Starting phenix.real_space_refine on Wed Aug 27 00:42:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xl7_38440/08_2025/8xl7_38440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xl7_38440/08_2025/8xl7_38440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xl7_38440/08_2025/8xl7_38440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xl7_38440/08_2025/8xl7_38440.map" model { file = "/net/cci-nas-00/data/ceres_data/8xl7_38440/08_2025/8xl7_38440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xl7_38440/08_2025/8xl7_38440.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 18 5.49 5 S 250 5.16 5 C 27976 2.51 5 N 7706 2.21 5 O 8364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44314 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1615 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain breaks: 1 Chain: "B" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4153 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "C" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1615 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain breaks: 1 Chain: "D" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4153 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "E" Number of atoms: 1615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1615 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain breaks: 1 Chain: "F" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4153 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "G" Number of atoms: 4517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4517 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 26, 'TRANS': 557} Chain breaks: 2 Chain: "H" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4153 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "I" Number of atoms: 5121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5121 Classifications: {'peptide': 660} Link IDs: {'PTRANS': 28, 'TRANS': 631} Chain breaks: 1 Chain: "J" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4153 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "K" Number of atoms: 4517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4517 Classifications: {'peptide': 584} Link IDs: {'PTRANS': 26, 'TRANS': 557} Chain breaks: 2 Chain: "L" Number of atoms: 4153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4153 Classifications: {'peptide': 541} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'ACO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 102 Unusual residues: {'ACO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'BTN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.85, per 1000 atoms: 0.20 Number of scatterers: 44314 At special positions: 0 Unit cell: (152.977, 160.518, 191.759, 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 250 16.00 P 18 15.00 O 8364 8.00 N 7706 7.00 C 27976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.95 Conformation dependent library (CDL) restraints added in 2.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10408 Finding SS restraints... Secondary structure from input PDB file: 215 helices and 64 sheets defined 40.7% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 504 through 529 removed outlier: 3.771A pdb=" N GLN A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'B' and resid 39 through 64 Processing helix chain 'B' and resid 68 through 77 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 114 through 117 removed outlier: 3.509A pdb=" N GLY B 117 " --> pdb=" O VAL B 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 114 through 117' Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 146 through 164 Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 191 through 202 removed outlier: 4.382A pdb=" N PHE B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.940A pdb=" N ALA B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 251 Processing helix chain 'B' and resid 256 through 261 Processing helix chain 'B' and resid 262 through 269 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 315 through 322 Processing helix chain 'B' and resid 331 through 339 removed outlier: 3.570A pdb=" N ARG B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 343 Processing helix chain 'B' and resid 377 through 395 removed outlier: 3.569A pdb=" N ALA B 381 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 417 removed outlier: 3.841A pdb=" N GLU B 414 " --> pdb=" O GLY B 410 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU B 416 " --> pdb=" O GLU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 432 removed outlier: 4.107A pdb=" N ALA B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 452 Processing helix chain 'B' and resid 454 through 458 removed outlier: 3.853A pdb=" N SER B 458 " --> pdb=" O ARG B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 491 Processing helix chain 'B' and resid 497 through 517 Proline residue: B 508 - end of helix removed outlier: 3.661A pdb=" N LYS B 512 " --> pdb=" O PRO B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.747A pdb=" N ARG B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 549 Processing helix chain 'C' and resid 504 through 529 removed outlier: 3.772A pdb=" N GLN C 529 " --> pdb=" O THR C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 Processing helix chain 'D' and resid 39 through 64 Processing helix chain 'D' and resid 68 through 77 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 114 through 117 removed outlier: 3.509A pdb=" N GLY D 117 " --> pdb=" O VAL D 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 114 through 117' Processing helix chain 'D' and resid 140 through 144 Processing helix chain 'D' and resid 146 through 164 Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'D' and resid 191 through 202 removed outlier: 4.382A pdb=" N PHE D 195 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 3.939A pdb=" N ALA D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 251 Processing helix chain 'D' and resid 256 through 261 Processing helix chain 'D' and resid 262 through 269 Processing helix chain 'D' and resid 279 through 293 Processing helix chain 'D' and resid 315 through 322 Processing helix chain 'D' and resid 331 through 339 removed outlier: 3.571A pdb=" N ARG D 337 " --> pdb=" O GLU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 343 Processing helix chain 'D' and resid 377 through 395 removed outlier: 3.570A pdb=" N ALA D 381 " --> pdb=" O PHE D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 417 removed outlier: 3.840A pdb=" N GLU D 414 " --> pdb=" O GLY D 410 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU D 416 " --> pdb=" O GLU D 412 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 432 removed outlier: 4.106A pdb=" N ALA D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET D 425 " --> pdb=" O ASP D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 452 Processing helix chain 'D' and resid 454 through 458 removed outlier: 3.854A pdb=" N SER D 458 " --> pdb=" O ARG D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 491 Processing helix chain 'D' and resid 497 through 517 Proline residue: D 508 - end of helix removed outlier: 3.660A pdb=" N LYS D 512 " --> pdb=" O PRO D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 525 removed outlier: 3.747A pdb=" N ARG D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 549 Processing helix chain 'E' and resid 504 through 529 removed outlier: 3.771A pdb=" N GLN E 529 " --> pdb=" O THR E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 638 Processing helix chain 'F' and resid 39 through 64 Processing helix chain 'F' and resid 68 through 77 Processing helix chain 'F' and resid 82 through 91 Processing helix chain 'F' and resid 114 through 117 removed outlier: 3.509A pdb=" N GLY F 117 " --> pdb=" O VAL F 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 114 through 117' Processing helix chain 'F' and resid 140 through 144 Processing helix chain 'F' and resid 146 through 164 Processing helix chain 'F' and resid 180 through 185 Processing helix chain 'F' and resid 191 through 202 removed outlier: 4.382A pdb=" N PHE F 195 " --> pdb=" O PHE F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 226 removed outlier: 3.941A pdb=" N ALA F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 251 Processing helix chain 'F' and resid 256 through 261 Processing helix chain 'F' and resid 262 through 269 Processing helix chain 'F' and resid 279 through 293 Processing helix chain 'F' and resid 315 through 322 Processing helix chain 'F' and resid 331 through 339 removed outlier: 3.571A pdb=" N ARG F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 343 Processing helix chain 'F' and resid 377 through 395 removed outlier: 3.569A pdb=" N ALA F 381 " --> pdb=" O PHE F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 417 removed outlier: 3.841A pdb=" N GLU F 414 " --> pdb=" O GLY F 410 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU F 416 " --> pdb=" O GLU F 412 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 432 removed outlier: 4.106A pdb=" N ALA F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET F 425 " --> pdb=" O ASP F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 452 Processing helix chain 'F' and resid 454 through 458 removed outlier: 3.854A pdb=" N SER F 458 " --> pdb=" O ARG F 455 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 491 Processing helix chain 'F' and resid 497 through 517 Proline residue: F 508 - end of helix removed outlier: 3.661A pdb=" N LYS F 512 " --> pdb=" O PRO F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 525 removed outlier: 3.748A pdb=" N ARG F 525 " --> pdb=" O TYR F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 549 Processing helix chain 'G' and resid 57 through 72 removed outlier: 3.753A pdb=" N ALA G 61 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 92 removed outlier: 4.044A pdb=" N ASP G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 106 Processing helix chain 'G' and resid 109 through 120 removed outlier: 3.947A pdb=" N ILE G 113 " --> pdb=" O SER G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 146 Processing helix chain 'G' and resid 153 through 159 removed outlier: 4.082A pdb=" N ASP G 159 " --> pdb=" O SER G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 172 Processing helix chain 'G' and resid 295 through 313 Processing helix chain 'G' and resid 343 through 352 removed outlier: 4.250A pdb=" N THR G 347 " --> pdb=" O GLU G 343 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET G 349 " --> pdb=" O PRO G 345 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE G 350 " --> pdb=" O VAL G 346 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 364 Processing helix chain 'G' and resid 371 through 375 removed outlier: 3.904A pdb=" N ILE G 375 " --> pdb=" O GLN G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 394 Processing helix chain 'G' and resid 443 through 456 Processing helix chain 'G' and resid 466 through 475 Processing helix chain 'G' and resid 476 through 482 Processing helix chain 'G' and resid 487 through 492 Processing helix chain 'G' and resid 493 through 496 Processing helix chain 'G' and resid 504 through 529 removed outlier: 3.771A pdb=" N GLN G 529 " --> pdb=" O THR G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 638 Processing helix chain 'H' and resid 39 through 64 Processing helix chain 'H' and resid 68 through 77 Processing helix chain 'H' and resid 82 through 91 Processing helix chain 'H' and resid 114 through 117 removed outlier: 3.509A pdb=" N GLY H 117 " --> pdb=" O VAL H 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 114 through 117' Processing helix chain 'H' and resid 140 through 144 Processing helix chain 'H' and resid 146 through 164 Processing helix chain 'H' and resid 180 through 185 Processing helix chain 'H' and resid 191 through 202 removed outlier: 4.382A pdb=" N PHE H 195 " --> pdb=" O PHE H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 226 removed outlier: 3.941A pdb=" N ALA H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 251 Processing helix chain 'H' and resid 256 through 261 Processing helix chain 'H' and resid 262 through 269 Processing helix chain 'H' and resid 279 through 293 Processing helix chain 'H' and resid 315 through 322 Processing helix chain 'H' and resid 331 through 339 removed outlier: 3.570A pdb=" N ARG H 337 " --> pdb=" O GLU H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 343 Processing helix chain 'H' and resid 377 through 395 removed outlier: 3.570A pdb=" N ALA H 381 " --> pdb=" O PHE H 377 " (cutoff:3.500A) Processing helix chain 'H' and resid 410 through 417 removed outlier: 3.841A pdb=" N GLU H 414 " --> pdb=" O GLY H 410 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU H 416 " --> pdb=" O GLU H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 432 removed outlier: 4.107A pdb=" N ALA H 423 " --> pdb=" O ALA H 419 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS H 424 " --> pdb=" O LYS H 420 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET H 425 " --> pdb=" O ASP H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 447 through 452 Processing helix chain 'H' and resid 454 through 458 removed outlier: 3.853A pdb=" N SER H 458 " --> pdb=" O ARG H 455 " (cutoff:3.500A) Processing helix chain 'H' and resid 474 through 491 removed outlier: 3.919A pdb=" N ALA H 478 " --> pdb=" O GLY H 474 " (cutoff:3.500A) Processing helix chain 'H' and resid 497 through 517 Proline residue: H 508 - end of helix removed outlier: 3.660A pdb=" N LYS H 512 " --> pdb=" O PRO H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 518 through 525 removed outlier: 3.748A pdb=" N ARG H 525 " --> pdb=" O TYR H 521 " (cutoff:3.500A) Processing helix chain 'H' and resid 536 through 549 Processing helix chain 'I' and resid 57 through 72 removed outlier: 3.753A pdb=" N ALA I 61 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 92 removed outlier: 4.044A pdb=" N ASP I 90 " --> pdb=" O SER I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 106 Processing helix chain 'I' and resid 109 through 120 removed outlier: 3.947A pdb=" N ILE I 113 " --> pdb=" O SER I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 146 Processing helix chain 'I' and resid 153 through 159 removed outlier: 4.082A pdb=" N ASP I 159 " --> pdb=" O SER I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 172 Processing helix chain 'I' and resid 187 through 199 Processing helix chain 'I' and resid 223 through 234 Processing helix chain 'I' and resid 234 through 239 removed outlier: 3.528A pdb=" N SER I 238 " --> pdb=" O GLU I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 313 Processing helix chain 'I' and resid 343 through 352 removed outlier: 4.250A pdb=" N THR I 347 " --> pdb=" O GLU I 343 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE I 350 " --> pdb=" O VAL I 346 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 364 Processing helix chain 'I' and resid 371 through 375 removed outlier: 3.903A pdb=" N ILE I 375 " --> pdb=" O GLN I 372 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 394 Processing helix chain 'I' and resid 443 through 456 Processing helix chain 'I' and resid 466 through 475 Processing helix chain 'I' and resid 476 through 482 Processing helix chain 'I' and resid 487 through 492 Processing helix chain 'I' and resid 493 through 496 Processing helix chain 'I' and resid 504 through 529 removed outlier: 3.771A pdb=" N GLN I 529 " --> pdb=" O THR I 525 " (cutoff:3.500A) Processing helix chain 'I' and resid 634 through 638 Processing helix chain 'J' and resid 39 through 64 Processing helix chain 'J' and resid 68 through 77 Processing helix chain 'J' and resid 82 through 91 Processing helix chain 'J' and resid 114 through 117 removed outlier: 3.509A pdb=" N GLY J 117 " --> pdb=" O VAL J 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 114 through 117' Processing helix chain 'J' and resid 140 through 144 Processing helix chain 'J' and resid 146 through 164 Processing helix chain 'J' and resid 191 through 202 removed outlier: 4.382A pdb=" N PHE J 195 " --> pdb=" O PHE J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 226 removed outlier: 3.940A pdb=" N ALA J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 251 Processing helix chain 'J' and resid 256 through 261 Processing helix chain 'J' and resid 262 through 269 Processing helix chain 'J' and resid 279 through 293 Processing helix chain 'J' and resid 315 through 322 Processing helix chain 'J' and resid 331 through 339 removed outlier: 3.571A pdb=" N ARG J 337 " --> pdb=" O GLU J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 343 Processing helix chain 'J' and resid 377 through 395 removed outlier: 3.570A pdb=" N ALA J 381 " --> pdb=" O PHE J 377 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 417 removed outlier: 3.841A pdb=" N GLU J 414 " --> pdb=" O GLY J 410 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU J 416 " --> pdb=" O GLU J 412 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 432 removed outlier: 4.106A pdb=" N ALA J 423 " --> pdb=" O ALA J 419 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS J 424 " --> pdb=" O LYS J 420 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET J 425 " --> pdb=" O ASP J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 447 through 452 Processing helix chain 'J' and resid 454 through 458 removed outlier: 3.854A pdb=" N SER J 458 " --> pdb=" O ARG J 455 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 491 removed outlier: 3.878A pdb=" N ALA J 478 " --> pdb=" O GLY J 474 " (cutoff:3.500A) Processing helix chain 'J' and resid 497 through 517 Proline residue: J 508 - end of helix removed outlier: 3.660A pdb=" N LYS J 512 " --> pdb=" O PRO J 508 " (cutoff:3.500A) Processing helix chain 'J' and resid 518 through 525 removed outlier: 3.747A pdb=" N ARG J 525 " --> pdb=" O TYR J 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 536 through 549 Processing helix chain 'K' and resid 57 through 72 removed outlier: 3.753A pdb=" N ALA K 61 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 92 removed outlier: 4.044A pdb=" N ASP K 90 " --> pdb=" O SER K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 106 Processing helix chain 'K' and resid 109 through 120 removed outlier: 3.947A pdb=" N ILE K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 146 Processing helix chain 'K' and resid 153 through 159 removed outlier: 4.083A pdb=" N ASP K 159 " --> pdb=" O SER K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 172 Processing helix chain 'K' and resid 295 through 313 Processing helix chain 'K' and resid 343 through 352 removed outlier: 4.249A pdb=" N THR K 347 " --> pdb=" O GLU K 343 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET K 349 " --> pdb=" O PRO K 345 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE K 350 " --> pdb=" O VAL K 346 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 364 Processing helix chain 'K' and resid 371 through 375 removed outlier: 3.904A pdb=" N ILE K 375 " --> pdb=" O GLN K 372 " (cutoff:3.500A) Processing helix chain 'K' and resid 391 through 394 Processing helix chain 'K' and resid 443 through 456 Processing helix chain 'K' and resid 466 through 475 Processing helix chain 'K' and resid 476 through 482 Processing helix chain 'K' and resid 487 through 492 Processing helix chain 'K' and resid 493 through 496 Processing helix chain 'K' and resid 504 through 529 removed outlier: 3.771A pdb=" N GLN K 529 " --> pdb=" O THR K 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 634 through 638 Processing helix chain 'L' and resid 39 through 64 Processing helix chain 'L' and resid 68 through 77 Processing helix chain 'L' and resid 82 through 91 Processing helix chain 'L' and resid 114 through 117 removed outlier: 3.508A pdb=" N GLY L 117 " --> pdb=" O VAL L 114 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 114 through 117' Processing helix chain 'L' and resid 140 through 144 Processing helix chain 'L' and resid 146 through 164 Processing helix chain 'L' and resid 180 through 185 Processing helix chain 'L' and resid 191 through 202 removed outlier: 4.382A pdb=" N PHE L 195 " --> pdb=" O PHE L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 226 removed outlier: 3.940A pdb=" N ALA L 225 " --> pdb=" O ALA L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 251 Processing helix chain 'L' and resid 256 through 261 Processing helix chain 'L' and resid 262 through 269 Processing helix chain 'L' and resid 279 through 293 Processing helix chain 'L' and resid 315 through 322 Processing helix chain 'L' and resid 331 through 339 removed outlier: 3.571A pdb=" N ARG L 337 " --> pdb=" O GLU L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 340 through 343 Processing helix chain 'L' and resid 377 through 395 removed outlier: 3.570A pdb=" N ALA L 381 " --> pdb=" O PHE L 377 " (cutoff:3.500A) Processing helix chain 'L' and resid 410 through 417 removed outlier: 3.841A pdb=" N GLU L 414 " --> pdb=" O GLY L 410 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLU L 416 " --> pdb=" O GLU L 412 " (cutoff:3.500A) Processing helix chain 'L' and resid 417 through 432 removed outlier: 4.105A pdb=" N ALA L 423 " --> pdb=" O ALA L 419 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS L 424 " --> pdb=" O LYS L 420 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET L 425 " --> pdb=" O ASP L 421 " (cutoff:3.500A) Processing helix chain 'L' and resid 447 through 452 Processing helix chain 'L' and resid 454 through 458 removed outlier: 3.853A pdb=" N SER L 458 " --> pdb=" O ARG L 455 " (cutoff:3.500A) Processing helix chain 'L' and resid 474 through 491 removed outlier: 3.557A pdb=" N ALA L 479 " --> pdb=" O GLY L 475 " (cutoff:3.500A) Processing helix chain 'L' and resid 497 through 517 Proline residue: L 508 - end of helix removed outlier: 3.661A pdb=" N LYS L 512 " --> pdb=" O PRO L 508 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 525 removed outlier: 3.748A pdb=" N ARG L 525 " --> pdb=" O TYR L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 536 through 549 Processing sheet with id=AA1, first strand: chain 'A' and resid 549 through 557 removed outlier: 4.619A pdb=" N TYR A 549 " --> pdb=" O TYR A 568 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY A 625 " --> pdb=" O SER A 622 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 650 through 651 removed outlier: 3.778A pdb=" N THR A 709 " --> pdb=" O ALA A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 684 through 688 removed outlier: 6.265A pdb=" N SER A 688 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER A 673 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU A 674 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL A 660 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 676 " --> pdb=" O GLU A 658 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 656 " --> pdb=" O ILE A 678 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 666 through 667 removed outlier: 6.804A pdb=" N GLU A 713 " --> pdb=" O LYS A 695 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.479A pdb=" N THR B 121 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS B 167 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL B 211 " --> pdb=" O CYS B 167 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR B 169 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU B 229 " --> pdb=" O GLN B 208 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN B 230 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA B 277 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 232 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 215 through 217 Processing sheet with id=AA7, first strand: chain 'B' and resid 345 through 347 removed outlier: 4.495A pdb=" N THR B 357 " --> pdb=" O PHE B 347 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU B 399 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY B 368 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU B 401 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 370 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE B 461 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 443 through 445 removed outlier: 3.625A pdb=" N SER B 471 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 549 through 557 removed outlier: 4.619A pdb=" N TYR C 549 " --> pdb=" O TYR C 568 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY C 625 " --> pdb=" O SER C 622 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 650 through 651 removed outlier: 3.778A pdb=" N THR C 709 " --> pdb=" O ALA C 651 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 684 through 688 removed outlier: 6.265A pdb=" N SER C 688 " --> pdb=" O SER C 673 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER C 673 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU C 674 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL C 660 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 676 " --> pdb=" O GLU C 658 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR C 656 " --> pdb=" O ILE C 678 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 666 through 667 removed outlier: 6.805A pdb=" N GLU C 713 " --> pdb=" O LYS C 695 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.480A pdb=" N THR D 121 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N CYS D 167 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL D 211 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR D 169 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU D 229 " --> pdb=" O GLN D 208 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASN D 230 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA D 277 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 232 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 215 through 217 Processing sheet with id=AB6, first strand: chain 'D' and resid 345 through 347 removed outlier: 4.495A pdb=" N THR D 357 " --> pdb=" O PHE D 347 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU D 399 " --> pdb=" O PRO D 366 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N GLY D 368 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU D 401 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL D 370 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE D 461 " --> pdb=" O LYS D 436 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 443 through 445 removed outlier: 3.625A pdb=" N SER D 471 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 549 through 557 removed outlier: 4.619A pdb=" N TYR E 549 " --> pdb=" O TYR E 568 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR E 596 " --> pdb=" O LEU E 611 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY E 625 " --> pdb=" O SER E 622 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 650 through 651 removed outlier: 3.778A pdb=" N THR E 709 " --> pdb=" O ALA E 651 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 684 through 688 removed outlier: 6.265A pdb=" N SER E 688 " --> pdb=" O SER E 673 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER E 673 " --> pdb=" O SER E 688 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU E 674 " --> pdb=" O VAL E 660 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL E 660 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL E 676 " --> pdb=" O GLU E 658 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR E 656 " --> pdb=" O ILE E 678 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 666 through 667 removed outlier: 6.805A pdb=" N GLU E 713 " --> pdb=" O LYS E 695 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 98 through 100 removed outlier: 4.480A pdb=" N THR F 121 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS F 167 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL F 211 " --> pdb=" O CYS F 167 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR F 169 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU F 229 " --> pdb=" O GLN F 208 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN F 230 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA F 277 " --> pdb=" O ASN F 230 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE F 232 " --> pdb=" O ALA F 277 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 215 through 217 Processing sheet with id=AC5, first strand: chain 'F' and resid 345 through 347 removed outlier: 4.495A pdb=" N THR F 357 " --> pdb=" O PHE F 347 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU F 399 " --> pdb=" O PRO F 366 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY F 368 " --> pdb=" O LEU F 399 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU F 401 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL F 370 " --> pdb=" O LEU F 401 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE F 461 " --> pdb=" O LYS F 436 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 443 through 445 removed outlier: 3.625A pdb=" N SER F 471 " --> pdb=" O SER F 444 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 148 through 149 removed outlier: 4.023A pdb=" N VAL G 78 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR G 75 " --> pdb=" O GLU G 94 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N TYR G 96 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA G 77 " --> pdb=" O TYR G 96 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA G 95 " --> pdb=" O ALA K 606 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY K 625 " --> pdb=" O SER K 622 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR K 549 " --> pdb=" O TYR K 568 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR K 596 " --> pdb=" O LEU K 611 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 268 through 275 removed outlier: 5.477A pdb=" N TYR G 270 " --> pdb=" O PHE G 261 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE G 261 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N PHE G 272 " --> pdb=" O GLN G 259 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN G 259 " --> pdb=" O PHE G 272 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE G 324 " --> pdb=" O PHE G 333 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N PHE G 333 " --> pdb=" O ILE G 324 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 279 through 280 Processing sheet with id=AD1, first strand: chain 'G' and resid 286 through 288 removed outlier: 6.726A pdb=" N HIS G 380 " --> pdb=" O TRP G 440 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP G 440 " --> pdb=" O HIS G 380 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE G 382 " --> pdb=" O VAL G 438 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL G 438 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA G 384 " --> pdb=" O LYS G 436 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS G 436 " --> pdb=" O ALA G 384 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ILE G 386 " --> pdb=" O ILE G 434 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 389 through 390 removed outlier: 3.671A pdb=" N MET G 396 " --> pdb=" O ASP G 390 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 404 through 406 Processing sheet with id=AD4, first strand: chain 'I' and resid 148 through 149 removed outlier: 4.023A pdb=" N VAL I 78 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR I 75 " --> pdb=" O GLU I 94 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N TYR I 96 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA I 77 " --> pdb=" O TYR I 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA I 95 " --> pdb=" O ALA G 606 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY G 625 " --> pdb=" O SER G 622 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR G 549 " --> pdb=" O TYR G 568 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR G 596 " --> pdb=" O LEU G 611 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 650 through 651 removed outlier: 3.778A pdb=" N THR G 709 " --> pdb=" O ALA G 651 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 684 through 688 removed outlier: 6.264A pdb=" N SER G 688 " --> pdb=" O SER G 673 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER G 673 " --> pdb=" O SER G 688 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU G 674 " --> pdb=" O VAL G 660 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL G 660 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL G 676 " --> pdb=" O GLU G 658 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR G 656 " --> pdb=" O ILE G 678 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 666 through 667 removed outlier: 6.804A pdb=" N GLU G 713 " --> pdb=" O LYS G 695 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 98 through 100 removed outlier: 4.480A pdb=" N THR H 121 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS H 167 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL H 211 " --> pdb=" O CYS H 167 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N TYR H 169 " --> pdb=" O VAL H 211 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU H 229 " --> pdb=" O GLN H 208 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN H 230 " --> pdb=" O HIS H 275 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA H 277 " --> pdb=" O ASN H 230 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE H 232 " --> pdb=" O ALA H 277 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 215 through 217 Processing sheet with id=AE1, first strand: chain 'H' and resid 345 through 347 removed outlier: 4.495A pdb=" N THR H 357 " --> pdb=" O PHE H 347 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU H 399 " --> pdb=" O PRO H 366 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY H 368 " --> pdb=" O LEU H 399 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU H 401 " --> pdb=" O GLY H 368 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL H 370 " --> pdb=" O LEU H 401 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE H 461 " --> pdb=" O LYS H 436 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 443 through 445 removed outlier: 3.626A pdb=" N SER H 471 " --> pdb=" O SER H 444 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 216 through 218 Processing sheet with id=AE4, first strand: chain 'I' and resid 268 through 275 removed outlier: 5.478A pdb=" N TYR I 270 " --> pdb=" O PHE I 261 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N PHE I 261 " --> pdb=" O TYR I 270 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE I 272 " --> pdb=" O GLN I 259 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN I 259 " --> pdb=" O PHE I 272 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE I 324 " --> pdb=" O PHE I 333 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE I 333 " --> pdb=" O ILE I 324 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 279 through 280 Processing sheet with id=AE6, first strand: chain 'I' and resid 286 through 288 removed outlier: 6.726A pdb=" N HIS I 380 " --> pdb=" O TRP I 440 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP I 440 " --> pdb=" O HIS I 380 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE I 382 " --> pdb=" O VAL I 438 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL I 438 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA I 384 " --> pdb=" O LYS I 436 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS I 436 " --> pdb=" O ALA I 384 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ILE I 386 " --> pdb=" O ILE I 434 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 389 through 390 removed outlier: 3.670A pdb=" N MET I 396 " --> pdb=" O ASP I 390 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 404 through 406 Processing sheet with id=AE9, first strand: chain 'K' and resid 148 through 149 removed outlier: 4.024A pdb=" N VAL K 78 " --> pdb=" O ILE K 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N THR K 75 " --> pdb=" O GLU K 94 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N TYR K 96 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA K 77 " --> pdb=" O TYR K 96 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA K 95 " --> pdb=" O ALA I 606 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY I 625 " --> pdb=" O SER I 622 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR I 549 " --> pdb=" O TYR I 568 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N THR I 596 " --> pdb=" O LEU I 611 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 650 through 651 removed outlier: 3.778A pdb=" N THR I 709 " --> pdb=" O ALA I 651 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 684 through 688 removed outlier: 6.265A pdb=" N SER I 688 " --> pdb=" O SER I 673 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER I 673 " --> pdb=" O SER I 688 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU I 674 " --> pdb=" O VAL I 660 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL I 660 " --> pdb=" O LEU I 674 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL I 676 " --> pdb=" O GLU I 658 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR I 656 " --> pdb=" O ILE I 678 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 666 through 667 removed outlier: 6.805A pdb=" N GLU I 713 " --> pdb=" O LYS I 695 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 98 through 100 removed outlier: 4.480A pdb=" N THR J 121 " --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS J 167 " --> pdb=" O ILE J 209 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL J 211 " --> pdb=" O CYS J 167 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR J 169 " --> pdb=" O VAL J 211 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU J 229 " --> pdb=" O GLN J 208 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN J 230 " --> pdb=" O HIS J 275 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA J 277 " --> pdb=" O ASN J 230 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE J 232 " --> pdb=" O ALA J 277 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 215 through 217 Processing sheet with id=AF6, first strand: chain 'J' and resid 345 through 347 removed outlier: 4.495A pdb=" N THR J 357 " --> pdb=" O PHE J 347 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU J 399 " --> pdb=" O PRO J 366 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY J 368 " --> pdb=" O LEU J 399 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU J 401 " --> pdb=" O GLY J 368 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL J 370 " --> pdb=" O LEU J 401 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE J 461 " --> pdb=" O LYS J 436 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 443 through 445 removed outlier: 3.625A pdb=" N SER J 471 " --> pdb=" O SER J 444 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 268 through 275 removed outlier: 5.477A pdb=" N TYR K 270 " --> pdb=" O PHE K 261 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE K 261 " --> pdb=" O TYR K 270 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N PHE K 272 " --> pdb=" O GLN K 259 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLN K 259 " --> pdb=" O PHE K 272 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE K 324 " --> pdb=" O PHE K 333 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N PHE K 333 " --> pdb=" O ILE K 324 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 279 through 280 Processing sheet with id=AG1, first strand: chain 'K' and resid 286 through 288 removed outlier: 6.726A pdb=" N HIS K 380 " --> pdb=" O TRP K 440 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N TRP K 440 " --> pdb=" O HIS K 380 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE K 382 " --> pdb=" O VAL K 438 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL K 438 " --> pdb=" O PHE K 382 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA K 384 " --> pdb=" O LYS K 436 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LYS K 436 " --> pdb=" O ALA K 384 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE K 386 " --> pdb=" O ILE K 434 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 389 through 390 removed outlier: 3.669A pdb=" N MET K 396 " --> pdb=" O ASP K 390 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 404 through 406 Processing sheet with id=AG4, first strand: chain 'K' and resid 650 through 651 removed outlier: 3.778A pdb=" N THR K 709 " --> pdb=" O ALA K 651 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'K' and resid 684 through 688 removed outlier: 6.265A pdb=" N SER K 688 " --> pdb=" O SER K 673 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER K 673 " --> pdb=" O SER K 688 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N LEU K 674 " --> pdb=" O VAL K 660 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL K 660 " --> pdb=" O LEU K 674 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL K 676 " --> pdb=" O GLU K 658 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR K 656 " --> pdb=" O ILE K 678 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 666 through 667 removed outlier: 6.805A pdb=" N GLU K 713 " --> pdb=" O LYS K 695 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 98 through 100 removed outlier: 4.480A pdb=" N THR L 121 " --> pdb=" O LEU L 100 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N CYS L 167 " --> pdb=" O ILE L 209 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL L 211 " --> pdb=" O CYS L 167 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR L 169 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU L 229 " --> pdb=" O GLN L 208 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN L 230 " --> pdb=" O HIS L 275 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA L 277 " --> pdb=" O ASN L 230 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE L 232 " --> pdb=" O ALA L 277 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 215 through 217 Processing sheet with id=AG9, first strand: chain 'L' and resid 345 through 347 removed outlier: 4.495A pdb=" N THR L 357 " --> pdb=" O PHE L 347 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU L 399 " --> pdb=" O PRO L 366 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLY L 368 " --> pdb=" O LEU L 399 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU L 401 " --> pdb=" O GLY L 368 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL L 370 " --> pdb=" O LEU L 401 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE L 461 " --> pdb=" O LYS L 436 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 443 through 445 removed outlier: 3.625A pdb=" N SER L 471 " --> pdb=" O SER L 444 " (cutoff:3.500A) 2086 hydrogen bonds defined for protein. 5811 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: 10.98 Time building geometry restraints manager: 4.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 7714 1.31 - 1.44: 11309 1.44 - 1.56: 25711 1.56 - 1.69: 42 1.69 - 1.81: 406 Bond restraints: 45182 Sorted by residual: bond pdb=" C3 BTN C 801 " pdb=" O3 BTN C 801 " ideal model delta sigma weight residual 1.220 1.406 -0.186 2.00e-02 2.50e+03 8.68e+01 bond pdb=" C3 BTN G 801 " pdb=" O3 BTN G 801 " ideal model delta sigma weight residual 1.220 1.406 -0.186 2.00e-02 2.50e+03 8.66e+01 bond pdb=" C3 BTN A 801 " pdb=" O3 BTN A 801 " ideal model delta sigma weight residual 1.220 1.406 -0.186 2.00e-02 2.50e+03 8.65e+01 bond pdb=" C3 BTN I 801 " pdb=" O3 BTN I 801 " ideal model delta sigma weight residual 1.220 1.406 -0.186 2.00e-02 2.50e+03 8.64e+01 bond pdb=" C3 BTN K 801 " pdb=" O3 BTN K 801 " ideal model delta sigma weight residual 1.220 1.406 -0.186 2.00e-02 2.50e+03 8.63e+01 ... (remaining 45177 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 60362 4.07 - 8.13: 626 8.13 - 12.20: 59 12.20 - 16.26: 17 16.26 - 20.33: 5 Bond angle restraints: 61069 Sorted by residual: angle pdb=" P1A ACO B 602 " pdb=" O3A ACO B 602 " pdb=" P2A ACO B 602 " ideal model delta sigma weight residual 136.83 116.50 20.33 1.00e+00 1.00e+00 4.13e+02 angle pdb=" P1A ACO F 601 " pdb=" O3A ACO F 601 " pdb=" P2A ACO F 601 " ideal model delta sigma weight residual 136.83 116.96 19.87 1.00e+00 1.00e+00 3.95e+02 angle pdb=" P1A ACO B 601 " pdb=" O3A ACO B 601 " pdb=" P2A ACO B 601 " ideal model delta sigma weight residual 136.83 117.85 18.98 1.00e+00 1.00e+00 3.60e+02 angle pdb=" P1A ACO L 601 " pdb=" O3A ACO L 601 " pdb=" P2A ACO L 601 " ideal model delta sigma weight residual 136.83 118.33 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" P1A ACO J 601 " pdb=" O3A ACO J 601 " pdb=" P2A ACO J 601 " ideal model delta sigma weight residual 136.83 120.42 16.41 1.00e+00 1.00e+00 2.69e+02 ... (remaining 61064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.28: 25794 22.28 - 44.56: 1403 44.56 - 66.83: 198 66.83 - 89.11: 70 89.11 - 111.39: 6 Dihedral angle restraints: 27471 sinusoidal: 11170 harmonic: 16301 Sorted by residual: dihedral pdb=" CA PHE B 185 " pdb=" C PHE B 185 " pdb=" N PRO B 186 " pdb=" CA PRO B 186 " ideal model delta harmonic sigma weight residual -180.00 -153.50 -26.50 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA PHE L 185 " pdb=" C PHE L 185 " pdb=" N PRO L 186 " pdb=" CA PRO L 186 " ideal model delta harmonic sigma weight residual -180.00 -153.53 -26.47 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA PHE J 185 " pdb=" C PHE J 185 " pdb=" N PRO J 186 " pdb=" CA PRO J 186 " ideal model delta harmonic sigma weight residual -180.00 -153.53 -26.47 0 5.00e+00 4.00e-02 2.80e+01 ... (remaining 27468 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 5942 0.106 - 0.212: 745 0.212 - 0.317: 51 0.317 - 0.423: 1 0.423 - 0.529: 6 Chirality restraints: 6745 Sorted by residual: chirality pdb=" CA PHE B 191 " pdb=" N PHE B 191 " pdb=" C PHE B 191 " pdb=" CB PHE B 191 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" CA PHE F 191 " pdb=" N PHE F 191 " pdb=" C PHE F 191 " pdb=" CB PHE F 191 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.00e+00 chirality pdb=" CA PHE L 191 " pdb=" N PHE L 191 " pdb=" C PHE L 191 " pdb=" CB PHE L 191 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.98e+00 ... (remaining 6742 not shown) Planarity restraints: 7927 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7P ACO J 602 " -0.360 2.00e-02 2.50e+03 3.08e-01 1.18e+03 pdb=" C9P ACO J 602 " 0.093 2.00e-02 2.50e+03 pdb=" CAP ACO J 602 " -0.123 2.00e-02 2.50e+03 pdb=" N8P ACO J 602 " 0.544 2.00e-02 2.50e+03 pdb=" O9P ACO J 602 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C7P ACO F 601 " -0.355 2.00e-02 2.50e+03 3.03e-01 1.15e+03 pdb=" C9P ACO F 601 " 0.090 2.00e-02 2.50e+03 pdb=" CAP ACO F 601 " -0.152 2.00e-02 2.50e+03 pdb=" N8P ACO F 601 " 0.538 2.00e-02 2.50e+03 pdb=" O9P ACO F 601 " -0.121 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3P ACO L 601 " -0.338 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C5P ACO L 601 " 0.080 2.00e-02 2.50e+03 pdb=" C6P ACO L 601 " -0.048 2.00e-02 2.50e+03 pdb=" N4P ACO L 601 " 0.510 2.00e-02 2.50e+03 pdb=" O5P ACO L 601 " -0.203 2.00e-02 2.50e+03 ... (remaining 7924 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 187 2.46 - 3.07: 27918 3.07 - 3.68: 65005 3.68 - 4.29: 100554 4.29 - 4.90: 170549 Nonbonded interactions: 364213 Sorted by model distance: nonbonded pdb=" O1A ACO F 601 " pdb=" OAP ACO F 601 " model vdw 1.846 3.040 nonbonded pdb=" O5A ACO J 602 " pdb=" OAP ACO J 602 " model vdw 1.852 3.040 nonbonded pdb=" O3A ACO B 602 " pdb=" OAP ACO B 602 " model vdw 1.854 3.040 nonbonded pdb=" NE2 GLN F 489 " pdb=" O9A ACO L 601 " model vdw 2.207 3.120 nonbonded pdb=" O6A ACO L 601 " pdb=" OAP ACO L 601 " model vdw 2.230 3.040 ... (remaining 364208 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 563) selection = chain 'D' selection = (chain 'F' and resid 23 through 563) selection = chain 'H' selection = (chain 'J' and resid 23 through 563) selection = (chain 'L' and resid 23 through 563) } ncs_group { reference = chain 'G' selection = (chain 'I' and (resid 49 through 174 or resid 251 through 801)) selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.850 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 38.920 Find NCS groups from input model: 1.080 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:7.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 : 0.013 0.186 45188 Z= 0.639 Angle : 1.161 20.331 61069 Z= 0.713 Chirality : 0.069 0.529 6745 Planarity : 0.012 0.308 7927 Dihedral : 14.123 111.392 17063 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.60 % Favored : 93.77 % Rotamer: Outliers : 1.35 % Allowed : 3.98 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.10), residues: 5664 helix: -1.54 (0.10), residues: 1986 sheet: -0.07 (0.14), residues: 1132 loop : -2.01 (0.11), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 525 TYR 0.035 0.003 TYR F 457 PHE 0.027 0.002 PHE D 407 TRP 0.015 0.002 TRP L 527 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.01317 (45182) covalent geometry : angle 1.16067 (61069) hydrogen bonds : bond 0.18359 ( 2086) hydrogen bonds : angle 7.12172 ( 5811) Misc. bond : bond 0.10980 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 992 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 929 time to evaluate : 1.327 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: B 183 ASP cc_start: 0.7440 (m-30) cc_final: 0.7208 (m-30) REVERT: C 653 MET cc_start: 0.6864 (ttt) cc_final: 0.5492 (mpp) REVERT: C 677 MET cc_start: 0.3698 (OUTLIER) cc_final: 0.2639 (ppp) REVERT: C 685 THR cc_start: 0.5225 (t) cc_final: 0.4892 (m) REVERT: E 653 MET cc_start: 0.4680 (ttt) cc_final: 0.4226 (mtm) REVERT: G 300 LYS cc_start: 0.5416 (mtmt) cc_final: 0.4858 (ptmm) REVERT: G 382 PHE cc_start: 0.6393 (m-80) cc_final: 0.6092 (m-80) REVERT: G 415 ARG cc_start: 0.6475 (ttm170) cc_final: 0.6063 (mtp85) REVERT: G 421 ARG cc_start: 0.5953 (mtm180) cc_final: 0.5725 (ttm170) REVERT: G 672 ASP cc_start: 0.4282 (OUTLIER) cc_final: 0.3967 (m-30) REVERT: H 251 THR cc_start: 0.7990 (p) cc_final: 0.7636 (t) REVERT: H 473 MET cc_start: 0.8912 (ptp) cc_final: 0.8652 (ptp) REVERT: H 510 ILE cc_start: 0.8617 (mt) cc_final: 0.8384 (pp) REVERT: I 458 TYR cc_start: 0.6094 (t80) cc_final: 0.5669 (t80) REVERT: I 682 MET cc_start: 0.5425 (OUTLIER) cc_final: 0.4620 (mtp) REVERT: I 713 GLU cc_start: 0.6805 (tp30) cc_final: 0.6516 (mt-10) REVERT: J 408 MET cc_start: 0.6141 (tpt) cc_final: 0.5825 (tpt) REVERT: K 270 TYR cc_start: 0.6673 (p90) cc_final: 0.6112 (p90) REVERT: K 431 ASP cc_start: 0.6779 (t70) cc_final: 0.6490 (m-30) REVERT: K 672 ASP cc_start: 0.3368 (OUTLIER) cc_final: 0.2026 (m-30) outliers start: 63 outliers final: 15 residues processed: 969 average time/residue: 0.8387 time to fit residues: 975.7656 Evaluate side-chains 539 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 520 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 682 MET Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 301 ASP Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain C residue 677 MET Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain G residue 672 ASP Chi-restraints excluded: chain H residue 301 ASP Chi-restraints excluded: chain I residue 672 ASP Chi-restraints excluded: chain I residue 682 MET Chi-restraints excluded: chain J residue 180 ARG Chi-restraints excluded: chain J residue 353 ASP Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 677 MET Chi-restraints excluded: chain K residue 709 THR Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 226 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 265 optimal weight: 0.9980 chunk 523 optimal weight: 0.9980 chunk 497 optimal weight: 4.9990 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 529 GLN A 531 HIS A 706 ASN B 43 GLN B 198 GLN B 489 GLN C 529 GLN C 531 HIS C 706 ASN D 34 GLN D 198 GLN D 489 GLN E 531 HIS E 706 ASN F 153 GLN F 198 GLN F 285 HIS F 449 ASN F 489 GLN G 282 HIS G 492 HIS G 493 HIS ** G 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 706 ASN H 198 GLN I 126 HIS I 329 HIS I 330 ASN ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 706 ASN J 34 GLN J 198 GLN J 489 GLN K 105 GLN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 279 GLN K 491 GLN K 531 HIS K 704 GLN K 706 ASN L 198 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.189858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.123690 restraints weight = 57974.099| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 2.56 r_work: 0.3268 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 45188 Z= 0.162 Angle : 0.677 9.961 61069 Z= 0.359 Chirality : 0.047 0.531 6745 Planarity : 0.005 0.058 7927 Dihedral : 8.696 120.368 6648 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.87 % Favored : 96.12 % Rotamer: Outliers : 2.65 % Allowed : 13.23 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.11), residues: 5664 helix: 0.15 (0.11), residues: 1999 sheet: 0.04 (0.14), residues: 1158 loop : -1.78 (0.11), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 234 TYR 0.017 0.001 TYR A 597 PHE 0.020 0.002 PHE G 323 TRP 0.009 0.001 TRP F 276 HIS 0.012 0.001 HIS I 380 Details of bonding type rmsd covalent geometry : bond 0.00356 (45182) covalent geometry : angle 0.67714 (61069) hydrogen bonds : bond 0.05054 ( 2086) hydrogen bonds : angle 5.22418 ( 5811) Misc. bond : bond 0.00906 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 576 time to evaluate : 1.775 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 528 LEU cc_start: 0.8005 (pp) cc_final: 0.7445 (mm) REVERT: A 591 SER cc_start: 0.8281 (m) cc_final: 0.7942 (t) REVERT: B 183 ASP cc_start: 0.8233 (m-30) cc_final: 0.7967 (m-30) REVERT: B 204 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8971 (mtpp) REVERT: B 469 ARG cc_start: 0.9098 (mmt-90) cc_final: 0.8819 (mpt180) REVERT: C 506 GLU cc_start: 0.7457 (mp0) cc_final: 0.6964 (pp20) REVERT: C 579 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6702 (mt-10) REVERT: C 592 GLU cc_start: 0.6588 (mt-10) cc_final: 0.6291 (pp20) REVERT: D 217 THR cc_start: 0.8917 (m) cc_final: 0.8588 (p) REVERT: D 292 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8351 (ttt-90) REVERT: D 393 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8625 (tt0) REVERT: D 414 GLU cc_start: 0.6666 (mm-30) cc_final: 0.6401 (tp30) REVERT: D 452 MET cc_start: 0.9370 (mmm) cc_final: 0.9021 (mmm) REVERT: E 680 MET cc_start: 0.5947 (mtp) cc_final: 0.5558 (ptp) REVERT: E 682 MET cc_start: 0.4966 (ptt) cc_final: 0.4643 (ptp) REVERT: G 84 ARG cc_start: 0.6857 (ttm110) cc_final: 0.5839 (mtt-85) REVERT: G 300 LYS cc_start: 0.4663 (mtmt) cc_final: 0.4316 (ptmt) REVERT: G 304 GLU cc_start: 0.5562 (OUTLIER) cc_final: 0.5281 (mp0) REVERT: G 349 MET cc_start: 0.4572 (mmm) cc_final: 0.4297 (mmm) REVERT: G 383 GLU cc_start: 0.6733 (tt0) cc_final: 0.5689 (pp20) REVERT: G 421 ARG cc_start: 0.5888 (mtm180) cc_final: 0.5175 (ttm110) REVERT: G 672 ASP cc_start: 0.3628 (OUTLIER) cc_final: 0.3274 (m-30) REVERT: G 675 MET cc_start: 0.3297 (ttm) cc_final: 0.3085 (ttp) REVERT: H 188 ARG cc_start: 0.7725 (ttp-110) cc_final: 0.7403 (ttt-90) REVERT: H 189 ASP cc_start: 0.8245 (p0) cc_final: 0.7745 (p0) REVERT: H 213 MET cc_start: 0.9205 (mtt) cc_final: 0.8818 (mtt) REVERT: H 473 MET cc_start: 0.8993 (ptp) cc_final: 0.8700 (ptm) REVERT: H 510 ILE cc_start: 0.8380 (mt) cc_final: 0.7849 (pp) REVERT: I 65 MET cc_start: 0.8192 (mtt) cc_final: 0.7834 (mtm) REVERT: I 74 GLN cc_start: 0.7217 (OUTLIER) cc_final: 0.6117 (mp10) REVERT: I 91 MET cc_start: 0.7208 (mtp) cc_final: 0.6955 (ttm) REVERT: I 110 MET cc_start: 0.3614 (mmm) cc_final: 0.3327 (mmm) REVERT: I 160 MET cc_start: 0.3354 (mmp) cc_final: 0.3003 (tmm) REVERT: I 163 LYS cc_start: 0.4992 (mmtt) cc_final: 0.4294 (mtmt) REVERT: I 373 GLU cc_start: 0.7434 (mt-10) cc_final: 0.6701 (pp20) REVERT: I 396 MET cc_start: 0.3625 (tmm) cc_final: 0.3112 (tmt) REVERT: I 458 TYR cc_start: 0.6663 (t80) cc_final: 0.6146 (t80) REVERT: I 480 GLU cc_start: 0.5814 (OUTLIER) cc_final: 0.5204 (mp0) REVERT: I 599 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8233 (ttpp) REVERT: I 682 MET cc_start: 0.6362 (mtp) cc_final: 0.6122 (mtp) REVERT: I 713 GLU cc_start: 0.6920 (tp30) cc_final: 0.6306 (mt-10) REVERT: K 94 GLU cc_start: 0.6032 (OUTLIER) cc_final: 0.5800 (tp30) REVERT: K 108 LEU cc_start: 0.5874 (OUTLIER) cc_final: 0.5655 (mp) REVERT: K 160 MET cc_start: 0.2066 (mpt) cc_final: 0.1531 (tmm) REVERT: K 270 TYR cc_start: 0.6187 (p90) cc_final: 0.5432 (p90) REVERT: K 367 LYS cc_start: 0.5909 (mppt) cc_final: 0.5645 (mmtt) REVERT: K 382 PHE cc_start: 0.6647 (m-80) cc_final: 0.6269 (m-10) REVERT: K 424 ASP cc_start: 0.5809 (m-30) cc_final: 0.5580 (m-30) REVERT: K 431 ASP cc_start: 0.7043 (t70) cc_final: 0.6814 (m-30) REVERT: K 492 HIS cc_start: 0.5781 (m-70) cc_final: 0.5432 (m170) REVERT: K 672 ASP cc_start: 0.3648 (OUTLIER) cc_final: 0.2146 (m-30) REVERT: L 292 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8529 (ttt90) REVERT: L 376 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8601 (tp) REVERT: L 408 MET cc_start: 0.7607 (tpt) cc_final: 0.7260 (tpt) outliers start: 123 outliers final: 35 residues processed: 647 average time/residue: 0.7233 time to fit residues: 573.8552 Evaluate side-chains 508 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 461 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 393 GLN Chi-restraints excluded: chain D residue 425 MET Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 346 VAL Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 672 ASP Chi-restraints excluded: chain G residue 678 ILE Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 425 MET Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 480 GLU Chi-restraints excluded: chain I residue 599 LYS Chi-restraints excluded: chain I residue 712 VAL Chi-restraints excluded: chain J residue 353 ASP Chi-restraints excluded: chain J residue 557 ASP Chi-restraints excluded: chain K residue 94 GLU Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 347 THR Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 627 ILE Chi-restraints excluded: chain K residue 672 ASP Chi-restraints excluded: chain K residue 697 VAL Chi-restraints excluded: chain K residue 709 THR Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 328 SER Chi-restraints excluded: chain L residue 376 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 67 optimal weight: 7.9990 chunk 554 optimal weight: 0.9980 chunk 258 optimal weight: 0.0870 chunk 181 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 389 optimal weight: 3.9990 chunk 336 optimal weight: 0.5980 chunk 434 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 132 optimal weight: 0.7980 chunk 440 optimal weight: 2.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN B 43 GLN C 529 GLN D 433 GLN F 75 HIS F 230 ASN G 126 HIS G 492 HIS G 493 HIS H 230 ASN ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 457 GLN I 495 GLN J 34 GLN J 230 ASN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.189286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.124195 restraints weight = 57522.950| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.54 r_work: 0.3275 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 45188 Z= 0.131 Angle : 0.605 13.282 61069 Z= 0.318 Chirality : 0.045 0.306 6745 Planarity : 0.004 0.052 7927 Dihedral : 8.312 103.655 6619 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.87 % Favored : 96.12 % Rotamer: Outliers : 2.97 % Allowed : 14.52 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.11), residues: 5664 helix: 0.78 (0.12), residues: 2003 sheet: 0.05 (0.14), residues: 1158 loop : -1.45 (0.12), residues: 2503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 234 TYR 0.019 0.001 TYR I 315 PHE 0.023 0.001 PHE G 323 TRP 0.008 0.001 TRP D 276 HIS 0.013 0.001 HIS G 493 Details of bonding type rmsd covalent geometry : bond 0.00292 (45182) covalent geometry : angle 0.60521 (61069) hydrogen bonds : bond 0.04156 ( 2086) hydrogen bonds : angle 4.84067 ( 5811) Misc. bond : bond 0.00168 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 497 time to evaluate : 1.233 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 528 LEU cc_start: 0.7904 (pp) cc_final: 0.7339 (mm) REVERT: A 543 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8321 (mmm-85) REVERT: A 577 GLN cc_start: 0.8027 (tt0) cc_final: 0.7601 (tp-100) REVERT: A 591 SER cc_start: 0.8381 (m) cc_final: 0.8056 (t) REVERT: A 599 LYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7129 (tttt) REVERT: A 602 VAL cc_start: 0.6525 (OUTLIER) cc_final: 0.6311 (t) REVERT: A 610 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7238 (ttmm) REVERT: B 43 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8116 (mp10) REVERT: B 64 LYS cc_start: 0.8319 (tmtt) cc_final: 0.7845 (tttt) REVERT: B 130 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: B 183 ASP cc_start: 0.8219 (m-30) cc_final: 0.7996 (m-30) REVERT: B 204 LYS cc_start: 0.9383 (OUTLIER) cc_final: 0.9159 (mttm) REVERT: B 213 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8862 (mtm) REVERT: B 469 ARG cc_start: 0.9058 (mmt-90) cc_final: 0.8854 (mpt180) REVERT: C 506 GLU cc_start: 0.7527 (mp0) cc_final: 0.6987 (pp20) REVERT: C 592 GLU cc_start: 0.6560 (mt-10) cc_final: 0.6074 (pp20) REVERT: C 617 THR cc_start: 0.7139 (m) cc_final: 0.6808 (p) REVERT: C 624 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6804 (mm-30) REVERT: C 683 GLU cc_start: 0.6182 (OUTLIER) cc_final: 0.5927 (pt0) REVERT: C 687 LYS cc_start: 0.5206 (OUTLIER) cc_final: 0.4951 (tttt) REVERT: D 217 THR cc_start: 0.8820 (m) cc_final: 0.8504 (p) REVERT: D 292 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8359 (ttt-90) REVERT: D 425 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8291 (tpt) REVERT: E 522 MET cc_start: 0.6829 (mtp) cc_final: 0.6548 (ttm) REVERT: E 682 MET cc_start: 0.5418 (ptt) cc_final: 0.5147 (ptt) REVERT: G 84 ARG cc_start: 0.6867 (ttm110) cc_final: 0.5853 (mtt-85) REVERT: G 160 MET cc_start: 0.4080 (tpp) cc_final: 0.3729 (tpt) REVERT: G 304 GLU cc_start: 0.5498 (OUTLIER) cc_final: 0.5183 (mp0) REVERT: G 349 MET cc_start: 0.4627 (mmm) cc_final: 0.4290 (mmm) REVERT: G 383 GLU cc_start: 0.6695 (tt0) cc_final: 0.6073 (pp20) REVERT: G 421 ARG cc_start: 0.5501 (mtm180) cc_final: 0.4769 (ttm170) REVERT: G 653 MET cc_start: 0.3627 (mtm) cc_final: 0.2553 (ttt) REVERT: G 675 MET cc_start: 0.3273 (ttm) cc_final: 0.2994 (ttm) REVERT: H 188 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7387 (ttt-90) REVERT: H 189 ASP cc_start: 0.8237 (p0) cc_final: 0.7679 (p0) REVERT: H 213 MET cc_start: 0.9193 (mtt) cc_final: 0.8823 (mtt) REVERT: H 324 ASN cc_start: 0.8530 (t0) cc_final: 0.8238 (t0) REVERT: H 473 MET cc_start: 0.9040 (ptp) cc_final: 0.8755 (ptm) REVERT: I 74 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6073 (mp10) REVERT: I 76 VAL cc_start: 0.8054 (OUTLIER) cc_final: 0.7738 (p) REVERT: I 91 MET cc_start: 0.7248 (mtp) cc_final: 0.6994 (ttm) REVERT: I 110 MET cc_start: 0.3727 (mmm) cc_final: 0.3481 (mmm) REVERT: I 163 LYS cc_start: 0.4934 (mmtt) cc_final: 0.4230 (mtmt) REVERT: I 373 GLU cc_start: 0.7406 (mt-10) cc_final: 0.6694 (pp20) REVERT: I 396 MET cc_start: 0.3483 (tmm) cc_final: 0.2815 (tmt) REVERT: I 433 MET cc_start: 0.6966 (OUTLIER) cc_final: 0.6414 (tpt) REVERT: I 480 GLU cc_start: 0.5870 (OUTLIER) cc_final: 0.5249 (mp0) REVERT: I 682 MET cc_start: 0.6369 (mtp) cc_final: 0.6100 (mtp) REVERT: I 713 GLU cc_start: 0.7023 (tp30) cc_final: 0.6342 (mt-10) REVERT: J 408 MET cc_start: 0.6617 (tpt) cc_final: 0.6334 (tpt) REVERT: K 113 ILE cc_start: 0.6182 (mm) cc_final: 0.5939 (mt) REVERT: K 135 ASN cc_start: 0.5644 (OUTLIER) cc_final: 0.5376 (t0) REVERT: K 160 MET cc_start: 0.2292 (mpt) cc_final: 0.1867 (mmm) REVERT: K 270 TYR cc_start: 0.6270 (p90) cc_final: 0.5555 (p90) REVERT: K 367 LYS cc_start: 0.6300 (mppt) cc_final: 0.6100 (mmtt) REVERT: K 424 ASP cc_start: 0.5873 (m-30) cc_final: 0.5473 (m-30) REVERT: K 431 ASP cc_start: 0.7109 (t70) cc_final: 0.6452 (p0) REVERT: K 487 ASP cc_start: 0.8062 (t0) cc_final: 0.7847 (OUTLIER) REVERT: K 492 HIS cc_start: 0.5891 (m-70) cc_final: 0.5490 (m170) REVERT: K 518 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.8113 (tmmt) REVERT: K 560 ASN cc_start: 0.7182 (OUTLIER) cc_final: 0.6948 (p0) outliers start: 138 outliers final: 48 residues processed: 580 average time/residue: 0.7473 time to fit residues: 530.4716 Evaluate side-chains 507 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 440 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 425 MET Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 189 ASP Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 678 ILE Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 188 ARG Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain I residue 480 GLU Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 672 ASP Chi-restraints excluded: chain I residue 684 HIS Chi-restraints excluded: chain I residue 712 VAL Chi-restraints excluded: chain J residue 353 ASP Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 304 GLU Chi-restraints excluded: chain K residue 347 THR Chi-restraints excluded: chain K residue 428 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 518 LYS Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 528 LEU Chi-restraints excluded: chain K residue 560 ASN Chi-restraints excluded: chain K residue 614 LEU Chi-restraints excluded: chain K residue 627 ILE Chi-restraints excluded: chain K residue 697 VAL Chi-restraints excluded: chain K residue 709 THR Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain L residue 140 VAL Chi-restraints excluded: chain L residue 251 THR Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 328 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 22 optimal weight: 0.2980 chunk 55 optimal weight: 0.3980 chunk 21 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 306 optimal weight: 10.0000 chunk 214 optimal weight: 0.0980 chunk 296 optimal weight: 0.9980 chunk 557 optimal weight: 5.9990 chunk 401 optimal weight: 3.9990 chunk 191 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 569 ASN B 449 ASN C 529 GLN ** C 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN G 492 HIS ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 457 GLN J 34 GLN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.188406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.124020 restraints weight = 57925.829| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.73 r_work: 0.3245 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 45188 Z= 0.127 Angle : 0.583 10.791 61069 Z= 0.304 Chirality : 0.045 0.299 6745 Planarity : 0.004 0.051 7927 Dihedral : 8.106 93.744 6614 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 3.10 % Allowed : 15.40 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.11), residues: 5664 helix: 0.92 (0.12), residues: 2066 sheet: 0.13 (0.14), residues: 1158 loop : -1.31 (0.12), residues: 2440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 268 TYR 0.022 0.001 TYR B 42 PHE 0.017 0.001 PHE K 333 TRP 0.013 0.001 TRP L 276 HIS 0.004 0.001 HIS I 255 Details of bonding type rmsd covalent geometry : bond 0.00286 (45182) covalent geometry : angle 0.58287 (61069) hydrogen bonds : bond 0.03869 ( 2086) hydrogen bonds : angle 4.66326 ( 5811) Misc. bond : bond 0.00048 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 485 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.7104 (mmm) cc_final: 0.6636 (OUTLIER) REVERT: A 528 LEU cc_start: 0.7914 (pp) cc_final: 0.7333 (mm) REVERT: A 543 ARG cc_start: 0.8717 (mmm-85) cc_final: 0.8394 (mmm-85) REVERT: A 577 GLN cc_start: 0.8037 (tt0) cc_final: 0.7556 (tp-100) REVERT: A 591 SER cc_start: 0.8396 (m) cc_final: 0.8071 (t) REVERT: A 599 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7210 (tttt) REVERT: A 602 VAL cc_start: 0.6583 (OUTLIER) cc_final: 0.6341 (t) REVERT: A 610 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7242 (ttmm) REVERT: B 64 LYS cc_start: 0.8434 (tmtt) cc_final: 0.8021 (tttm) REVERT: B 183 ASP cc_start: 0.8289 (m-30) cc_final: 0.8026 (m-30) REVERT: B 213 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8887 (mtm) REVERT: B 217 THR cc_start: 0.8158 (p) cc_final: 0.7799 (t) REVERT: B 259 ASP cc_start: 0.7503 (p0) cc_final: 0.7138 (p0) REVERT: B 269 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8068 (mttt) REVERT: B 404 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8406 (OUTLIER) REVERT: C 506 GLU cc_start: 0.7561 (mp0) cc_final: 0.6975 (pp20) REVERT: C 592 GLU cc_start: 0.6503 (mt-10) cc_final: 0.6025 (pp20) REVERT: C 617 THR cc_start: 0.7330 (m) cc_final: 0.7057 (p) REVERT: C 624 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6982 (pp20) REVERT: C 680 MET cc_start: 0.5109 (ptm) cc_final: 0.4772 (ptm) REVERT: C 687 LYS cc_start: 0.5408 (OUTLIER) cc_final: 0.5140 (tttt) REVERT: D 217 THR cc_start: 0.8770 (m) cc_final: 0.8453 (p) REVERT: D 292 ARG cc_start: 0.8804 (OUTLIER) cc_final: 0.8376 (ttt-90) REVERT: D 425 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8412 (tpt) REVERT: E 682 MET cc_start: 0.5414 (ptt) cc_final: 0.5102 (OUTLIER) REVERT: F 130 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: F 189 ASP cc_start: 0.7871 (t0) cc_final: 0.7300 (p0) REVERT: F 425 MET cc_start: 0.8826 (ttt) cc_final: 0.8625 (ttt) REVERT: F 511 LYS cc_start: 0.8123 (ptmm) cc_final: 0.7489 (ptpt) REVERT: G 84 ARG cc_start: 0.6884 (ttm110) cc_final: 0.6001 (mtt-85) REVERT: G 304 GLU cc_start: 0.5455 (OUTLIER) cc_final: 0.5170 (mp0) REVERT: G 349 MET cc_start: 0.4932 (mmm) cc_final: 0.4601 (mmm) REVERT: G 383 GLU cc_start: 0.6853 (tt0) cc_final: 0.6136 (pp20) REVERT: G 672 ASP cc_start: 0.3524 (OUTLIER) cc_final: 0.3141 (m-30) REVERT: G 675 MET cc_start: 0.3356 (ttm) cc_final: 0.3015 (ttm) REVERT: H 188 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7612 (ttt-90) REVERT: H 213 MET cc_start: 0.9231 (mtt) cc_final: 0.8843 (mtt) REVERT: H 411 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7079 (ttm-80) REVERT: H 473 MET cc_start: 0.9038 (ptp) cc_final: 0.8762 (ptm) REVERT: I 74 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.5959 (mt0) REVERT: I 76 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7736 (p) REVERT: I 91 MET cc_start: 0.7301 (mtp) cc_final: 0.7072 (ttm) REVERT: I 110 MET cc_start: 0.3801 (mmm) cc_final: 0.3537 (mmm) REVERT: I 163 LYS cc_start: 0.5020 (mmtt) cc_final: 0.4356 (mtmt) REVERT: I 287 GLU cc_start: 0.7941 (tt0) cc_final: 0.7610 (tt0) REVERT: I 373 GLU cc_start: 0.7385 (mt-10) cc_final: 0.6656 (pp20) REVERT: I 396 MET cc_start: 0.3298 (tmm) cc_final: 0.2590 (tmt) REVERT: I 433 MET cc_start: 0.7058 (ttt) cc_final: 0.6489 (tpt) REVERT: I 480 GLU cc_start: 0.5933 (OUTLIER) cc_final: 0.5291 (mp0) REVERT: I 653 MET cc_start: 0.6884 (OUTLIER) cc_final: 0.5799 (mtp) REVERT: I 682 MET cc_start: 0.6399 (mtp) cc_final: 0.6050 (mtp) REVERT: I 713 GLU cc_start: 0.7024 (tp30) cc_final: 0.6327 (mt-10) REVERT: J 183 ASP cc_start: 0.8187 (m-30) cc_final: 0.7968 (m-30) REVERT: J 458 SER cc_start: 0.9084 (m) cc_final: 0.8770 (p) REVERT: K 97 SER cc_start: 0.5305 (OUTLIER) cc_final: 0.5034 (t) REVERT: K 135 ASN cc_start: 0.5312 (OUTLIER) cc_final: 0.5014 (t0) REVERT: K 160 MET cc_start: 0.2367 (mpt) cc_final: 0.1944 (mmm) REVERT: K 270 TYR cc_start: 0.6265 (p90) cc_final: 0.5559 (p90) REVERT: K 295 LYS cc_start: 0.4255 (mmtt) cc_final: 0.3865 (mtpp) REVERT: K 301 LYS cc_start: 0.7186 (mmmm) cc_final: 0.6915 (mmmm) REVERT: K 396 MET cc_start: 0.4519 (ttm) cc_final: 0.3858 (ppp) REVERT: K 424 ASP cc_start: 0.5910 (m-30) cc_final: 0.5581 (m-30) REVERT: K 431 ASP cc_start: 0.7134 (t70) cc_final: 0.6427 (p0) REVERT: K 487 ASP cc_start: 0.8050 (t0) cc_final: 0.7791 (OUTLIER) REVERT: K 492 HIS cc_start: 0.5790 (m-70) cc_final: 0.5527 (m170) REVERT: K 560 ASN cc_start: 0.7190 (OUTLIER) cc_final: 0.6966 (p0) REVERT: K 683 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.6179 (pp20) REVERT: L 278 LEU cc_start: 0.8916 (mp) cc_final: 0.8567 (mt) outliers start: 144 outliers final: 54 residues processed: 573 average time/residue: 0.8099 time to fit residues: 569.9168 Evaluate side-chains 512 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 440 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 425 MET Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 631 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain G residue 286 ILE Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 672 ASP Chi-restraints excluded: chain G residue 678 ILE Chi-restraints excluded: chain G residue 684 HIS Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 188 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain H residue 411 ARG Chi-restraints excluded: chain H residue 510 ILE Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 480 GLU Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 684 HIS Chi-restraints excluded: chain I residue 712 VAL Chi-restraints excluded: chain J residue 421 ASP Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 112 LYS Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 347 THR Chi-restraints excluded: chain K residue 428 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 528 LEU Chi-restraints excluded: chain K residue 560 ASN Chi-restraints excluded: chain K residue 627 ILE Chi-restraints excluded: chain K residue 683 GLU Chi-restraints excluded: chain K residue 697 VAL Chi-restraints excluded: chain K residue 709 THR Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain L residue 178 LEU Chi-restraints excluded: chain L residue 255 VAL Chi-restraints excluded: chain L residue 328 SER Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 275 optimal weight: 6.9990 chunk 563 optimal weight: 5.9990 chunk 277 optimal weight: 9.9990 chunk 290 optimal weight: 2.9990 chunk 425 optimal weight: 0.9980 chunk 327 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 557 optimal weight: 3.9990 chunk 105 optimal weight: 0.0980 chunk 94 optimal weight: 10.0000 chunk 431 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 529 GLN ** C 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN F 389 GLN G 492 HIS H 57 HIS ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 457 GLN J 34 GLN ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.185610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.120864 restraints weight = 57301.211| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.70 r_work: 0.3194 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 45188 Z= 0.195 Angle : 0.630 10.004 61069 Z= 0.329 Chirality : 0.047 0.293 6745 Planarity : 0.004 0.054 7927 Dihedral : 8.026 76.737 6610 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.10 % Favored : 95.89 % Rotamer: Outliers : 3.46 % Allowed : 15.85 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.11), residues: 5664 helix: 0.91 (0.12), residues: 2074 sheet: 0.09 (0.14), residues: 1148 loop : -1.22 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 268 TYR 0.020 0.002 TYR J 457 PHE 0.022 0.002 PHE I 537 TRP 0.006 0.001 TRP G 358 HIS 0.008 0.001 HIS A 684 Details of bonding type rmsd covalent geometry : bond 0.00464 (45182) covalent geometry : angle 0.62988 (61069) hydrogen bonds : bond 0.04575 ( 2086) hydrogen bonds : angle 4.71003 ( 5811) Misc. bond : bond 0.00028 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 450 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 MET cc_start: 0.7093 (mmm) cc_final: 0.6721 (tpp) REVERT: A 528 LEU cc_start: 0.7923 (pp) cc_final: 0.7400 (mm) REVERT: A 543 ARG cc_start: 0.8807 (mmm-85) cc_final: 0.8553 (mmm-85) REVERT: A 577 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.7567 (tp-100) REVERT: A 591 SER cc_start: 0.8400 (m) cc_final: 0.8072 (t) REVERT: A 599 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7281 (tttt) REVERT: A 602 VAL cc_start: 0.6943 (OUTLIER) cc_final: 0.6715 (t) REVERT: A 610 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7237 (ttmm) REVERT: B 64 LYS cc_start: 0.8555 (tmtt) cc_final: 0.8128 (tttm) REVERT: B 183 ASP cc_start: 0.8373 (m-30) cc_final: 0.8138 (m-30) REVERT: B 204 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.9016 (mttp) REVERT: B 217 THR cc_start: 0.8221 (p) cc_final: 0.7884 (t) REVERT: B 269 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8044 (mttt) REVERT: C 506 GLU cc_start: 0.7780 (mp0) cc_final: 0.7323 (pp20) REVERT: C 522 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6358 (mmp) REVERT: C 592 GLU cc_start: 0.6496 (mt-10) cc_final: 0.6041 (pp20) REVERT: C 617 THR cc_start: 0.7502 (m) cc_final: 0.7201 (p) REVERT: C 624 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6979 (pp20) REVERT: C 687 LYS cc_start: 0.5504 (OUTLIER) cc_final: 0.5253 (tttt) REVERT: D 217 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8483 (p) REVERT: D 292 ARG cc_start: 0.8790 (ttm-80) cc_final: 0.8323 (ttt-90) REVERT: E 613 ILE cc_start: 0.6825 (mt) cc_final: 0.6053 (pp) REVERT: E 682 MET cc_start: 0.5287 (ptt) cc_final: 0.5016 (ptt) REVERT: F 130 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: F 297 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.8278 (tt0) REVERT: F 346 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: F 511 LYS cc_start: 0.8167 (ptmm) cc_final: 0.7473 (ptpt) REVERT: G 304 GLU cc_start: 0.5438 (OUTLIER) cc_final: 0.5140 (mp0) REVERT: G 383 GLU cc_start: 0.6794 (tt0) cc_final: 0.6263 (pp20) REVERT: G 672 ASP cc_start: 0.3223 (OUTLIER) cc_final: 0.2870 (m-30) REVERT: G 675 MET cc_start: 0.3587 (ttm) cc_final: 0.3312 (ttm) REVERT: H 213 MET cc_start: 0.9264 (OUTLIER) cc_final: 0.8879 (mtt) REVERT: H 324 ASN cc_start: 0.8497 (t0) cc_final: 0.8239 (t0) REVERT: H 411 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.6984 (ttm-80) REVERT: H 473 MET cc_start: 0.9037 (ptp) cc_final: 0.8818 (ptp) REVERT: I 74 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6113 (mt0) REVERT: I 110 MET cc_start: 0.4207 (mmm) cc_final: 0.3903 (mmm) REVERT: I 163 LYS cc_start: 0.4950 (mmtt) cc_final: 0.4334 (mtmt) REVERT: I 287 GLU cc_start: 0.8015 (tt0) cc_final: 0.7678 (tt0) REVERT: I 389 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.6036 (pm20) REVERT: I 396 MET cc_start: 0.3296 (tmm) cc_final: 0.2834 (tmm) REVERT: I 433 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.6703 (tpt) REVERT: I 458 TYR cc_start: 0.7216 (t80) cc_final: 0.6488 (t80) REVERT: I 653 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6001 (mtp) REVERT: I 682 MET cc_start: 0.6409 (mtp) cc_final: 0.6107 (mtp) REVERT: I 713 GLU cc_start: 0.6906 (tp30) cc_final: 0.6265 (mt-10) REVERT: J 34 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8123 (tm-30) REVERT: J 458 SER cc_start: 0.9131 (m) cc_final: 0.8791 (p) REVERT: K 97 SER cc_start: 0.5394 (OUTLIER) cc_final: 0.5181 (t) REVERT: K 135 ASN cc_start: 0.5415 (OUTLIER) cc_final: 0.5099 (t0) REVERT: K 160 MET cc_start: 0.2531 (mpt) cc_final: 0.1929 (mmm) REVERT: K 270 TYR cc_start: 0.6223 (p90) cc_final: 0.5529 (p90) REVERT: K 295 LYS cc_start: 0.4044 (mmtt) cc_final: 0.3673 (mtpp) REVERT: K 354 ASP cc_start: 0.5945 (t0) cc_final: 0.5375 (t0) REVERT: K 396 MET cc_start: 0.4446 (ttm) cc_final: 0.3742 (ppp) REVERT: K 405 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8019 (tm) REVERT: K 424 ASP cc_start: 0.5906 (m-30) cc_final: 0.5588 (m-30) REVERT: K 431 ASP cc_start: 0.7114 (t70) cc_final: 0.6605 (t70) REVERT: K 487 ASP cc_start: 0.8061 (t0) cc_final: 0.7812 (OUTLIER) REVERT: K 518 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8236 (tmmt) REVERT: K 683 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.6161 (pp20) REVERT: L 420 LYS cc_start: 0.8353 (tttm) cc_final: 0.8133 (tttp) outliers start: 161 outliers final: 62 residues processed: 554 average time/residue: 0.7407 time to fit residues: 507.1807 Evaluate side-chains 511 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 424 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 404 ILE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 425 MET Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 631 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 346 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 672 ASP Chi-restraints excluded: chain G residue 678 ILE Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 213 MET Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain H residue 411 ARG Chi-restraints excluded: chain H residue 510 ILE Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 389 GLU Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 433 MET Chi-restraints excluded: chain I residue 556 LYS Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 684 HIS Chi-restraints excluded: chain I residue 712 VAL Chi-restraints excluded: chain J residue 34 GLN Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 421 ASP Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 97 SER Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 347 THR Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 428 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 518 LYS Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 528 LEU Chi-restraints excluded: chain K residue 627 ILE Chi-restraints excluded: chain K residue 637 LEU Chi-restraints excluded: chain K residue 683 GLU Chi-restraints excluded: chain K residue 697 VAL Chi-restraints excluded: chain K residue 709 THR Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 328 SER Chi-restraints excluded: chain L residue 353 ASP Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 98 optimal weight: 2.9990 chunk 406 optimal weight: 0.7980 chunk 363 optimal weight: 8.9990 chunk 460 optimal weight: 4.9990 chunk 484 optimal weight: 8.9990 chunk 354 optimal weight: 0.0070 chunk 101 optimal weight: 1.9990 chunk 316 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 508 optimal weight: 5.9990 chunk 375 optimal weight: 1.9990 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 550 ASN C 529 GLN ** C 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 459 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.185123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.116764 restraints weight = 56996.941| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.01 r_work: 0.3202 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 45188 Z= 0.184 Angle : 0.621 10.051 61069 Z= 0.323 Chirality : 0.046 0.297 6745 Planarity : 0.004 0.056 7927 Dihedral : 7.962 76.696 6610 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.15 % Favored : 95.83 % Rotamer: Outliers : 3.42 % Allowed : 16.45 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.22 (0.11), residues: 5664 helix: 0.96 (0.12), residues: 2077 sheet: -0.03 (0.14), residues: 1159 loop : -1.14 (0.13), residues: 2428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 234 TYR 0.018 0.002 TYR J 457 PHE 0.027 0.001 PHE K 333 TRP 0.007 0.001 TRP J 276 HIS 0.007 0.001 HIS K 344 Details of bonding type rmsd covalent geometry : bond 0.00439 (45182) covalent geometry : angle 0.62121 (61069) hydrogen bonds : bond 0.04387 ( 2086) hydrogen bonds : angle 4.65566 ( 5811) Misc. bond : bond 0.00023 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 451 time to evaluate : 1.795 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 522 MET cc_start: 0.7046 (mmm) cc_final: 0.6749 (tpp) REVERT: A 543 ARG cc_start: 0.8765 (mmm-85) cc_final: 0.8493 (mmm-85) REVERT: A 577 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7564 (tp-100) REVERT: A 591 SER cc_start: 0.8338 (m) cc_final: 0.8024 (t) REVERT: A 599 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7265 (tttt) REVERT: A 610 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7241 (ttmm) REVERT: B 64 LYS cc_start: 0.8466 (tmtt) cc_final: 0.8059 (tttm) REVERT: B 132 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8781 (tpt) REVERT: B 183 ASP cc_start: 0.8248 (m-30) cc_final: 0.8006 (m-30) REVERT: B 204 LYS cc_start: 0.9399 (OUTLIER) cc_final: 0.8959 (mttp) REVERT: B 217 THR cc_start: 0.8162 (p) cc_final: 0.7811 (t) REVERT: B 269 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8008 (mttt) REVERT: C 506 GLU cc_start: 0.7790 (mp0) cc_final: 0.7348 (pp20) REVERT: C 522 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.6366 (mmp) REVERT: C 526 PHE cc_start: 0.7720 (t80) cc_final: 0.7483 (t80) REVERT: C 543 ARG cc_start: 0.8356 (tpp80) cc_final: 0.8113 (tpp80) REVERT: C 592 GLU cc_start: 0.6385 (mt-10) cc_final: 0.5984 (pp20) REVERT: C 617 THR cc_start: 0.7698 (m) cc_final: 0.7444 (p) REVERT: C 624 GLU cc_start: 0.7427 (mt-10) cc_final: 0.6892 (pp20) REVERT: C 677 MET cc_start: 0.4832 (ttm) cc_final: 0.4457 (ttm) REVERT: C 683 GLU cc_start: 0.6481 (pt0) cc_final: 0.6116 (pp20) REVERT: C 687 LYS cc_start: 0.5607 (OUTLIER) cc_final: 0.5296 (mttt) REVERT: D 217 THR cc_start: 0.8728 (OUTLIER) cc_final: 0.8385 (p) REVERT: D 292 ARG cc_start: 0.8822 (ttm-80) cc_final: 0.8311 (ttt-90) REVERT: D 555 LYS cc_start: 0.8399 (tmtm) cc_final: 0.8182 (tppt) REVERT: E 613 ILE cc_start: 0.6880 (mt) cc_final: 0.6084 (pp) REVERT: E 682 MET cc_start: 0.5364 (ptt) cc_final: 0.5103 (ptt) REVERT: F 130 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: F 240 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7335 (p90) REVERT: F 346 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.7836 (tp30) REVERT: G 304 GLU cc_start: 0.5483 (OUTLIER) cc_final: 0.5169 (mp0) REVERT: G 349 MET cc_start: 0.5312 (mmm) cc_final: 0.4856 (mtt) REVERT: G 383 GLU cc_start: 0.6831 (tt0) cc_final: 0.6225 (pp20) REVERT: G 421 ARG cc_start: 0.6646 (mtm180) cc_final: 0.5775 (mtm180) REVERT: G 478 GLU cc_start: 0.5511 (tt0) cc_final: 0.4728 (tm-30) REVERT: G 672 ASP cc_start: 0.3312 (OUTLIER) cc_final: 0.2929 (m-30) REVERT: G 675 MET cc_start: 0.3775 (ttm) cc_final: 0.3456 (ttm) REVERT: H 213 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.8887 (mtt) REVERT: H 353 ASP cc_start: 0.8468 (p0) cc_final: 0.8150 (p0) REVERT: H 473 MET cc_start: 0.8972 (ptp) cc_final: 0.8749 (ptp) REVERT: I 74 GLN cc_start: 0.6941 (OUTLIER) cc_final: 0.5991 (mt0) REVERT: I 110 MET cc_start: 0.4394 (mmm) cc_final: 0.4084 (mmm) REVERT: I 163 LYS cc_start: 0.4791 (mmtt) cc_final: 0.4385 (mtmt) REVERT: I 287 GLU cc_start: 0.8045 (tt0) cc_final: 0.7784 (tt0) REVERT: I 417 GLU cc_start: 0.5813 (pm20) cc_final: 0.5586 (mp0) REVERT: I 433 MET cc_start: 0.7444 (ttt) cc_final: 0.6629 (tpt) REVERT: I 559 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.7951 (mmtt) REVERT: I 653 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6037 (mtp) REVERT: I 682 MET cc_start: 0.6406 (mtp) cc_final: 0.6071 (mtp) REVERT: I 713 GLU cc_start: 0.7157 (tp30) cc_final: 0.6490 (mt-10) REVERT: J 240 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7038 (p90) REVERT: J 299 LYS cc_start: 0.8815 (tptt) cc_final: 0.8479 (ttmm) REVERT: J 476 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6575 (mp0) REVERT: K 84 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.5919 (ttt90) REVERT: K 135 ASN cc_start: 0.5511 (OUTLIER) cc_final: 0.5187 (t0) REVERT: K 160 MET cc_start: 0.2460 (mpt) cc_final: 0.1810 (mmm) REVERT: K 270 TYR cc_start: 0.6210 (p90) cc_final: 0.5576 (p90) REVERT: K 295 LYS cc_start: 0.3904 (mmtt) cc_final: 0.3602 (mtpp) REVERT: K 333 PHE cc_start: 0.5101 (t80) cc_final: 0.4444 (t80) REVERT: K 354 ASP cc_start: 0.6075 (t0) cc_final: 0.5454 (t0) REVERT: K 383 GLU cc_start: 0.6694 (tt0) cc_final: 0.5960 (tt0) REVERT: K 390 ASP cc_start: 0.5972 (t0) cc_final: 0.5615 (t0) REVERT: K 396 MET cc_start: 0.4583 (ttm) cc_final: 0.3846 (ppp) REVERT: K 405 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7985 (tm) REVERT: K 424 ASP cc_start: 0.5928 (m-30) cc_final: 0.5638 (m-30) REVERT: K 431 ASP cc_start: 0.7027 (t70) cc_final: 0.6577 (t70) REVERT: K 433 MET cc_start: 0.5790 (tmm) cc_final: 0.4741 (ttp) REVERT: K 487 ASP cc_start: 0.8071 (t0) cc_final: 0.7802 (OUTLIER) REVERT: K 518 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8185 (tmmt) REVERT: L 278 LEU cc_start: 0.8951 (mp) cc_final: 0.8652 (mt) REVERT: L 376 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8732 (tp) REVERT: L 420 LYS cc_start: 0.8320 (tttm) cc_final: 0.8094 (tttp) outliers start: 159 outliers final: 62 residues processed: 549 average time/residue: 0.6488 time to fit residues: 440.3554 Evaluate side-chains 519 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 433 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 555 LYS Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 425 MET Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 631 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 346 GLU Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 672 ASP Chi-restraints excluded: chain G residue 678 ILE Chi-restraints excluded: chain G residue 684 HIS Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 213 MET Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain H residue 510 ILE Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 556 LYS Chi-restraints excluded: chain I residue 559 LYS Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 684 HIS Chi-restraints excluded: chain I residue 712 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 240 PHE Chi-restraints excluded: chain J residue 421 ASP Chi-restraints excluded: chain J residue 476 GLU Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 347 THR Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 518 LYS Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 528 LEU Chi-restraints excluded: chain K residue 553 MET Chi-restraints excluded: chain K residue 627 ILE Chi-restraints excluded: chain K residue 709 THR Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 328 SER Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 376 LEU Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 290 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 302 optimal weight: 3.9990 chunk 372 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 528 optimal weight: 0.5980 chunk 350 optimal weight: 20.0000 chunk 181 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 295 optimal weight: 2.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 529 GLN ** C 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 341 GLN ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 457 GLN J 34 GLN ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.186431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118322 restraints weight = 56937.482| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.02 r_work: 0.3224 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 45188 Z= 0.129 Angle : 0.580 9.752 61069 Z= 0.304 Chirality : 0.045 0.297 6745 Planarity : 0.004 0.056 7927 Dihedral : 7.812 76.408 6610 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.92 % Rotamer: Outliers : 2.88 % Allowed : 17.31 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.11), residues: 5664 helix: 1.16 (0.12), residues: 2064 sheet: 0.04 (0.14), residues: 1145 loop : -1.09 (0.13), residues: 2455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 234 TYR 0.014 0.001 TYR D 457 PHE 0.024 0.001 PHE I 333 TRP 0.009 0.001 TRP B 276 HIS 0.005 0.001 HIS K 344 Details of bonding type rmsd covalent geometry : bond 0.00297 (45182) covalent geometry : angle 0.58001 (61069) hydrogen bonds : bond 0.03883 ( 2086) hydrogen bonds : angle 4.52045 ( 5811) Misc. bond : bond 0.00020 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 460 time to evaluate : 1.944 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: A 522 MET cc_start: 0.7035 (mmm) cc_final: 0.6796 (tpp) REVERT: A 543 ARG cc_start: 0.8755 (mmm-85) cc_final: 0.8484 (mmm-85) REVERT: A 577 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7681 (tp-100) REVERT: A 591 SER cc_start: 0.8325 (m) cc_final: 0.8023 (t) REVERT: A 610 LYS cc_start: 0.8030 (OUTLIER) cc_final: 0.7221 (ttmm) REVERT: B 64 LYS cc_start: 0.8508 (tmtt) cc_final: 0.8121 (tttm) REVERT: B 183 ASP cc_start: 0.8212 (m-30) cc_final: 0.7973 (m-30) REVERT: B 204 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8950 (mttp) REVERT: B 217 THR cc_start: 0.8069 (p) cc_final: 0.7703 (t) REVERT: B 269 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7995 (mttt) REVERT: C 506 GLU cc_start: 0.7755 (mp0) cc_final: 0.7382 (pp20) REVERT: C 522 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6368 (mmp) REVERT: C 526 PHE cc_start: 0.7796 (t80) cc_final: 0.7543 (t80) REVERT: C 543 ARG cc_start: 0.8340 (tpp80) cc_final: 0.8121 (tpp80) REVERT: C 579 GLU cc_start: 0.7213 (pt0) cc_final: 0.6655 (mm-30) REVERT: C 592 GLU cc_start: 0.6263 (mt-10) cc_final: 0.5878 (pp20) REVERT: C 617 THR cc_start: 0.7684 (m) cc_final: 0.7421 (p) REVERT: C 624 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6855 (pp20) REVERT: C 677 MET cc_start: 0.5049 (ttm) cc_final: 0.4645 (ttm) REVERT: C 683 GLU cc_start: 0.6388 (pt0) cc_final: 0.6032 (pp20) REVERT: C 687 LYS cc_start: 0.5534 (OUTLIER) cc_final: 0.5215 (mttt) REVERT: D 217 THR cc_start: 0.8664 (m) cc_final: 0.8336 (p) REVERT: D 292 ARG cc_start: 0.8801 (ttm-80) cc_final: 0.8317 (ttt-90) REVERT: D 425 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8293 (tpt) REVERT: E 613 ILE cc_start: 0.6837 (mt) cc_final: 0.6012 (pp) REVERT: F 130 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: G 304 GLU cc_start: 0.5629 (OUTLIER) cc_final: 0.5298 (mp0) REVERT: G 334 MET cc_start: 0.3460 (mpt) cc_final: 0.2723 (ptt) REVERT: G 349 MET cc_start: 0.5314 (mmm) cc_final: 0.4987 (mtt) REVERT: G 383 GLU cc_start: 0.6866 (tt0) cc_final: 0.6384 (tm-30) REVERT: G 421 ARG cc_start: 0.6728 (mtm180) cc_final: 0.5898 (mtm180) REVERT: G 478 GLU cc_start: 0.6639 (tt0) cc_final: 0.6231 (tp30) REVERT: G 488 PHE cc_start: 0.4751 (t80) cc_final: 0.4511 (t80) REVERT: G 672 ASP cc_start: 0.3327 (OUTLIER) cc_final: 0.2956 (m-30) REVERT: G 675 MET cc_start: 0.4208 (ttm) cc_final: 0.3916 (ttm) REVERT: H 213 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8846 (mtt) REVERT: H 353 ASP cc_start: 0.8448 (p0) cc_final: 0.8137 (p0) REVERT: H 473 MET cc_start: 0.9005 (ptp) cc_final: 0.8775 (ptp) REVERT: I 74 GLN cc_start: 0.6904 (OUTLIER) cc_final: 0.6014 (mt0) REVERT: I 76 VAL cc_start: 0.7934 (OUTLIER) cc_final: 0.7616 (p) REVERT: I 110 MET cc_start: 0.4357 (mmm) cc_final: 0.4113 (mmm) REVERT: I 163 LYS cc_start: 0.4691 (mmtt) cc_final: 0.4295 (mtmt) REVERT: I 287 GLU cc_start: 0.7961 (tt0) cc_final: 0.7634 (tt0) REVERT: I 328 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7827 (ptpt) REVERT: I 417 GLU cc_start: 0.6109 (pm20) cc_final: 0.4455 (tp30) REVERT: I 433 MET cc_start: 0.7377 (ttt) cc_final: 0.6722 (tpt) REVERT: I 559 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.7890 (mmtt) REVERT: I 653 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.5927 (mtp) REVERT: I 682 MET cc_start: 0.6289 (mtp) cc_final: 0.6033 (mtp) REVERT: I 713 GLU cc_start: 0.7165 (tp30) cc_final: 0.6468 (mt-10) REVERT: J 34 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7722 (tp40) REVERT: J 299 LYS cc_start: 0.8825 (tptt) cc_final: 0.8465 (ttmm) REVERT: J 458 SER cc_start: 0.9081 (m) cc_final: 0.8735 (p) REVERT: J 476 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6543 (mp0) REVERT: K 135 ASN cc_start: 0.5548 (OUTLIER) cc_final: 0.5241 (t0) REVERT: K 160 MET cc_start: 0.2563 (mpt) cc_final: 0.2062 (mmm) REVERT: K 270 TYR cc_start: 0.6340 (p90) cc_final: 0.5713 (p90) REVERT: K 295 LYS cc_start: 0.3956 (mmtt) cc_final: 0.3601 (mtpp) REVERT: K 333 PHE cc_start: 0.5013 (t80) cc_final: 0.4413 (t80) REVERT: K 354 ASP cc_start: 0.6058 (t0) cc_final: 0.5406 (t0) REVERT: K 383 GLU cc_start: 0.6725 (tt0) cc_final: 0.6036 (tt0) REVERT: K 396 MET cc_start: 0.4299 (ttm) cc_final: 0.3582 (ppp) REVERT: K 405 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7962 (tm) REVERT: K 424 ASP cc_start: 0.5891 (m-30) cc_final: 0.5549 (m-30) REVERT: K 431 ASP cc_start: 0.7002 (t70) cc_final: 0.6559 (t70) REVERT: K 487 ASP cc_start: 0.8085 (t0) cc_final: 0.7816 (OUTLIER) REVERT: K 518 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8202 (tmmt) REVERT: L 278 LEU cc_start: 0.8934 (mp) cc_final: 0.8643 (mt) REVERT: L 420 LYS cc_start: 0.8323 (tttm) cc_final: 0.8095 (tttp) outliers start: 134 outliers final: 57 residues processed: 547 average time/residue: 0.5187 time to fit residues: 352.3084 Evaluate side-chains 511 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 434 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 425 MET Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 631 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 672 ASP Chi-restraints excluded: chain G residue 678 ILE Chi-restraints excluded: chain G residue 684 HIS Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 213 MET Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain H residue 510 ILE Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 556 LYS Chi-restraints excluded: chain I residue 559 LYS Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 684 HIS Chi-restraints excluded: chain I residue 712 VAL Chi-restraints excluded: chain J residue 34 GLN Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 421 ASP Chi-restraints excluded: chain J residue 476 GLU Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 347 THR Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 428 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 518 LYS Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 528 LEU Chi-restraints excluded: chain K residue 627 ILE Chi-restraints excluded: chain K residue 637 LEU Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 328 SER Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 378 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 234 optimal weight: 0.9990 chunk 415 optimal weight: 2.9990 chunk 532 optimal weight: 0.7980 chunk 496 optimal weight: 0.9990 chunk 506 optimal weight: 1.9990 chunk 391 optimal weight: 0.2980 chunk 380 optimal weight: 6.9990 chunk 266 optimal weight: 4.9990 chunk 202 optimal weight: 4.9990 chunk 14 optimal weight: 0.1980 chunk 143 optimal weight: 9.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN ** C 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN D 449 ASN E 684 HIS ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN I 341 GLN ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 457 GLN I 616 ASN J 34 GLN ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 459 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.187034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.123050 restraints weight = 57366.178| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.66 r_work: 0.3231 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 45188 Z= 0.117 Angle : 0.577 9.986 61069 Z= 0.301 Chirality : 0.045 0.398 6745 Planarity : 0.004 0.056 7927 Dihedral : 7.699 75.790 6609 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.96 % Rotamer: Outliers : 2.60 % Allowed : 17.66 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.11), residues: 5664 helix: 1.36 (0.12), residues: 2022 sheet: 0.06 (0.15), residues: 1143 loop : -1.07 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 469 TYR 0.013 0.001 TYR J 318 PHE 0.025 0.001 PHE I 333 TRP 0.009 0.001 TRP B 276 HIS 0.004 0.001 HIS K 404 Details of bonding type rmsd covalent geometry : bond 0.00266 (45182) covalent geometry : angle 0.57665 (61069) hydrogen bonds : bond 0.03638 ( 2086) hydrogen bonds : angle 4.44243 ( 5811) Misc. bond : bond 0.00016 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 456 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8177 (tt) REVERT: A 543 ARG cc_start: 0.8823 (mmm-85) cc_final: 0.8553 (mmm-85) REVERT: A 577 GLN cc_start: 0.8205 (OUTLIER) cc_final: 0.7737 (tp40) REVERT: A 591 SER cc_start: 0.8356 (m) cc_final: 0.8050 (t) REVERT: A 610 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7237 (ttmm) REVERT: B 64 LYS cc_start: 0.8541 (tmtt) cc_final: 0.8170 (tttm) REVERT: B 183 ASP cc_start: 0.8409 (m-30) cc_final: 0.8184 (m-30) REVERT: B 204 LYS cc_start: 0.9406 (OUTLIER) cc_final: 0.9128 (mttp) REVERT: B 217 THR cc_start: 0.8004 (p) cc_final: 0.7658 (t) REVERT: B 269 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8051 (mttt) REVERT: B 378 SER cc_start: 0.8893 (OUTLIER) cc_final: 0.8645 (m) REVERT: C 506 GLU cc_start: 0.7755 (mp0) cc_final: 0.7345 (pp20) REVERT: C 522 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6358 (mmp) REVERT: C 526 PHE cc_start: 0.7743 (t80) cc_final: 0.7534 (t80) REVERT: C 529 GLN cc_start: 0.6743 (mm-40) cc_final: 0.6377 (tp40) REVERT: C 579 GLU cc_start: 0.7231 (pt0) cc_final: 0.6684 (mm-30) REVERT: C 592 GLU cc_start: 0.6293 (mt-10) cc_final: 0.5842 (pp20) REVERT: C 614 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7452 (tm) REVERT: C 617 THR cc_start: 0.7678 (m) cc_final: 0.7401 (p) REVERT: C 624 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6760 (pp20) REVERT: C 677 MET cc_start: 0.4948 (ttm) cc_final: 0.4488 (ttm) REVERT: C 683 GLU cc_start: 0.6325 (pt0) cc_final: 0.5950 (pp20) REVERT: C 687 LYS cc_start: 0.5470 (OUTLIER) cc_final: 0.5138 (mttt) REVERT: D 217 THR cc_start: 0.8616 (m) cc_final: 0.8326 (p) REVERT: D 292 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8364 (ttt-90) REVERT: D 425 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8408 (tpt) REVERT: F 69 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6620 (tp30) REVERT: F 130 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: F 240 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7268 (p90) REVERT: F 511 LYS cc_start: 0.7963 (ptmm) cc_final: 0.7290 (ptpt) REVERT: G 84 ARG cc_start: 0.7572 (mtm110) cc_final: 0.7130 (ttm110) REVERT: G 304 GLU cc_start: 0.5660 (OUTLIER) cc_final: 0.5342 (mp0) REVERT: G 334 MET cc_start: 0.3417 (mpt) cc_final: 0.2645 (ppp) REVERT: G 374 GLU cc_start: 0.4697 (mm-30) cc_final: 0.4314 (tp30) REVERT: G 383 GLU cc_start: 0.6871 (tt0) cc_final: 0.6600 (tm-30) REVERT: G 402 LEU cc_start: 0.7195 (mp) cc_final: 0.6817 (mp) REVERT: G 421 ARG cc_start: 0.6709 (mtm180) cc_final: 0.5555 (mtm110) REVERT: G 672 ASP cc_start: 0.3133 (OUTLIER) cc_final: 0.2839 (m-30) REVERT: G 675 MET cc_start: 0.4004 (ttm) cc_final: 0.3750 (ttm) REVERT: H 213 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8878 (mtt) REVERT: H 297 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7635 (tm-30) REVERT: H 353 ASP cc_start: 0.8559 (p0) cc_final: 0.8223 (p0) REVERT: H 473 MET cc_start: 0.9075 (ptp) cc_final: 0.8811 (ptp) REVERT: I 74 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.5998 (mt0) REVERT: I 76 VAL cc_start: 0.7996 (OUTLIER) cc_final: 0.7682 (p) REVERT: I 110 MET cc_start: 0.4278 (mmm) cc_final: 0.3981 (mmm) REVERT: I 163 LYS cc_start: 0.4673 (mmtt) cc_final: 0.4279 (mtmt) REVERT: I 287 GLU cc_start: 0.7924 (tt0) cc_final: 0.7504 (tt0) REVERT: I 328 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7767 (ptpt) REVERT: I 417 GLU cc_start: 0.5810 (pm20) cc_final: 0.4039 (tp30) REVERT: I 433 MET cc_start: 0.7363 (ttt) cc_final: 0.6694 (tpt) REVERT: I 559 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.7911 (mmtt) REVERT: I 682 MET cc_start: 0.6206 (mtp) cc_final: 0.5874 (mtp) REVERT: I 713 GLU cc_start: 0.7303 (tp30) cc_final: 0.6541 (mt-10) REVERT: J 240 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.6804 (p90) REVERT: J 299 LYS cc_start: 0.8816 (tptt) cc_final: 0.8509 (ttmm) REVERT: J 407 PHE cc_start: 0.6967 (OUTLIER) cc_final: 0.6732 (m-80) REVERT: J 458 SER cc_start: 0.9066 (m) cc_final: 0.8760 (p) REVERT: K 135 ASN cc_start: 0.5477 (OUTLIER) cc_final: 0.5196 (t0) REVERT: K 160 MET cc_start: 0.2416 (mpt) cc_final: 0.1874 (mmm) REVERT: K 270 TYR cc_start: 0.6318 (p90) cc_final: 0.5710 (p90) REVERT: K 295 LYS cc_start: 0.3917 (mmtt) cc_final: 0.3522 (mtpp) REVERT: K 325 MET cc_start: 0.4495 (ptt) cc_final: 0.4220 (pp-130) REVERT: K 333 PHE cc_start: 0.5142 (t80) cc_final: 0.4465 (t80) REVERT: K 354 ASP cc_start: 0.5852 (t0) cc_final: 0.5225 (t0) REVERT: K 396 MET cc_start: 0.4232 (ttm) cc_final: 0.3674 (ppp) REVERT: K 424 ASP cc_start: 0.6139 (m-30) cc_final: 0.5714 (m-30) REVERT: K 431 ASP cc_start: 0.7029 (t70) cc_final: 0.6566 (t70) REVERT: K 433 MET cc_start: 0.5066 (tmm) cc_final: 0.4572 (ttp) REVERT: K 458 TYR cc_start: 0.6228 (OUTLIER) cc_final: 0.4817 (m-80) REVERT: K 487 ASP cc_start: 0.8029 (t0) cc_final: 0.7780 (t0) REVERT: K 518 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8230 (tmmt) REVERT: L 278 LEU cc_start: 0.8931 (mp) cc_final: 0.8619 (mt) REVERT: L 376 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8724 (tp) outliers start: 121 outliers final: 54 residues processed: 538 average time/residue: 0.5090 time to fit residues: 339.6501 Evaluate side-chains 517 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 436 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain C residue 712 VAL Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 425 MET Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 672 ASP Chi-restraints excluded: chain G residue 678 ILE Chi-restraints excluded: chain G residue 684 HIS Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 188 ARG Chi-restraints excluded: chain H residue 213 MET Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain H residue 416 GLU Chi-restraints excluded: chain H residue 510 ILE Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 556 LYS Chi-restraints excluded: chain I residue 559 LYS Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 684 HIS Chi-restraints excluded: chain I residue 712 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 240 PHE Chi-restraints excluded: chain J residue 407 PHE Chi-restraints excluded: chain J residue 421 ASP Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 347 THR Chi-restraints excluded: chain K residue 428 VAL Chi-restraints excluded: chain K residue 458 TYR Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 518 LYS Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 528 LEU Chi-restraints excluded: chain K residue 553 MET Chi-restraints excluded: chain K residue 627 ILE Chi-restraints excluded: chain K residue 637 LEU Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 328 SER Chi-restraints excluded: chain L residue 376 LEU Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain L residue 404 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 536 optimal weight: 1.9990 chunk 398 optimal weight: 8.9990 chunk 565 optimal weight: 0.6980 chunk 303 optimal weight: 0.6980 chunk 428 optimal weight: 0.0970 chunk 501 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 145 optimal weight: 1.9990 chunk 347 optimal weight: 0.3980 chunk 552 optimal weight: 1.9990 chunk 187 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN ** C 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 HIS H 230 ASN ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 457 GLN I 616 ASN ** J 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 297 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.187837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.125721 restraints weight = 57126.809| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.74 r_work: 0.3246 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 45188 Z= 0.109 Angle : 0.573 9.761 61069 Z= 0.297 Chirality : 0.044 0.296 6745 Planarity : 0.004 0.055 7927 Dihedral : 7.584 75.201 6609 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.99 % Favored : 95.97 % Rotamer: Outliers : 2.15 % Allowed : 18.24 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.15 (0.11), residues: 5664 helix: 1.47 (0.12), residues: 2028 sheet: 0.05 (0.14), residues: 1157 loop : -1.03 (0.13), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 327 TYR 0.013 0.001 TYR J 318 PHE 0.030 0.001 PHE K 323 TRP 0.010 0.001 TRP B 276 HIS 0.005 0.001 HIS G 492 Details of bonding type rmsd covalent geometry : bond 0.00243 (45182) covalent geometry : angle 0.57275 (61069) hydrogen bonds : bond 0.03441 ( 2086) hydrogen bonds : angle 4.37174 ( 5811) Misc. bond : bond 0.00020 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 457 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8166 (tt) REVERT: A 543 ARG cc_start: 0.8807 (mmm-85) cc_final: 0.8531 (mmm-85) REVERT: A 552 ASN cc_start: 0.8410 (m-40) cc_final: 0.8110 (m110) REVERT: A 577 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7771 (tp40) REVERT: A 591 SER cc_start: 0.8337 (m) cc_final: 0.8047 (t) REVERT: A 610 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7243 (ttmm) REVERT: B 64 LYS cc_start: 0.8557 (tmtt) cc_final: 0.8173 (tttm) REVERT: B 189 ASP cc_start: 0.8338 (m-30) cc_final: 0.8126 (t0) REVERT: B 204 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9118 (mttm) REVERT: B 217 THR cc_start: 0.7897 (p) cc_final: 0.7581 (t) REVERT: B 269 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8043 (mttt) REVERT: B 378 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8600 (m) REVERT: C 506 GLU cc_start: 0.7777 (mp0) cc_final: 0.7349 (pp20) REVERT: C 522 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6311 (mmp) REVERT: C 529 GLN cc_start: 0.6726 (mm-40) cc_final: 0.6378 (tp40) REVERT: C 579 GLU cc_start: 0.7152 (pt0) cc_final: 0.6680 (mm-30) REVERT: C 592 GLU cc_start: 0.6280 (mt-10) cc_final: 0.5798 (pp20) REVERT: C 614 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7459 (tm) REVERT: C 617 THR cc_start: 0.7685 (m) cc_final: 0.7391 (p) REVERT: C 624 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6695 (pp20) REVERT: C 658 GLU cc_start: 0.6165 (tp30) cc_final: 0.5569 (mt-10) REVERT: C 677 MET cc_start: 0.5127 (ttm) cc_final: 0.4671 (ttm) REVERT: C 683 GLU cc_start: 0.6233 (pt0) cc_final: 0.5968 (pp20) REVERT: C 687 LYS cc_start: 0.5493 (OUTLIER) cc_final: 0.5144 (mttt) REVERT: D 217 THR cc_start: 0.8704 (m) cc_final: 0.8394 (p) REVERT: D 240 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7388 (p90) REVERT: D 292 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8369 (ttt-90) REVERT: D 425 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8470 (tpt) REVERT: F 69 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6644 (tp30) REVERT: F 240 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7121 (p90) REVERT: F 511 LYS cc_start: 0.8000 (ptmm) cc_final: 0.7314 (ptpt) REVERT: G 84 ARG cc_start: 0.7560 (mtm110) cc_final: 0.7119 (ttm110) REVERT: G 281 ARG cc_start: 0.5404 (mtp180) cc_final: 0.5099 (mmt90) REVERT: G 334 MET cc_start: 0.3413 (mpt) cc_final: 0.2722 (ppp) REVERT: G 336 MET cc_start: 0.4418 (ptp) cc_final: 0.3968 (pmt) REVERT: G 349 MET cc_start: 0.5275 (mmm) cc_final: 0.4921 (mtt) REVERT: G 383 GLU cc_start: 0.6882 (tt0) cc_final: 0.6642 (tm-30) REVERT: G 402 LEU cc_start: 0.7189 (mp) cc_final: 0.6816 (mp) REVERT: G 421 ARG cc_start: 0.6693 (mtm180) cc_final: 0.5436 (mtm110) REVERT: G 478 GLU cc_start: 0.5483 (pt0) cc_final: 0.4796 (tp30) REVERT: G 488 PHE cc_start: 0.4505 (t80) cc_final: 0.4073 (t80) REVERT: G 672 ASP cc_start: 0.3164 (OUTLIER) cc_final: 0.2864 (m-30) REVERT: G 675 MET cc_start: 0.4087 (ttm) cc_final: 0.3819 (ttm) REVERT: H 213 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8891 (mtt) REVERT: H 297 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7607 (tm-30) REVERT: H 353 ASP cc_start: 0.8510 (p0) cc_final: 0.8180 (p0) REVERT: H 411 ARG cc_start: 0.7785 (tmm-80) cc_final: 0.7257 (ttm-80) REVERT: H 473 MET cc_start: 0.9074 (ptp) cc_final: 0.8802 (ptp) REVERT: I 74 GLN cc_start: 0.6914 (OUTLIER) cc_final: 0.5989 (mt0) REVERT: I 76 VAL cc_start: 0.8075 (OUTLIER) cc_final: 0.7738 (p) REVERT: I 110 MET cc_start: 0.4234 (mmm) cc_final: 0.3963 (mmm) REVERT: I 163 LYS cc_start: 0.4794 (mmtt) cc_final: 0.4284 (mtmt) REVERT: I 328 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7812 (ptpt) REVERT: I 417 GLU cc_start: 0.5817 (pm20) cc_final: 0.4036 (tp30) REVERT: I 433 MET cc_start: 0.7366 (ttt) cc_final: 0.6702 (tpt) REVERT: I 559 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.7948 (mmtt) REVERT: I 653 MET cc_start: 0.5298 (OUTLIER) cc_final: 0.4813 (ptm) REVERT: I 682 MET cc_start: 0.6247 (mtp) cc_final: 0.5991 (mtp) REVERT: I 713 GLU cc_start: 0.7320 (tp30) cc_final: 0.6557 (mt-10) REVERT: J 299 LYS cc_start: 0.8815 (tptt) cc_final: 0.8512 (ttmm) REVERT: J 458 SER cc_start: 0.9051 (m) cc_final: 0.8745 (p) REVERT: J 473 MET cc_start: 0.8921 (ptp) cc_final: 0.8627 (ptm) REVERT: K 135 ASN cc_start: 0.5461 (OUTLIER) cc_final: 0.5223 (t0) REVERT: K 160 MET cc_start: 0.2310 (mpt) cc_final: 0.1798 (mmm) REVERT: K 270 TYR cc_start: 0.6449 (p90) cc_final: 0.5800 (p90) REVERT: K 295 LYS cc_start: 0.3882 (mmtt) cc_final: 0.3489 (mtpp) REVERT: K 325 MET cc_start: 0.4487 (ptt) cc_final: 0.4220 (pp-130) REVERT: K 333 PHE cc_start: 0.5118 (t80) cc_final: 0.4497 (t80) REVERT: K 354 ASP cc_start: 0.5844 (t0) cc_final: 0.5216 (t0) REVERT: K 396 MET cc_start: 0.4364 (ttm) cc_final: 0.3797 (ppp) REVERT: K 424 ASP cc_start: 0.6072 (m-30) cc_final: 0.5680 (m-30) REVERT: K 431 ASP cc_start: 0.7031 (t70) cc_final: 0.6547 (t70) REVERT: K 433 MET cc_start: 0.5051 (tmm) cc_final: 0.4611 (ttp) REVERT: K 458 TYR cc_start: 0.6235 (OUTLIER) cc_final: 0.4797 (m-80) REVERT: K 487 ASP cc_start: 0.8055 (t0) cc_final: 0.7806 (t0) REVERT: L 278 LEU cc_start: 0.8919 (mp) cc_final: 0.8574 (mt) outliers start: 100 outliers final: 49 residues processed: 523 average time/residue: 0.4783 time to fit residues: 311.2383 Evaluate side-chains 505 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 433 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 425 MET Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 633 VAL Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 672 ASP Chi-restraints excluded: chain G residue 678 ILE Chi-restraints excluded: chain G residue 684 HIS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 188 ARG Chi-restraints excluded: chain H residue 213 MET Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain H residue 416 GLU Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 559 LYS Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 684 HIS Chi-restraints excluded: chain I residue 712 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 421 ASP Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 347 THR Chi-restraints excluded: chain K residue 428 VAL Chi-restraints excluded: chain K residue 458 TYR Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 528 LEU Chi-restraints excluded: chain K residue 553 MET Chi-restraints excluded: chain K residue 627 ILE Chi-restraints excluded: chain K residue 637 LEU Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 328 SER Chi-restraints excluded: chain L residue 375 VAL Chi-restraints excluded: chain L residue 510 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 93 optimal weight: 0.6980 chunk 193 optimal weight: 3.9990 chunk 467 optimal weight: 10.0000 chunk 544 optimal weight: 0.6980 chunk 278 optimal weight: 7.9990 chunk 440 optimal weight: 0.7980 chunk 425 optimal weight: 0.9990 chunk 377 optimal weight: 5.9990 chunk 506 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 165 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN ** C 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN F 230 ASN ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 HIS H 230 ASN ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 616 ASN J 230 ASN ** K 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.187534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.119906 restraints weight = 57529.589| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.36 r_work: 0.3232 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 45188 Z= 0.116 Angle : 0.578 9.760 61069 Z= 0.299 Chirality : 0.044 0.295 6745 Planarity : 0.004 0.055 7927 Dihedral : 7.519 74.537 6609 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 1.89 % Allowed : 18.75 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.11), residues: 5664 helix: 1.48 (0.12), residues: 2037 sheet: 0.06 (0.14), residues: 1167 loop : -0.99 (0.13), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 327 TYR 0.013 0.001 TYR J 318 PHE 0.029 0.001 PHE C 526 TRP 0.009 0.001 TRP J 276 HIS 0.007 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00266 (45182) covalent geometry : angle 0.57818 (61069) hydrogen bonds : bond 0.03516 ( 2086) hydrogen bonds : angle 4.35711 ( 5811) Misc. bond : bond 0.00019 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11328 Ramachandran restraints generated. 5664 Oldfield, 0 Emsley, 5664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 443 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8213 (tt) REVERT: A 543 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.8436 (mmm-85) REVERT: A 552 ASN cc_start: 0.8392 (m-40) cc_final: 0.8099 (m110) REVERT: A 577 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7702 (tp40) REVERT: A 591 SER cc_start: 0.8310 (m) cc_final: 0.8023 (t) REVERT: A 610 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7231 (ttmm) REVERT: B 64 LYS cc_start: 0.8520 (tmtt) cc_final: 0.8151 (tttm) REVERT: B 204 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9105 (mttp) REVERT: B 217 THR cc_start: 0.7813 (p) cc_final: 0.7451 (t) REVERT: B 269 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8031 (mttt) REVERT: B 378 SER cc_start: 0.8798 (OUTLIER) cc_final: 0.8573 (m) REVERT: B 477 GLN cc_start: 0.7270 (mp10) cc_final: 0.6615 (mp10) REVERT: C 506 GLU cc_start: 0.7743 (mp0) cc_final: 0.7328 (pp20) REVERT: C 522 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.6298 (mmp) REVERT: C 529 GLN cc_start: 0.6608 (mm-40) cc_final: 0.6305 (tp40) REVERT: C 579 GLU cc_start: 0.7074 (pt0) cc_final: 0.6706 (mm-30) REVERT: C 592 GLU cc_start: 0.6277 (mt-10) cc_final: 0.5780 (pp20) REVERT: C 617 THR cc_start: 0.7652 (m) cc_final: 0.7379 (p) REVERT: C 624 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6709 (pp20) REVERT: C 658 GLU cc_start: 0.6242 (tp30) cc_final: 0.5602 (mt-10) REVERT: C 677 MET cc_start: 0.5168 (ttm) cc_final: 0.4713 (ttm) REVERT: C 683 GLU cc_start: 0.6242 (pt0) cc_final: 0.5945 (pp20) REVERT: C 687 LYS cc_start: 0.5534 (OUTLIER) cc_final: 0.5062 (ttpt) REVERT: D 217 THR cc_start: 0.8623 (m) cc_final: 0.8314 (p) REVERT: D 240 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7327 (p90) REVERT: D 292 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8366 (ttt-90) REVERT: D 425 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8378 (tpt) REVERT: F 69 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6591 (tp30) REVERT: F 240 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7046 (p90) REVERT: F 511 LYS cc_start: 0.7958 (ptmm) cc_final: 0.7279 (ptpt) REVERT: G 281 ARG cc_start: 0.5429 (mtp180) cc_final: 0.5112 (mmt90) REVERT: G 334 MET cc_start: 0.3261 (mpt) cc_final: 0.2650 (ppp) REVERT: G 383 GLU cc_start: 0.6836 (tt0) cc_final: 0.6531 (tm-30) REVERT: G 402 LEU cc_start: 0.7141 (mp) cc_final: 0.6774 (mp) REVERT: G 421 ARG cc_start: 0.6635 (mtm180) cc_final: 0.5296 (mtm180) REVERT: G 672 ASP cc_start: 0.3179 (OUTLIER) cc_final: 0.2883 (m-30) REVERT: G 675 MET cc_start: 0.3884 (ttm) cc_final: 0.3628 (ttm) REVERT: G 682 MET cc_start: 0.4814 (ptm) cc_final: 0.4102 (ptp) REVERT: H 213 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8917 (mtt) REVERT: H 297 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: H 353 ASP cc_start: 0.8502 (p0) cc_final: 0.8198 (p0) REVERT: H 411 ARG cc_start: 0.7721 (tmm-80) cc_final: 0.7227 (ttm-80) REVERT: H 473 MET cc_start: 0.8999 (ptp) cc_final: 0.8753 (ptp) REVERT: I 74 GLN cc_start: 0.6765 (OUTLIER) cc_final: 0.5881 (mt0) REVERT: I 76 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7667 (p) REVERT: I 163 LYS cc_start: 0.4772 (mmtt) cc_final: 0.4344 (mtmm) REVERT: I 203 MET cc_start: 0.2236 (pp-130) cc_final: 0.1088 (pmt) REVERT: I 328 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7824 (ptpt) REVERT: I 373 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6611 (pp20) REVERT: I 417 GLU cc_start: 0.5827 (pm20) cc_final: 0.4009 (tp30) REVERT: I 433 MET cc_start: 0.7408 (ttt) cc_final: 0.6705 (tpt) REVERT: I 653 MET cc_start: 0.5364 (OUTLIER) cc_final: 0.4829 (ptm) REVERT: I 682 MET cc_start: 0.6132 (mtp) cc_final: 0.5903 (mtp) REVERT: I 713 GLU cc_start: 0.7221 (tp30) cc_final: 0.6458 (mt-10) REVERT: J 299 LYS cc_start: 0.8781 (tptt) cc_final: 0.8437 (ttmm) REVERT: J 407 PHE cc_start: 0.6785 (OUTLIER) cc_final: 0.6228 (m-80) REVERT: J 408 MET cc_start: 0.6552 (tpt) cc_final: 0.6282 (tpt) REVERT: J 458 SER cc_start: 0.9048 (m) cc_final: 0.8727 (p) REVERT: J 473 MET cc_start: 0.8728 (ptp) cc_final: 0.8498 (ptm) REVERT: K 94 GLU cc_start: 0.6711 (tp30) cc_final: 0.6397 (tp30) REVERT: K 135 ASN cc_start: 0.5282 (OUTLIER) cc_final: 0.5066 (t0) REVERT: K 160 MET cc_start: 0.2291 (mpt) cc_final: 0.1785 (mmm) REVERT: K 270 TYR cc_start: 0.6399 (p90) cc_final: 0.5777 (p90) REVERT: K 295 LYS cc_start: 0.3823 (mmtt) cc_final: 0.3447 (mtpp) REVERT: K 325 MET cc_start: 0.4437 (ptt) cc_final: 0.4153 (pp-130) REVERT: K 333 PHE cc_start: 0.4957 (t80) cc_final: 0.4380 (t80) REVERT: K 354 ASP cc_start: 0.5822 (t0) cc_final: 0.5244 (t0) REVERT: K 383 GLU cc_start: 0.6770 (tt0) cc_final: 0.6064 (tt0) REVERT: K 396 MET cc_start: 0.4474 (ttm) cc_final: 0.3892 (ppp) REVERT: K 424 ASP cc_start: 0.5894 (m-30) cc_final: 0.5556 (m-30) REVERT: K 431 ASP cc_start: 0.7008 (t70) cc_final: 0.6499 (t70) REVERT: K 433 MET cc_start: 0.4956 (tmm) cc_final: 0.4477 (ttp) REVERT: K 458 TYR cc_start: 0.6084 (OUTLIER) cc_final: 0.3846 (m-80) REVERT: K 487 ASP cc_start: 0.8027 (t0) cc_final: 0.7779 (t0) REVERT: L 278 LEU cc_start: 0.8899 (mp) cc_final: 0.8567 (mt) outliers start: 88 outliers final: 50 residues processed: 502 average time/residue: 0.4816 time to fit residues: 299.1856 Evaluate side-chains 504 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 432 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 577 GLN Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 610 LYS Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain D residue 44 GLU Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 425 MET Chi-restraints excluded: chain E residue 582 THR Chi-restraints excluded: chain E residue 602 VAL Chi-restraints excluded: chain E residue 618 ILE Chi-restraints excluded: chain E residue 631 ILE Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 615 GLU Chi-restraints excluded: chain G residue 672 ASP Chi-restraints excluded: chain G residue 678 ILE Chi-restraints excluded: chain G residue 684 HIS Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 188 ARG Chi-restraints excluded: chain H residue 213 MET Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 297 GLN Chi-restraints excluded: chain H residue 378 SER Chi-restraints excluded: chain H residue 416 GLU Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 328 LYS Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 614 LEU Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 684 HIS Chi-restraints excluded: chain I residue 712 VAL Chi-restraints excluded: chain J residue 63 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 407 PHE Chi-restraints excluded: chain J residue 421 ASP Chi-restraints excluded: chain K residue 78 VAL Chi-restraints excluded: chain K residue 133 SER Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 347 THR Chi-restraints excluded: chain K residue 428 VAL Chi-restraints excluded: chain K residue 458 TYR Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 484 VAL Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 528 LEU Chi-restraints excluded: chain K residue 553 MET Chi-restraints excluded: chain K residue 627 ILE Chi-restraints excluded: chain K residue 637 LEU Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 328 SER Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain L residue 510 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 200 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 361 optimal weight: 0.9990 chunk 511 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 174 optimal weight: 0.5980 chunk 494 optimal weight: 7.9990 chunk 275 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 181 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN C 684 HIS D 433 GLN F 230 ASN G 378 GLN ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 HIS H 230 ASN ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 616 ASN ** K 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.186296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120678 restraints weight = 57862.760| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 2.53 r_work: 0.3212 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45188 Z= 0.142 Angle : 0.597 9.909 61069 Z= 0.309 Chirality : 0.045 0.295 6745 Planarity : 0.004 0.055 7927 Dihedral : 7.523 74.220 6609 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % Rotamer: Outliers : 1.87 % Allowed : 18.84 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.11), residues: 5664 helix: 1.34 (0.12), residues: 2073 sheet: 0.13 (0.15), residues: 1137 loop : -1.01 (0.13), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 327 TYR 0.015 0.001 TYR J 457 PHE 0.036 0.001 PHE K 323 TRP 0.009 0.001 TRP J 276 HIS 0.007 0.001 HIS F 190 Details of bonding type rmsd covalent geometry : bond 0.00333 (45182) covalent geometry : angle 0.59737 (61069) hydrogen bonds : bond 0.03824 ( 2086) hydrogen bonds : angle 4.41225 ( 5811) Misc. bond : bond 0.00022 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17876.84 seconds wall clock time: 303 minutes 51.33 seconds (18231.33 seconds total)