weight residual 112.00 107.50 4.50 1.40e+00 5.10e-01 1.03e+01 angle pdb=" C VAL E 448 " pdb=" N PRO E 449 " pdb=" CD PRO E 449 " ideal model delta sigma weight residual 125.00 114.27 10.73 4.10e+00 5.95e-02 6.85e+00 angle pdb=" N ASN J 81 " pdb=" CA ASN J 81 " pdb=" C ASN J 81 " ideal model delta sigma weight residual 114.09 110.10 3.99 1.55e+00 4.16e-01 6.61e+00 angle pdb=" N VAL E 448 " pdb=" CA VAL E 448 " pdb=" C VAL E 448 " ideal model delta sigma weight residual 108.88 113.98 -5.10 2.16e+00 2.14e-01 5.58e+00 angle pdb=" CA LEU E 508 " pdb=" C LEU E 508 " pdb=" N VAL E 509 " ideal model delta sigma weight residual 114.17 117.60 -3.43 1.45e+00 4.76e-01 5.58e+00 ... (remaining 50891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 12173 17.93 - 35.87: 1169 35.87 - 53.80: 418 53.80 - 71.73: 66 71.73 - 89.66: 20 Dihedral angle restraints: 13846 sinusoidal: 7355 harmonic: 6491 Sorted by residual: dihedral pdb=" CB CYS J 109 " pdb=" SG CYS J 109 " pdb=" SG CYS J 134 " pdb=" CB CYS J 134 " ideal model delta sinusoidal sigma weight residual -86.00 -175.36 89.36 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS E 239 " pdb=" SG CYS E 239 " pdb=" SG CYS E 307 " pdb=" CB CYS E 307 " ideal model delta sinusoidal sigma weight residual 93.00 157.52 -64.52 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CA VAL E 448 " pdb=" C VAL E 448 " pdb=" N PRO E 449 " pdb=" CA PRO E 449 " ideal model delta harmonic sigma weight residual -180.00 -146.31 -33.69 0 5.00e+00 4.00e-02 4.54e+01 ... (remaining 13843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.189: 2416 0.189 - 0.378: 2 0.378 - 0.567: 0 0.567 - 0.756: 0 0.756 - 0.944: 1 Chirality restraints: 2419 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN E 451 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.46 -0.94 2.00e-01 2.50e+01 2.23e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C 263 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 65 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 2416 not shown) Planarity restraints: 4426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 448 " 0.100 5.00e-02 4.00e+02 1.51e-01 3.66e+01 pdb=" N PRO E 449 " -0.262 5.00e-02 4.00e+02 pdb=" CA PRO E 449 " 0.084 5.00e-02 4.00e+02 pdb=" CD PRO E 449 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 28 " -0.054 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO J 29 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO J 29 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO J 29 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 308 " 0.031 5.00e-02 4.00e+02 4.64e-02 3.44e+00 pdb=" N PRO A 309 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 309 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 309 " 0.026 5.00e-02 4.00e+02 ... (remaining 4423 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 859 2.13 - 2.75: 49173 2.75 - 3.36: 73285 3.36 - 3.98: 97787 3.98 - 4.60: 148311 Nonbonded interactions: 369415 Sorted by model distance: nonbonded pdb=" HE1 TRP A 383 " pdb=" OG SER A 415 " model vdw 1.512 2.450 nonbonded pdb=" O VAL R 98 " pdb=" H TRP R 183 " model vdw 1.562 2.450 nonbonded pdb="HE21 GLN S 38 " pdb=" OE1 GLU S 49 " model vdw 1.578 2.450 nonbonded pdb=" O PRO R 8 " pdb=" HG SER R 91 " model vdw 1.584 2.450 nonbonded pdb=" O LYS S 73 " pdb=" HH TYR S 77 " model vdw 1.586 2.450 ... (remaining 369410 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' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 256 through 421 or (r \ esid 422 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 423 through 425 or (resid 426 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 427 through 445 or (resid 4 \ 46 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 447 through 449 or (resid 450 and (name N or name CA or name C or name \ O or name CB or name H or name HA )) or resid 451 through 464)) selection = (chain 'B' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 256 through 259 or (r \ esid 260 through 261 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 262 through 345 or (resid 346 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 347 through 356 \ or (resid 357 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 358 through 404 or (resid 405 through 406 and (name N or n \ ame CA or name C or name O or name CB or name H or name HA )) or resid 407 throu \ gh 449 or (resid 450 and (name N or name CA or name C or name O or name CB or na \ me H or name HA )) or resid 451 through 453 or resid 456 through 464)) selection = (chain 'C' and (resid 242 through 310 or (resid 311 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 312 through 345 or (r \ esid 346 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 347 through 356 or (resid 357 and (name N or name CA or name C o \ r name O or name CB or name H or name HA )) or resid 358 through 424 or (resid 4 \ 25 through 426 and (name N or name CA or name C or name O or name CB or name H o \ r name HA )) or resid 427 through 449 or (resid 450 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 451 through 453 or (r \ esid 456 and (name N or name CA or name C or name O or name CB or name OG1 or na \ me CG2 or name HA or name HB or name HG1 or name HG21 or name HG22 or name HG23) \ ) or resid 457 through 464)) selection = (chain 'D' and (resid 242 through 254 or (resid 255 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 256 through 262 or (r \ esid 263 and (name N or name CA or name C or name O or name CB or name CG or nam \ e OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or \ resid 264 through 356 or (resid 357 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 358 through 445 or (resid 446 and (n \ ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \ 447 through 453 or (resid 456 and (name N or name CA or name C or name O or nam \ e CB or name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or n \ ame HG22 or name HG23)) or resid 457 through 464)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'R' selection = chain 'S' } 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: 8.180 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: 0.170 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 30.260 Find NCS groups from input model: 0.360 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: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 : 0.004 0.078 14862 Z= 0.166 Angle : 0.620 12.562 20406 Z= 0.307 Chirality : 0.047 0.944 2419 Planarity : 0.005 0.151 2606 Dihedral : 15.955 89.665 5279 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.69 % Favored : 93.20 % Rotamer: Outliers : 0.41 % Allowed : 25.68 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -1.08 (0.20), residues: 1927 helix: -0.50 (0.60), residues: 93 sheet: -0.12 (0.19), residues: 773 loop : -1.19 (0.19), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 89 TYR 0.009 0.001 TYR C 327 PHE 0.016 0.001 PHE E 75 TRP 0.009 0.001 TRP B 281 HIS 0.003 0.001 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00377 (14821) covalent geometry : angle 0.59768 (20312) SS BOND : bond 0.00346 ( 29) SS BOND : angle 1.20087 ( 58) hydrogen bonds : bond 0.13649 ( 329) hydrogen bonds : angle 6.75669 ( 789) link_BETA1-4 : bond 0.01150 ( 4) link_BETA1-4 : angle 3.88288 ( 12) link_NAG-ASN : bond 0.00504 ( 8) link_NAG-ASN : angle 3.72940 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 126 average time/residue: 0.2761 time to fit residues: 51.7250 Evaluate side-chains 122 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain E residue 230 ASP Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain D residue 431 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.4980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.224670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.175314 restraints weight = 50771.554| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 3.63 r_work: 0.3823 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.0433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14862 Z= 0.142 Angle : 0.573 11.270 20406 Z= 0.278 Chirality : 0.044 0.607 2419 Planarity : 0.005 0.152 2606 Dihedral : 6.037 59.738 2329 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.80 % Favored : 93.15 % Rotamer: Outliers : 1.29 % Allowed : 24.80 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -1.12 (0.19), residues: 1927 helix: -0.64 (0.56), residues: 97 sheet: -0.16 (0.19), residues: 779 loop : -1.19 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 450 TYR 0.008 0.001 TYR B 472 PHE 0.015 0.001 PHE E 75 TRP 0.009 0.001 TRP E 366 HIS 0.003 0.001 HIS E 465 Details of bonding type rmsd covalent geometry : bond 0.00348 (14821) covalent geometry : angle 0.55727 (20312) SS BOND : bond 0.00311 ( 29) SS BOND : angle 1.05826 ( 58) hydrogen bonds : bond 0.03188 ( 329) hydrogen bonds : angle 5.86478 ( 789) link_BETA1-4 : bond 0.00504 ( 4) link_BETA1-4 : angle 2.29870 ( 12) link_NAG-ASN : bond 0.00534 ( 8) link_NAG-ASN : angle 3.37828 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 89 ARG cc_start: 0.7545 (mtp180) cc_final: 0.7233 (ttm170) REVERT: D 400 SER cc_start: 0.7743 (OUTLIER) cc_final: 0.7246 (t) outliers start: 19 outliers final: 12 residues processed: 138 average time/residue: 0.2673 time to fit residues: 55.9534 Evaluate side-chains 132 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 119 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 475 LYS Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain D residue 431 SER Chi-restraints excluded: chain J residue 113 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 4 optimal weight: 0.5980 chunk 191 optimal weight: 0.9990 chunk 108 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 182 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 126 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4650 r_free = 0.4650 target = 0.223866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.173447 restraints weight = 50709.629| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 3.91 r_work: 0.3816 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.0604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14862 Z= 0.136 Angle : 0.559 10.920 20406 Z= 0.270 Chirality : 0.044 0.559 2419 Planarity : 0.005 0.150 2606 Dihedral : 5.703 56.922 2327 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.90 % Favored : 93.05 % Rotamer: Outliers : 2.18 % Allowed : 24.18 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -1.19 (0.19), residues: 1927 helix: -0.66 (0.55), residues: 98 sheet: -0.27 (0.19), residues: 759 loop : -1.18 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG S 171 TYR 0.008 0.001 TYR B 472 PHE 0.015 0.001 PHE E 75 TRP 0.010 0.001 TRP E 366 HIS 0.003 0.001 HIS E 465 Details of bonding type rmsd covalent geometry : bond 0.00335 (14821) covalent geometry : angle 0.54360 (20312) SS BOND : bond 0.00300 ( 29) SS BOND : angle 1.06393 ( 58) hydrogen bonds : bond 0.02796 ( 329) hydrogen bonds : angle 5.65336 ( 789) link_BETA1-4 : bond 0.00514 ( 4) link_BETA1-4 : angle 2.14915 ( 12) link_NAG-ASN : bond 0.00474 ( 8) link_NAG-ASN : angle 3.17799 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6303 (mtm-85) REVERT: B 264 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5197 (tt) REVERT: R 89 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7327 (ttm170) REVERT: D 400 SER cc_start: 0.7854 (OUTLIER) cc_final: 0.7312 (t) outliers start: 32 outliers final: 19 residues processed: 146 average time/residue: 0.2715 time to fit residues: 59.7607 Evaluate side-chains 139 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 450 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 475 LYS Chi-restraints excluded: chain E residue 478 CYS Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain J residue 89 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 136 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 104 optimal weight: 0.0570 chunk 158 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.224736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.173946 restraints weight = 50668.719| |-----------------------------------------------------------------------------| r_work (start): 0.4192 rms_B_bonded: 4.00 r_work: 0.3839 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14862 Z= 0.139 Angle : 0.556 10.615 20406 Z= 0.269 Chirality : 0.043 0.540 2419 Planarity : 0.005 0.149 2606 Dihedral : 5.545 56.239 2326 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.11 % Favored : 92.84 % Rotamer: Outliers : 2.52 % Allowed : 23.77 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -1.21 (0.19), residues: 1927 helix: -0.60 (0.56), residues: 98 sheet: -0.31 (0.19), residues: 758 loop : -1.17 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 24 TYR 0.010 0.001 TYR E 421 PHE 0.015 0.001 PHE E 75 TRP 0.011 0.001 TRP E 366 HIS 0.003 0.001 HIS E 465 Details of bonding type rmsd covalent geometry : bond 0.00343 (14821) covalent geometry : angle 0.54165 (20312) SS BOND : bond 0.00350 ( 29) SS BOND : angle 1.09329 ( 58) hydrogen bonds : bond 0.02611 ( 329) hydrogen bonds : angle 5.54661 ( 789) link_BETA1-4 : bond 0.00512 ( 4) link_BETA1-4 : angle 1.91120 ( 12) link_NAG-ASN : bond 0.00469 ( 8) link_NAG-ASN : angle 3.10157 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 118 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6217 (mtm-85) REVERT: R 89 ARG cc_start: 0.7793 (mtp180) cc_final: 0.7403 (ttm170) REVERT: D 400 SER cc_start: 0.7793 (OUTLIER) cc_final: 0.7239 (t) outliers start: 37 outliers final: 26 residues processed: 146 average time/residue: 0.2559 time to fit residues: 56.8950 Evaluate side-chains 145 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 117 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 450 ARG Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 475 LYS Chi-restraints excluded: chain E residue 478 CYS Chi-restraints excluded: chain E residue 526 CYS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 113 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 149 optimal weight: 8.9990 chunk 182 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 184 optimal weight: 0.5980 chunk 11 optimal weight: 0.0980 chunk 111 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 144 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4671 r_free = 0.4671 target = 0.227764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.176812 restraints weight = 50471.282| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 3.66 r_work: 0.3837 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14862 Z= 0.143 Angle : 0.555 10.387 20406 Z= 0.269 Chirality : 0.043 0.524 2419 Planarity : 0.005 0.147 2606 Dihedral : 5.506 56.602 2326 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.47 % Favored : 92.48 % Rotamer: Outliers : 3.20 % Allowed : 23.16 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -1.23 (0.19), residues: 1927 helix: -0.52 (0.56), residues: 98 sheet: -0.37 (0.19), residues: 764 loop : -1.16 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 24 TYR 0.010 0.001 TYR E 524 PHE 0.016 0.001 PHE E 75 TRP 0.010 0.001 TRP E 366 HIS 0.003 0.001 HIS E 465 Details of bonding type rmsd covalent geometry : bond 0.00352 (14821) covalent geometry : angle 0.54225 (20312) SS BOND : bond 0.00361 ( 29) SS BOND : angle 1.02303 ( 58) hydrogen bonds : bond 0.02510 ( 329) hydrogen bonds : angle 5.46348 ( 789) link_BETA1-4 : bond 0.00519 ( 4) link_BETA1-4 : angle 1.75725 ( 12) link_NAG-ASN : bond 0.00463 ( 8) link_NAG-ASN : angle 3.04024 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 120 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.6935 (OUTLIER) cc_final: 0.6298 (mtm-85) REVERT: B 368 THR cc_start: 0.7590 (OUTLIER) cc_final: 0.7329 (m) REVERT: E 446 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7588 (mt) REVERT: R 89 ARG cc_start: 0.7713 (mtp180) cc_final: 0.7364 (ttm170) REVERT: D 400 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7314 (t) outliers start: 47 outliers final: 35 residues processed: 159 average time/residue: 0.2693 time to fit residues: 65.8187 Evaluate side-chains 156 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 450 ARG Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 475 LYS Chi-restraints excluded: chain E residue 478 CYS Chi-restraints excluded: chain E residue 526 CYS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 113 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 134 optimal weight: 0.6980 chunk 39 optimal weight: 0.0980 chunk 146 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.223344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.173702 restraints weight = 51152.710| |-----------------------------------------------------------------------------| r_work (start): 0.4184 rms_B_bonded: 3.99 r_work: 0.3803 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14862 Z= 0.193 Angle : 0.589 10.279 20406 Z= 0.288 Chirality : 0.044 0.529 2419 Planarity : 0.005 0.146 2606 Dihedral : 5.655 57.627 2324 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.50 % Favored : 90.45 % Rotamer: Outliers : 3.81 % Allowed : 22.55 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -1.38 (0.19), residues: 1927 helix: -0.63 (0.56), residues: 98 sheet: -0.45 (0.19), residues: 763 loop : -1.27 (0.19), residues: 1066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 250 TYR 0.012 0.001 TYR E 36 PHE 0.020 0.002 PHE E 75 TRP 0.011 0.001 TRP E 324 HIS 0.003 0.001 HIS E 465 Details of bonding type rmsd covalent geometry : bond 0.00469 (14821) covalent geometry : angle 0.57510 (20312) SS BOND : bond 0.00443 ( 29) SS BOND : angle 1.22633 ( 58) hydrogen bonds : bond 0.02690 ( 329) hydrogen bonds : angle 5.55091 ( 789) link_BETA1-4 : bond 0.00544 ( 4) link_BETA1-4 : angle 1.66008 ( 12) link_NAG-ASN : bond 0.00576 ( 8) link_NAG-ASN : angle 3.22351 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.6996 (OUTLIER) cc_final: 0.6358 (mtm-85) REVERT: E 446 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7621 (mt) REVERT: R 89 ARG cc_start: 0.7898 (mtp180) cc_final: 0.7571 (ttm170) REVERT: C 348 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7695 (mm-30) REVERT: D 400 SER cc_start: 0.7899 (OUTLIER) cc_final: 0.7365 (t) outliers start: 56 outliers final: 42 residues processed: 165 average time/residue: 0.2493 time to fit residues: 63.3981 Evaluate side-chains 159 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 114 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 450 ARG Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 324 TRP Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 475 LYS Chi-restraints excluded: chain E residue 478 CYS Chi-restraints excluded: chain E residue 526 CYS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain J residue 71 LYS Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 89 SER Chi-restraints excluded: chain J residue 113 VAL Chi-restraints excluded: chain J residue 125 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 107 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 0.0970 chunk 79 optimal weight: 0.9990 chunk 104 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 445 ASN C 291 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.224615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.176714 restraints weight = 50895.852| |-----------------------------------------------------------------------------| r_work (start): 0.4248 rms_B_bonded: 3.38 r_work: 0.3842 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14862 Z= 0.114 Angle : 0.564 9.917 20406 Z= 0.273 Chirality : 0.043 0.503 2419 Planarity : 0.005 0.145 2606 Dihedral : 5.507 55.454 2324 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.69 % Favored : 93.25 % Rotamer: Outliers : 3.41 % Allowed : 23.37 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % 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: -1.27 (0.19), residues: 1927 helix: -0.54 (0.56), residues: 98 sheet: -0.40 (0.19), residues: 764 loop : -1.18 (0.19), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 450 TYR 0.018 0.001 TYR J 135 PHE 0.013 0.001 PHE E 75 TRP 0.011 0.001 TRP E 366 HIS 0.003 0.000 HIS B 350 Details of bonding type rmsd covalent geometry : bond 0.00288 (14821) covalent geometry : angle 0.54576 (20312) SS BOND : bond 0.00285 ( 29) SS BOND : angle 1.77683 ( 58) hydrogen bonds : bond 0.02350 ( 329) hydrogen bonds : angle 5.38520 ( 789) link_BETA1-4 : bond 0.00529 ( 4) link_BETA1-4 : angle 1.69018 ( 12) link_NAG-ASN : bond 0.00437 ( 8) link_NAG-ASN : angle 2.97857 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3854 Ramachandran restraints generated. 1927 Oldfield, 0 Emsley, 1927 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Residue LYS 361 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 446 is missing expected H atoms. Skipping. Residue MET 7 is missing expected H atoms. Skipping. Residue SER 11 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Residue SER 45 is missing expected H atoms. Skipping. Residue TYR 86 is missing expected H atoms. Skipping. Residue LYS 104 is missing expected H atoms. Skipping. Residue LEU 115 is missing expected H atoms. Skipping. Residue MET 116 is missing expected H atoms. Skipping. Residue SER 158 is missing expected H atoms. Skipping. Residue LEU 164 is missing expected H atoms. Skipping. Residue LEU 192 is missing expected H atoms. Skipping. Residue SER 260 is missing expected H atoms. Skipping. Residue LEU 271 is missing expected H atoms. Skipping. Residue SER 275 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LEU 298 is missing expected H atoms. Skipping. Residue TYR 302 is missing expected H atoms. Skipping. Residue LYS 319 is missing expected H atoms. Skipping. Residue SER 330 is missing expected H atoms. Skipping. Residue LYS 331 is missing expected H atoms. Skipping. Residue LEU 338 is missing expected H atoms. Skipping. Residue SER 339 is missing expected H atoms. Skipping. Residue SER 341 is missing expected H atoms. Skipping. Residue LYS 377 is missing expected H atoms. Skipping. Residue LYS 394 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 425 is missing expected H atoms. Skipping. Residue LYS 426 is missing expected H atoms. Skipping. Residue LYS 454 is missing expected H atoms. Skipping. Evaluate side-chains 167 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 117 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 450 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6329 (mtm-85) REVERT: E 446 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7564 (mt) REVERT: R 89 ARG cc_start: 0.7792 (mtp180) cc_final: 0.7433 (ttm170) REVERT: C 348 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7667 (mm-30) REVERT: D 400 SER cc_start: 0.7755 (OUTLIER) cc_final: 0.7214 (t) outliers start: 50 outliers final: 40 residues processed: 160 average time/residue: 0.2631 time to fit residues: 63.3905 Evaluate side-chains 158 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 SER Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 450 ARG Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 378 ASP Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 83 SER Chi-restraints excluded: chain E residue 227 VAL Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 324 TRP Chi-restraints excluded: chain E residue 398 LEU Chi-restraints excluded: chain E residue 435 VAL Chi-restraints excluded: chain E residue 446 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 475 LYS Chi-restraints excluded: chain E residue 478 CYS Chi-restraints excluded: chain E residue 526 CYS Chi-restraints excluded: chain E residue 540 VAL Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 80 GLN Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain S residue 114 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 327 TYR Chi-restraints excluded: chain D residue 357 GLU Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain J residue 71 LYS Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 113 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- 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: 61.989 > 50: distance: 65 - 79: 10.634 distance: 79 - 80: 6.720 distance: 79 - 86: 11.156 distance: 80 - 81: 8.673 distance: 80 - 83: 9.057 distance: 80 - 87: 9.085 distance: 81 - 82: 21.001 distance: 81 - 95: 17.703 distance: 83 - 84: 13.286 distance: 83 - 85: 33.010 distance: 83 - 88: 17.324 distance: 84 - 89: 21.879 distance: 84 - 90: 20.497 distance: 84 - 91: 10.572 distance: 85 - 92: 16.939 distance: 85 - 93: 22.207 distance: 85 - 94: 27.042 distance: 95 - 96: 14.915 distance: 95 - 106: 5.134 distance: 95 - 389: 13.732 distance: 96 - 97: 8.210 distance: 96 - 99: 8.675 distance: 96 - 107: 18.177 distance: 97 - 98: 3.677 distance: 97 - 119: 6.300 distance: 98 - 386: 22.736 distance: 99 - 100: 12.783 distance: 99 - 108: 3.868 distance: 99 - 109: 6.364 distance: 100 - 101: 14.994 distance: 100 - 110: 11.561 distance: 100 - 111: 11.280 distance: 101 - 102: 12.065 distance: 101 - 112: 5.049 distance: 101 - 113: 3.554 distance: 102 - 103: 16.519 distance: 102 - 114: 5.982 distance: 103 - 104: 10.089 distance: 103 - 105: 10.829 distance: 104 - 115: 7.432 distance: 104 - 116: 14.273 distance: 105 - 117: 7.134 distance: 105 - 118: 14.653 distance: 119 - 120: 5.853 distance: 119 - 133: 6.893 distance: 120 - 121: 7.572 distance: 120 - 134: 3.674 distance: 121 - 122: 15.309 distance: 121 - 143: 8.214 distance: 123 - 124: 3.385 distance: 123 - 136: 4.258 distance: 124 - 125: 4.460 distance: 124 - 126: 5.012 distance: 125 - 127: 8.007 distance: 125 - 137: 3.763 distance: 126 - 128: 11.016 distance: 126 - 129: 3.820 distance: 127 - 128: 6.679 distance: 127 - 138: 4.121 distance: 128 - 130: 8.556 distance: 129 - 131: 8.333 distance: 129 - 139: 3.956 distance: 130 - 140: 6.505 distance: 131 - 132: 8.545 distance: 132 - 142: 5.859 distance: 143 - 144: 12.746 distance: 143 - 151: 4.319 distance: 143 - 368: 17.051 distance: 144 - 145: 8.034 distance: 144 - 147: 5.900 distance: 144 - 152: 16.877 distance: 145 - 146: 12.385 distance: 145 - 162: 7.377 distance: 146 - 365: 15.529 distance: 147 - 148: 7.356 distance: 147 - 153: 5.194 distance: 147 - 154: 5.278 distance: 148 - 149: 4.563 distance: 148 - 150: 9.530 distance: 148 - 155: 9.497 distance: 149 - 156: 9.297 distance: 149 - 157: 7.919 distance: 149 - 158: 3.644 distance: 150 - 159: 16.286 distance: 150 - 160: 5.034 distance: 150 - 161: 19.403 distance: 162 - 171: 5.583 distance: 162 - 200: 29.685 distance: 163 - 164: 4.503 distance: 163 - 166: 13.271 distance: 163 - 172: 10.921 distance: 164 - 165: 15.575 distance: 164 - 179: 4.393 distance: 165 - 197: 14.912 distance: 166 - 167: 29.114 distance: 166 - 173: 20.495 distance: 166 - 174: 10.822 distance: 167 - 168: 5.980 distance: 167 - 175: 7.397 distance: 167 - 176: 15.531 distance: 168 - 169: 12.123 distance: 168 - 170: 11.461 distance: 170 - 177: 17.741 distance: 179 - 180: 5.603 distance: 179 - 183: 6.384 distance: 180 - 181: 7.599 distance: 180 - 184: 9.375 distance: 180 - 185: 12.013 distance: 181 - 182: 24.970 distance: 181 - 186: 9.919 distance: 186 - 187: 10.006 distance: 186 - 192: 15.449 distance: 187 - 188: 7.366 distance: 187 - 190: 12.936 distance: 187 - 193: 20.965 distance: 188 - 189: 19.441 distance: 188 - 197: 13.385 distance: 190 - 191: 3.505 distance: 190 - 194: 34.494 distance: 190 - 195: 9.547 distance: 191 - 196: 31.925 distance: 197 - 198: 12.017 distance: 197 - 202: 13.168 distance: 198 - 199: 19.493 distance: 198 - 201: 13.657 distance: 198 - 203: 18.040 distance: 199 - 200: 26.625 distance: 199 - 204: 14.890 distance: 204 - 205: 9.078 distance: 204 - 213: 8.390 distance: 205 - 206: 18.189 distance: 205 - 208: 18.192 distance: 205 - 214: 15.328 distance: 206 - 207: 10.961 distance: 206 - 219: 4.541 distance: 208 - 209: 5.552 distance: 208 - 215: 5.004 distance: 209 - 210: 31.879 distance: 210 - 211: 26.174 distance: 210 - 212: 10.585 distance: 219 - 227: 50.191 distance: 220 - 221: 20.303 distance: 220 - 223: 22.465 distance: 220 - 228: 13.557 distance: 221 - 222: 11.357 distance: 221 - 238: 20.899 distance: 223 - 224: 21.483 distance: 223 - 229: 16.863 distance: 223 - 230: 6.941 distance: 224 - 225: 20.997 distance: 224 - 226: 42.548 distance: 224 - 231: 20.361 distance: 225 - 232: 9.285 distance: 225 - 233: 17.106 distance: 225 - 234: 14.462 distance: 226 - 235: 3.137 distance: 226 - 236: 18.842 distance: 226 - 237: 21.278