Starting phenix.real_space_refine on Mon May 26 06:37:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sku_40567/05_2025/8sku_40567_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sku_40567/05_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_40567/05_2025/8sku_40567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sku_40567/05_2025/8sku_40567.map" model { file = "/net/cci-nas-00/data/ceres_data/8sku_40567/05_2025/8sku_40567_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sku_40567/05_2025/8sku_40567_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.017 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 5} 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: {'GLN:plan1': 1, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 4} 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: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 5} 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: {'GLN:plan1': 2, 'ASP:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 6} 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, 'ASN:plan1': 1, 'ASP:plan': 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: 14.89, per 1000 atoms: 0.53 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: 8.56 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 3.03 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: 11.94 Time building geometry restraints manager: 10.15 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: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.540 Extract box with map and model: 1.220 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 66.790 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.120 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:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.670 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), 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 TRP 0.009 0.001 TRP B 281 HIS 0.003 0.001 HIS B 350 PHE 0.016 0.001 PHE E 75 TYR 0.009 0.001 TYR C 327 ARG 0.003 0.000 ARG E 89 Details of bonding type rmsd link_NAG-ASN : bond 0.00504 ( 8) link_NAG-ASN : angle 3.72940 ( 24) link_BETA1-4 : bond 0.01150 ( 4) link_BETA1-4 : angle 3.88288 ( 12) hydrogen bonds : bond 0.13649 ( 329) hydrogen bonds : angle 6.75669 ( 789) SS BOND : bond 0.00346 ( 29) SS BOND : angle 1.20087 ( 58) covalent geometry : bond 0.00377 (14821) covalent geometry : angle 0.59768 (20312) *********************** 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 : 2.181 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: 0.5525 time to fit residues: 104.1520 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 : 2.154 ------------------------------------------------------------------------------- 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 163 optimal weight: 9.9990 chunk 147 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 99 optimal weight: 20.0000 chunk 78 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 176 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4639 r_free = 0.4639 target = 0.222719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.172063 restraints weight = 50884.715| |-----------------------------------------------------------------------------| r_work (start): 0.4177 rms_B_bonded: 4.09 r_work: 0.3787 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.0506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 14862 Z= 0.188 Angle : 0.602 11.449 20406 Z= 0.295 Chirality : 0.045 0.611 2419 Planarity : 0.005 0.152 2606 Dihedral : 6.148 59.103 2329 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.25 % Favored : 91.70 % Rotamer: Outliers : 1.77 % Allowed : 24.66 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.19), residues: 1927 helix: -0.68 (0.56), residues: 96 sheet: -0.25 (0.19), residues: 781 loop : -1.28 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 366 HIS 0.004 0.001 HIS E 465 PHE 0.018 0.001 PHE E 75 TYR 0.011 0.001 TYR C 395 ARG 0.004 0.000 ARG C 450 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 8) link_NAG-ASN : angle 3.49621 ( 24) link_BETA1-4 : bond 0.00455 ( 4) link_BETA1-4 : angle 2.18102 ( 12) hydrogen bonds : bond 0.03105 ( 329) hydrogen bonds : angle 5.93017 ( 789) SS BOND : bond 0.00407 ( 29) SS BOND : angle 1.18804 ( 58) covalent geometry : bond 0.00455 (14821) covalent geometry : angle 0.58526 (20312) *********************** 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 148 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 2.181 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: A 450 ARG cc_start: 0.6958 (OUTLIER) cc_final: 0.6333 (mtm-85) REVERT: B 264 LEU cc_start: 0.5676 (OUTLIER) cc_final: 0.5252 (tt) REVERT: R 89 ARG cc_start: 0.7688 (mtp180) cc_final: 0.7332 (ttm170) REVERT: D 400 SER cc_start: 0.7783 (OUTLIER) cc_final: 0.7288 (t) outliers start: 26 outliers final: 16 residues processed: 143 average time/residue: 0.5324 time to fit residues: 114.5855 Evaluate side-chains 135 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 2.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 398 LEU Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 475 LYS 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 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 89 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 39 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 179 optimal weight: 0.5980 chunk 155 optimal weight: 20.0000 chunk 75 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.224090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.163152 restraints weight = 50678.345| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 3.22 r_work: 0.3853 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.0679 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= 0.126 Angle : 0.558 10.900 20406 Z= 0.270 Chirality : 0.043 0.553 2419 Planarity : 0.005 0.150 2606 Dihedral : 5.735 56.741 2327 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.38 % Favored : 93.57 % Rotamer: Outliers : 2.18 % Allowed : 24.25 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.19), residues: 1927 helix: -0.73 (0.55), residues: 98 sheet: -0.30 (0.19), residues: 758 loop : -1.22 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 366 HIS 0.003 0.001 HIS B 350 PHE 0.013 0.001 PHE E 75 TYR 0.009 0.001 TYR E 365 ARG 0.007 0.000 ARG J 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00467 ( 8) link_NAG-ASN : angle 3.18148 ( 24) link_BETA1-4 : bond 0.00457 ( 4) link_BETA1-4 : angle 2.19418 ( 12) hydrogen bonds : bond 0.02795 ( 329) hydrogen bonds : angle 5.67392 ( 789) SS BOND : bond 0.00320 ( 29) SS BOND : angle 1.08318 ( 58) covalent geometry : bond 0.00310 (14821) covalent geometry : angle 0.54249 (20312) *********************** 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 151 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 119 time to evaluate : 2.380 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: 0.6876 (OUTLIER) cc_final: 0.6247 (mtm-85) REVERT: B 264 LEU cc_start: 0.5767 (OUTLIER) cc_final: 0.5257 (tt) REVERT: R 89 ARG cc_start: 0.7741 (mtp180) cc_final: 0.7368 (ttm170) REVERT: D 400 SER cc_start: 0.7791 (OUTLIER) cc_final: 0.7258 (t) outliers start: 32 outliers final: 21 residues processed: 143 average time/residue: 0.5366 time to fit residues: 116.5709 Evaluate side-chains 141 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 2.115 ------------------------------------------------------------------------------- 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 378 ASP 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 26 ILE 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 113 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.224444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.173710 restraints weight = 51088.408| |-----------------------------------------------------------------------------| r_work (start): 0.4169 rms_B_bonded: 4.00 r_work: 0.3811 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3683 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14862 Z= 0.145 Angle : 0.558 10.671 20406 Z= 0.271 Chirality : 0.044 0.543 2419 Planarity : 0.005 0.149 2606 Dihedral : 5.589 56.890 2326 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.63 % Favored : 92.32 % Rotamer: Outliers : 2.86 % Allowed : 23.57 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.19), residues: 1927 helix: -0.66 (0.55), residues: 98 sheet: -0.35 (0.19), residues: 759 loop : -1.23 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 366 HIS 0.003 0.001 HIS E 465 PHE 0.016 0.001 PHE E 75 TYR 0.010 0.001 TYR E 421 ARG 0.003 0.000 ARG A 450 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 8) link_NAG-ASN : angle 3.12617 ( 24) link_BETA1-4 : bond 0.00522 ( 4) link_BETA1-4 : angle 1.87298 ( 12) hydrogen bonds : bond 0.02617 ( 329) hydrogen bonds : angle 5.58677 ( 789) SS BOND : bond 0.00635 ( 29) SS BOND : angle 1.13531 ( 58) covalent geometry : bond 0.00357 (14821) covalent geometry : angle 0.54390 (20312) *********************** 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 161 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 119 time to evaluate : 2.116 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: 0.6863 (OUTLIER) cc_final: 0.6240 (mtm-85) REVERT: B 264 LEU cc_start: 0.5855 (OUTLIER) cc_final: 0.5407 (tt) REVERT: B 368 THR cc_start: 0.7668 (OUTLIER) cc_final: 0.7404 (m) REVERT: E 446 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7748 (mt) REVERT: R 89 ARG cc_start: 0.7830 (mtp180) cc_final: 0.7441 (ttm170) REVERT: D 400 SER cc_start: 0.7832 (OUTLIER) cc_final: 0.7277 (t) outliers start: 42 outliers final: 31 residues processed: 153 average time/residue: 0.5028 time to fit residues: 118.9570 Evaluate side-chains 154 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 2.091 ------------------------------------------------------------------------------- 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 307 VAL Chi-restraints excluded: chain B residue 316 ASN Chi-restraints excluded: chain B residue 324 THR 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 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 327 TYR Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain J residue 87 THR 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 53 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 38 optimal weight: 0.0470 chunk 140 optimal weight: 0.0010 chunk 166 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 124 optimal weight: 1.9990 overall best weight: 0.5084 ------------------------------------------------------------------------------- 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 = 0.4676 r_free = 0.4676 target = 0.226541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.176596 restraints weight = 50782.485| |-----------------------------------------------------------------------------| r_work (start): 0.4211 rms_B_bonded: 3.72 r_work: 0.3867 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14862 Z= 0.103 Angle : 0.535 10.317 20406 Z= 0.257 Chirality : 0.043 0.512 2419 Planarity : 0.005 0.148 2606 Dihedral : 5.351 53.816 2326 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.08 % Rotamer: Outliers : 2.86 % Allowed : 23.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.19), residues: 1927 helix: -0.52 (0.56), residues: 98 sheet: -0.30 (0.19), residues: 759 loop : -1.13 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 366 HIS 0.002 0.000 HIS B 350 PHE 0.012 0.001 PHE E 75 TYR 0.007 0.001 TYR E 365 ARG 0.003 0.000 ARG A 450 Details of bonding type rmsd link_NAG-ASN : bond 0.00426 ( 8) link_NAG-ASN : angle 2.94150 ( 24) link_BETA1-4 : bond 0.00541 ( 4) link_BETA1-4 : angle 1.81871 ( 12) hydrogen bonds : bond 0.02391 ( 329) hydrogen bonds : angle 5.40874 ( 789) SS BOND : bond 0.00247 ( 29) SS BOND : angle 0.90960 ( 58) covalent geometry : bond 0.00262 (14821) covalent geometry : angle 0.52199 (20312) *********************** 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 163 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 121 time to evaluate : 2.114 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: symmetry clash REVERT: B 264 LEU cc_start: 0.6028 (OUTLIER) cc_final: 0.5479 (tt) REVERT: E 446 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7608 (mt) REVERT: R 89 ARG cc_start: 0.7616 (mtp180) cc_final: 0.7300 (ttm170) REVERT: D 400 SER cc_start: 0.7721 (OUTLIER) cc_final: 0.7171 (t) outliers start: 42 outliers final: 30 residues processed: 157 average time/residue: 0.5289 time to fit residues: 126.9331 Evaluate side-chains 151 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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 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 378 ASP Chi-restraints excluded: chain B residue 405 SER Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain E residue 52 SER 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 99 optimal weight: 0.0980 chunk 171 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 119 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 144 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4669 r_free = 0.4669 target = 0.225461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.175610 restraints weight = 51192.008| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 3.86 r_work: 0.3855 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 14862 Z= 0.122 Angle : 0.538 10.098 20406 Z= 0.259 Chirality : 0.043 0.507 2419 Planarity : 0.005 0.146 2606 Dihedral : 5.323 53.560 2326 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.27 % Favored : 92.68 % Rotamer: Outliers : 3.27 % Allowed : 22.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.19), residues: 1927 helix: -0.46 (0.56), residues: 98 sheet: -0.32 (0.19), residues: 760 loop : -1.14 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 366 HIS 0.002 0.001 HIS B 436 PHE 0.015 0.001 PHE E 75 TYR 0.007 0.001 TYR B 472 ARG 0.005 0.000 ARG C 250 Details of bonding type rmsd link_NAG-ASN : bond 0.00440 ( 8) link_NAG-ASN : angle 2.92788 ( 24) link_BETA1-4 : bond 0.00521 ( 4) link_BETA1-4 : angle 1.67906 ( 12) hydrogen bonds : bond 0.02392 ( 329) hydrogen bonds : angle 5.30826 ( 789) SS BOND : bond 0.00282 ( 29) SS BOND : angle 0.96269 ( 58) covalent geometry : bond 0.00304 (14821) covalent geometry : angle 0.52526 (20312) *********************** 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 168 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 120 time to evaluate : 2.358 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: 0.6815 (OUTLIER) cc_final: 0.6204 (mtm-85) REVERT: E 446 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7603 (mt) REVERT: R 89 ARG cc_start: 0.7753 (mtp180) cc_final: 0.7409 (ttm170) REVERT: D 400 SER cc_start: 0.7835 (OUTLIER) cc_final: 0.7239 (t) outliers start: 48 outliers final: 36 residues processed: 161 average time/residue: 0.4991 time to fit residues: 124.7491 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 : 2.048 ------------------------------------------------------------------------------- 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 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 70 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 142 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 291 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.225064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.174866 restraints weight = 50851.199| |-----------------------------------------------------------------------------| r_work (start): 0.4187 rms_B_bonded: 3.65 r_work: 0.3827 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14862 Z= 0.182 Angle : 0.575 10.092 20406 Z= 0.280 Chirality : 0.044 0.514 2419 Planarity : 0.005 0.145 2606 Dihedral : 5.536 59.718 2324 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.93 % Favored : 91.02 % Rotamer: Outliers : 3.68 % Allowed : 22.68 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 1927 helix: -0.57 (0.56), residues: 98 sheet: -0.45 (0.19), residues: 762 loop : -1.19 (0.19), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 324 HIS 0.003 0.001 HIS E 465 PHE 0.020 0.002 PHE E 75 TYR 0.011 0.001 TYR E 36 ARG 0.003 0.000 ARG A 401 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 8) link_NAG-ASN : angle 3.10057 ( 24) link_BETA1-4 : bond 0.00535 ( 4) link_BETA1-4 : angle 1.63750 ( 12) hydrogen bonds : bond 0.02590 ( 329) hydrogen bonds : angle 5.42308 ( 789) SS BOND : bond 0.00443 ( 29) SS BOND : angle 1.08621 ( 58) covalent geometry : bond 0.00446 (14821) covalent geometry : angle 0.56149 (20312) *********************** 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 171 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 117 time to evaluate : 2.038 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: A 450 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6345 (mtm-85) REVERT: B 368 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7417 (m) REVERT: E 446 LEU cc_start: 0.7919 (OUTLIER) cc_final: 0.7568 (mt) REVERT: R 89 ARG cc_start: 0.7866 (mtp180) cc_final: 0.7542 (ttm170) REVERT: D 400 SER cc_start: 0.7866 (OUTLIER) cc_final: 0.7308 (t) outliers start: 54 outliers final: 41 residues processed: 164 average time/residue: 0.4913 time to fit residues: 124.2779 Evaluate side-chains 160 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 2.018 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 113 optimal weight: 30.0000 chunk 69 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 164 optimal weight: 9.9990 chunk 193 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.223832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.177786 restraints weight = 50155.925| |-----------------------------------------------------------------------------| r_work (start): 0.4221 rms_B_bonded: 3.10 r_work: 0.3859 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1234 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= 0.138 Angle : 0.567 9.861 20406 Z= 0.275 Chirality : 0.043 0.502 2419 Planarity : 0.005 0.144 2606 Dihedral : 5.523 57.276 2324 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.52 % Favored : 92.42 % Rotamer: Outliers : 3.34 % Allowed : 23.30 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.19), residues: 1927 helix: -0.55 (0.56), residues: 98 sheet: -0.44 (0.19), residues: 767 loop : -1.18 (0.19), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 366 HIS 0.003 0.001 HIS B 350 PHE 0.015 0.001 PHE E 75 TYR 0.019 0.001 TYR J 135 ARG 0.003 0.000 ARG A 450 Details of bonding type rmsd link_NAG-ASN : bond 0.00466 ( 8) link_NAG-ASN : angle 3.00266 ( 24) link_BETA1-4 : bond 0.00541 ( 4) link_BETA1-4 : angle 1.64129 ( 12) hydrogen bonds : bond 0.02413 ( 329) hydrogen bonds : angle 5.34604 ( 789) SS BOND : bond 0.00328 ( 29) SS BOND : angle 1.30851 ( 58) covalent geometry : bond 0.00343 (14821) covalent geometry : angle 0.55339 (20312) *********************** REFINEMENT MACRO_CYCLE 8 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 164 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 115 time to evaluate : 2.040 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: A 450 ARG cc_start: 0.6957 (OUTLIER) cc_final: 0.6360 (mtm-85) REVERT: E 446 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7562 (mt) REVERT: R 89 ARG cc_start: 0.7796 (mtp180) cc_final: 0.7524 (ttm170) REVERT: D 400 SER cc_start: 0.7812 (OUTLIER) cc_final: 0.7264 (t) outliers start: 49 outliers final: 42 residues processed: 160 average time/residue: 0.5320 time to fit residues: 131.5629 Evaluate side-chains 158 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 2.138 ------------------------------------------------------------------------------- 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 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 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 357 GLU Chi-restraints excluded: chain D residue 400 SER Chi-restraints excluded: chain J residue 71 LYS Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 89 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 193 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 49 optimal weight: 0.4980 chunk 130 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 80 optimal weight: 0.0070 chunk 140 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 150 optimal weight: 0.0030 chunk 167 optimal weight: 6.9990 overall best weight: 0.3808 ------------------------------------------------------------------------------- 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 = 0.4674 r_free = 0.4674 target = 0.225924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.181236 restraints weight = 51323.200| |-----------------------------------------------------------------------------| r_work (start): 0.4255 rms_B_bonded: 3.06 r_work: 0.3876 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 14862 Z= 0.097 Angle : 0.535 9.509 20406 Z= 0.258 Chirality : 0.043 0.484 2419 Planarity : 0.005 0.144 2606 Dihedral : 5.212 52.386 2324 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.02 % Favored : 93.93 % Rotamer: Outliers : 2.66 % Allowed : 23.91 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.20), residues: 1927 helix: -0.41 (0.57), residues: 98 sheet: -0.31 (0.19), residues: 762 loop : -1.09 (0.20), residues: 1067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 366 HIS 0.003 0.000 HIS B 436 PHE 0.011 0.001 PHE E 75 TYR 0.021 0.001 TYR J 110 ARG 0.003 0.000 ARG A 450 Details of bonding type rmsd link_NAG-ASN : bond 0.00404 ( 8) link_NAG-ASN : angle 2.76593 ( 24) link_BETA1-4 : bond 0.00549 ( 4) link_BETA1-4 : angle 1.62506 ( 12) hydrogen bonds : bond 0.02202 ( 329) hydrogen bonds : angle 5.18624 ( 789) SS BOND : bond 0.00235 ( 29) SS BOND : angle 1.08410 ( 58) covalent geometry : bond 0.00249 (14821) covalent geometry : angle 0.52354 (20312) *********************** REFINEMENT MACRO_CYCLE 9 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 159 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 120 time to evaluate : 2.003 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: A 450 ARG cc_start: 0.6894 (OUTLIER) cc_final: 0.6334 (mtm-85) REVERT: E 446 LEU cc_start: 0.7819 (OUTLIER) cc_final: 0.7487 (mt) REVERT: R 89 ARG cc_start: 0.7690 (mtp180) cc_final: 0.7374 (ttm170) outliers start: 39 outliers final: 36 residues processed: 154 average time/residue: 0.5054 time to fit residues: 117.9152 Evaluate side-chains 155 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 2.034 ------------------------------------------------------------------------------- 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 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 405 SER Chi-restraints excluded: chain B residue 466 GLU Chi-restraints excluded: chain E residue 2 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 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 357 GLU Chi-restraints excluded: chain J residue 71 LYS Chi-restraints excluded: chain J residue 82 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 63 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 181 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 128 optimal weight: 0.0970 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.4674 r_free = 0.4674 target = 0.223911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.177141 restraints weight = 50292.462| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 3.24 r_work: 0.3843 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14862 Z= 0.143 Angle : 0.552 9.430 20406 Z= 0.267 Chirality : 0.043 0.492 2419 Planarity : 0.005 0.142 2606 Dihedral : 5.333 55.625 2324 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.73 % Favored : 92.22 % Rotamer: Outliers : 2.93 % Allowed : 23.64 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.20), residues: 1927 helix: -0.44 (0.56), residues: 98 sheet: -0.40 (0.19), residues: 764 loop : -1.13 (0.20), residues: 1065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 324 HIS 0.002 0.001 HIS B 350 PHE 0.016 0.001 PHE E 75 TYR 0.011 0.001 TYR J 110 ARG 0.003 0.000 ARG A 450 Details of bonding type rmsd link_NAG-ASN : bond 0.00460 ( 8) link_NAG-ASN : angle 2.90051 ( 24) link_BETA1-4 : bond 0.00516 ( 4) link_BETA1-4 : angle 1.58196 ( 12) hydrogen bonds : bond 0.02336 ( 329) hydrogen bonds : angle 5.24233 ( 789) SS BOND : bond 0.00315 ( 29) SS BOND : angle 1.29780 ( 58) covalent geometry : bond 0.00356 (14821) covalent geometry : angle 0.53843 (20312) ********************** REFINEMENT MACRO_CYCLE 10 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 160 residues out of total 1685 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 117 time to evaluate : 2.165 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: A 450 ARG cc_start: 0.6926 (OUTLIER) cc_final: 0.6340 (mtm-85) REVERT: E 446 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7507 (mt) REVERT: R 89 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7455 (ttm170) outliers start: 43 outliers final: 41 residues processed: 154 average time/residue: 0.4981 time to fit residues: 117.7904 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 : 2.040 ------------------------------------------------------------------------------- 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 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 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 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 J residue 71 LYS Chi-restraints excluded: chain J residue 82 GLN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 157 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 11 optimal weight: 0.0970 chunk 47 optimal weight: 0.9990 chunk 128 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 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 = 0.4659 r_free = 0.4659 target = 0.223755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.179416 restraints weight = 51257.885| |-----------------------------------------------------------------------------| r_work (start): 0.4293 rms_B_bonded: 3.13 r_work: 0.3898 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 14862 Z= 0.138 Angle : 0.553 9.223 20406 Z= 0.268 Chirality : 0.043 0.489 2419 Planarity : 0.005 0.142 2606 Dihedral : 5.378 56.126 2324 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.32 % Favored : 92.63 % Rotamer: Outliers : 3.20 % Allowed : 23.64 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.20), residues: 1927 helix: -0.44 (0.56), residues: 98 sheet: -0.40 (0.19), residues: 766 loop : -1.14 (0.20), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 324 HIS 0.003 0.001 HIS B 350 PHE 0.016 0.001 PHE E 75 TYR 0.011 0.001 TYR E 524 ARG 0.003 0.000 ARG A 450 Details of bonding type rmsd link_NAG-ASN : bond 0.00447 ( 8) link_NAG-ASN : angle 2.89881 ( 24) link_BETA1-4 : bond 0.00523 ( 4) link_BETA1-4 : angle 1.60319 ( 12) hydrogen bonds : bond 0.02319 ( 329) hydrogen bonds : angle 5.24640 ( 789) SS BOND : bond 0.00307 ( 29) SS BOND : angle 1.22271 ( 58) covalent geometry : bond 0.00342 (14821) covalent geometry : angle 0.53970 (20312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14420.34 seconds wall clock time: 247 minutes 42.70 seconds (14862.70 seconds total)