Starting phenix.real_space_refine on Thu Dec 26 09:07:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xl7_38440/12_2024/8xl7_38440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xl7_38440/12_2024/8xl7_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_38440/12_2024/8xl7_38440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xl7_38440/12_2024/8xl7_38440.map" model { file = "/net/cci-nas-00/data/ceres_data/8xl7_38440/12_2024/8xl7_38440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xl7_38440/12_2024/8xl7_38440.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.089 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): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 25.42, per 1000 atoms: 0.57 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: 11.39 Conformation dependent library (CDL) restraints added in 6.2 seconds 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: 6.40 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: 23.35 Time building geometry restraints manager: 12.80 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 715 or resid 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: 7.890 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: 0.040 Extract box with map and model: 1.860 Check model and map are aligned: 0.350 Set scattering table: 0.450 Process input model: 103.660 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.280 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: 0.020 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.620 ------------------------------------------------------------------------------- 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 45182 Z= 0.864 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.002 TRP L 527 HIS 0.007 0.001 HIS B 75 PHE 0.027 0.002 PHE D 407 TYR 0.035 0.003 TYR F 457 ARG 0.007 0.001 ARG B 525 *********************** 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 : 4.959 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: 1.9007 time to fit residues: 2215.2436 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 : 5.600 ------------------------------------------------------------------------------- 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 480 optimal weight: 4.9990 chunk 431 optimal weight: 0.8980 chunk 239 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 290 optimal weight: 0.4980 chunk 230 optimal weight: 0.9990 chunk 445 optimal weight: 0.8980 chunk 172 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 chunk 331 optimal weight: 10.0000 chunk 516 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 45182 Z= 0.233 Angle : 0.677 10.002 61069 Z= 0.360 Chirality : 0.047 0.517 6745 Planarity : 0.005 0.059 7927 Dihedral : 8.705 120.085 6648 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.85 % Favored : 96.13 % Rotamer: Outliers : 2.73 % Allowed : 13.03 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.11), residues: 5664 helix: 0.16 (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 TRP 0.009 0.001 TRP F 276 HIS 0.012 0.001 HIS I 380 PHE 0.020 0.002 PHE G 323 TYR 0.017 0.001 TYR A 597 ARG 0.008 0.001 ARG K 421 *********************** 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 704 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 577 time to evaluate : 5.274 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: 0.7887 (pp) cc_final: 0.7651 (mm) REVERT: A 690 LYS cc_start: 0.2777 (pttp) cc_final: 0.2371 (mptp) REVERT: B 183 ASP cc_start: 0.7587 (m-30) cc_final: 0.7371 (m-30) REVERT: B 204 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8628 (mtpp) REVERT: C 579 GLU cc_start: 0.6309 (mt-10) cc_final: 0.6052 (mt-10) REVERT: C 712 VAL cc_start: 0.4868 (OUTLIER) cc_final: 0.4653 (m) REVERT: E 653 MET cc_start: 0.4358 (ttt) cc_final: 0.3950 (mtm) REVERT: E 677 MET cc_start: 0.4023 (ttm) cc_final: 0.3804 (ttm) REVERT: E 680 MET cc_start: 0.5604 (mtp) cc_final: 0.5207 (ptp) REVERT: E 682 MET cc_start: 0.5063 (ptt) cc_final: 0.4753 (ptp) REVERT: G 84 ARG cc_start: 0.6478 (ttm110) cc_final: 0.5668 (mtt-85) REVERT: G 143 LYS cc_start: 0.5308 (OUTLIER) cc_final: 0.5055 (ptmt) REVERT: G 300 LYS cc_start: 0.5417 (mtmt) cc_final: 0.4755 (ptmt) REVERT: G 304 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5613 (mp0) REVERT: G 349 MET cc_start: 0.5568 (mmm) cc_final: 0.5362 (mmm) REVERT: G 421 ARG cc_start: 0.6150 (mtm180) cc_final: 0.5606 (ttm110) REVERT: G 672 ASP cc_start: 0.4223 (OUTLIER) cc_final: 0.3742 (m-30) REVERT: G 675 MET cc_start: 0.4816 (ttm) cc_final: 0.4451 (ttp) REVERT: H 188 ARG cc_start: 0.7428 (ttp-110) cc_final: 0.7094 (ttt-90) REVERT: H 189 ASP cc_start: 0.7398 (p0) cc_final: 0.6808 (p0) REVERT: H 213 MET cc_start: 0.8672 (mtt) cc_final: 0.8251 (mtt) REVERT: H 473 MET cc_start: 0.8799 (ptp) cc_final: 0.8528 (ptm) REVERT: H 510 ILE cc_start: 0.8640 (mt) cc_final: 0.8282 (pp) REVERT: I 65 MET cc_start: 0.8506 (mtt) cc_final: 0.8296 (mtm) REVERT: I 74 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.6559 (mp10) REVERT: I 110 MET cc_start: 0.4411 (mmm) cc_final: 0.4096 (mmm) REVERT: I 160 MET cc_start: 0.3375 (mmp) cc_final: 0.3052 (tmm) REVERT: I 163 LYS cc_start: 0.5187 (mmtt) cc_final: 0.4467 (mtmt) REVERT: I 396 MET cc_start: 0.4291 (tmm) cc_final: 0.3708 (tmt) REVERT: I 458 TYR cc_start: 0.6399 (t80) cc_final: 0.6189 (t80) REVERT: I 480 GLU cc_start: 0.5641 (OUTLIER) cc_final: 0.4895 (mp0) REVERT: I 599 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7668 (ttpp) REVERT: I 713 GLU cc_start: 0.7154 (tp30) cc_final: 0.6595 (mt-10) REVERT: K 160 MET cc_start: 0.2374 (mpt) cc_final: 0.1957 (tmm) REVERT: K 270 TYR cc_start: 0.6677 (p90) cc_final: 0.6129 (p90) REVERT: K 301 LYS cc_start: 0.7118 (mmmm) cc_final: 0.6913 (mmmm) REVERT: K 382 PHE cc_start: 0.7688 (m-80) cc_final: 0.7465 (m-10) REVERT: K 431 ASP cc_start: 0.6808 (t70) cc_final: 0.6400 (m-30) REVERT: K 672 ASP cc_start: 0.3729 (OUTLIER) cc_final: 0.2320 (m-30) REVERT: L 376 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8393 (tp) outliers start: 127 outliers final: 37 residues processed: 650 average time/residue: 1.7472 time to fit residues: 1399.4872 Evaluate side-chains 503 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 456 time to evaluate : 5.202 ------------------------------------------------------------------------------- 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 C residue 712 VAL 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 F residue 509 ILE Chi-restraints excluded: chain G residue 143 LYS 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 677 MET 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 97 SER 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 287 optimal weight: 5.9990 chunk 160 optimal weight: 0.9990 chunk 430 optimal weight: 0.6980 chunk 351 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 517 optimal weight: 3.9990 chunk 559 optimal weight: 3.9990 chunk 461 optimal weight: 4.9990 chunk 513 optimal weight: 0.9980 chunk 176 optimal weight: 0.9990 chunk 415 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 B 449 ASN 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 45182 Z= 0.212 Angle : 0.615 13.402 61069 Z= 0.323 Chirality : 0.045 0.296 6745 Planarity : 0.004 0.053 7927 Dihedral : 8.320 103.925 6619 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.92 % Favored : 96.06 % Rotamer: Outliers : 2.99 % Allowed : 14.60 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.11), residues: 5664 helix: 0.75 (0.12), residues: 2003 sheet: 0.03 (0.14), residues: 1164 loop : -1.45 (0.12), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 276 HIS 0.013 0.001 HIS G 493 PHE 0.023 0.001 PHE G 323 TYR 0.019 0.001 TYR I 315 ARG 0.007 0.000 ARG H 234 *********************** 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 626 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 487 time to evaluate : 5.204 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: 0.7837 (pp) cc_final: 0.7556 (mm) REVERT: A 599 LYS cc_start: 0.7513 (OUTLIER) cc_final: 0.7151 (tttt) REVERT: B 130 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.6751 (mt-10) REVERT: B 183 ASP cc_start: 0.7599 (m-30) cc_final: 0.7391 (m-30) REVERT: B 425 MET cc_start: 0.8126 (ttt) cc_final: 0.7844 (ttt) REVERT: C 687 LYS cc_start: 0.5404 (OUTLIER) cc_final: 0.5093 (tttt) REVERT: C 713 GLU cc_start: 0.5287 (mp0) cc_final: 0.4894 (mp0) REVERT: D 425 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7662 (tpt) REVERT: E 677 MET cc_start: 0.4169 (ttm) cc_final: 0.3870 (ttm) REVERT: E 682 MET cc_start: 0.5096 (ptt) cc_final: 0.4782 (ptp) REVERT: F 130 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6947 (mt-10) REVERT: F 297 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7551 (tt0) REVERT: F 414 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.6204 (mt-10) REVERT: G 84 ARG cc_start: 0.6509 (ttm110) cc_final: 0.5689 (mtt-85) REVERT: G 304 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5548 (mp0) REVERT: G 349 MET cc_start: 0.5733 (mmm) cc_final: 0.5464 (mmm) REVERT: G 421 ARG cc_start: 0.5819 (mtm180) cc_final: 0.5234 (ttm110) REVERT: G 675 MET cc_start: 0.4828 (ttm) cc_final: 0.4256 (ttm) REVERT: H 188 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7084 (ttt-90) REVERT: H 189 ASP cc_start: 0.7486 (p0) cc_final: 0.6882 (p0) REVERT: H 213 MET cc_start: 0.8656 (OUTLIER) cc_final: 0.8239 (mtt) REVERT: H 473 MET cc_start: 0.8840 (ptp) cc_final: 0.8565 (ptm) REVERT: I 74 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.6412 (mp10) REVERT: I 76 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.7988 (p) REVERT: I 110 MET cc_start: 0.4516 (mmm) cc_final: 0.4269 (mmm) REVERT: I 163 LYS cc_start: 0.5150 (mmtt) cc_final: 0.4360 (mtmt) REVERT: I 334 MET cc_start: 0.3864 (OUTLIER) cc_final: 0.3542 (mtp) REVERT: I 396 MET cc_start: 0.4367 (tmm) cc_final: 0.3567 (tmt) REVERT: I 433 MET cc_start: 0.6831 (OUTLIER) cc_final: 0.6469 (tpt) REVERT: I 480 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.4997 (mp0) REVERT: I 713 GLU cc_start: 0.7251 (tp30) cc_final: 0.6635 (mt-10) REVERT: K 113 ILE cc_start: 0.7253 (mm) cc_final: 0.6908 (mt) REVERT: K 135 ASN cc_start: 0.6963 (OUTLIER) cc_final: 0.6601 (t0) REVERT: K 160 MET cc_start: 0.2581 (mpt) cc_final: 0.2223 (mmm) REVERT: K 270 TYR cc_start: 0.6730 (p90) cc_final: 0.6241 (p90) REVERT: K 334 MET cc_start: 0.5451 (mmt) cc_final: 0.5206 (mmt) REVERT: K 431 ASP cc_start: 0.6848 (t70) cc_final: 0.6611 (p0) REVERT: L 563 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7128 (mpp) outliers start: 139 outliers final: 51 residues processed: 576 average time/residue: 1.7214 time to fit residues: 1217.6250 Evaluate side-chains 496 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 428 time to evaluate : 5.267 ------------------------------------------------------------------------------- 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 633 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 140 VAL 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 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 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 E residue 709 THR Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 408 MET Chi-restraints excluded: chain F residue 414 GLU Chi-restraints excluded: chain F residue 509 ILE Chi-restraints excluded: chain G residue 304 GLU Chi-restraints excluded: chain G residue 346 VAL 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 213 MET Chi-restraints excluded: chain H residue 378 SER 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 334 MET 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 347 THR Chi-restraints excluded: chain K residue 428 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 487 ASP Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 528 LEU 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 Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain L residue 563 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 511 optimal weight: 9.9990 chunk 389 optimal weight: 3.9990 chunk 268 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 247 optimal weight: 6.9990 chunk 347 optimal weight: 0.7980 chunk 519 optimal weight: 5.9990 chunk 549 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 492 optimal weight: 9.9990 chunk 148 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 ** C 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN ** E 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN G 492 HIS H 57 HIS H 162 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 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** K 485 HIS K 491 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 45182 Z= 0.386 Angle : 0.694 13.136 61069 Z= 0.361 Chirality : 0.048 0.310 6745 Planarity : 0.005 0.057 7927 Dihedral : 8.345 88.060 6615 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 3.94 % Allowed : 15.03 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.11), residues: 5664 helix: 0.60 (0.11), residues: 2077 sheet: -0.07 (0.14), residues: 1164 loop : -1.37 (0.12), residues: 2423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 358 HIS 0.009 0.001 HIS B 190 PHE 0.028 0.002 PHE I 537 TYR 0.023 0.002 TYR J 457 ARG 0.010 0.001 ARG B 268 *********************** 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 638 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 455 time to evaluate : 5.160 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: 0.7966 (pp) cc_final: 0.7646 (mm) REVERT: A 599 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7260 (tptm) REVERT: B 183 ASP cc_start: 0.7606 (m-30) cc_final: 0.7392 (m-30) REVERT: B 204 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8663 (mttp) REVERT: B 269 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7654 (mttt) REVERT: C 687 LYS cc_start: 0.5689 (OUTLIER) cc_final: 0.5334 (mttt) REVERT: C 713 GLU cc_start: 0.5222 (mp0) cc_final: 0.4789 (mp0) REVERT: E 613 ILE cc_start: 0.7158 (mt) cc_final: 0.6685 (pp) REVERT: E 653 MET cc_start: 0.3173 (OUTLIER) cc_final: 0.2205 (mtt) REVERT: F 130 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7088 (mt-10) REVERT: F 178 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8285 (mm) REVERT: F 297 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7687 (tt0) REVERT: F 346 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7214 (tp30) REVERT: F 515 GLU cc_start: 0.7224 (OUTLIER) cc_final: 0.6948 (tt0) REVERT: G 304 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5569 (mp0) REVERT: G 672 ASP cc_start: 0.4063 (OUTLIER) cc_final: 0.3432 (m-30) REVERT: G 675 MET cc_start: 0.4812 (ttm) cc_final: 0.4261 (ttm) REVERT: H 188 ARG cc_start: 0.7694 (ttp-110) cc_final: 0.7482 (ttt-90) REVERT: H 213 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8272 (mtt) REVERT: H 411 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7486 (ttm-80) REVERT: H 473 MET cc_start: 0.8813 (ptp) cc_final: 0.8611 (ptp) REVERT: I 74 GLN cc_start: 0.7561 (OUTLIER) cc_final: 0.6459 (mt0) REVERT: I 104 GLN cc_start: 0.5745 (OUTLIER) cc_final: 0.5480 (mp10) REVERT: I 110 MET cc_start: 0.4788 (mmm) cc_final: 0.4459 (mmm) REVERT: I 163 LYS cc_start: 0.5105 (mmtt) cc_final: 0.4410 (mtmt) REVERT: I 331 PHE cc_start: 0.6514 (OUTLIER) cc_final: 0.5606 (p90) REVERT: I 433 MET cc_start: 0.7067 (OUTLIER) cc_final: 0.6690 (tpt) REVERT: I 480 GLU cc_start: 0.5716 (OUTLIER) cc_final: 0.5048 (mp0) REVERT: I 559 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7384 (mmtt) REVERT: I 672 ASP cc_start: 0.3498 (OUTLIER) cc_final: 0.3212 (m-30) REVERT: I 713 GLU cc_start: 0.7196 (tp30) cc_final: 0.6702 (mt-10) REVERT: J 555 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8032 (ttpt) REVERT: K 84 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.5898 (ttt90) REVERT: K 135 ASN cc_start: 0.6767 (OUTLIER) cc_final: 0.6388 (t0) REVERT: K 160 MET cc_start: 0.2691 (mpt) cc_final: 0.2149 (mmm) REVERT: K 270 TYR cc_start: 0.6808 (p90) cc_final: 0.6358 (p90) REVERT: K 295 LYS cc_start: 0.4306 (mmtt) cc_final: 0.3891 (mtpp) REVERT: K 301 LYS cc_start: 0.7246 (mmmm) cc_final: 0.6279 (tmtm) REVERT: K 354 ASP cc_start: 0.6521 (t0) cc_final: 0.6123 (t0) REVERT: K 383 GLU cc_start: 0.7045 (tt0) cc_final: 0.6817 (tt0) REVERT: K 396 MET cc_start: 0.4607 (ttm) cc_final: 0.4077 (ppp) REVERT: K 431 ASP cc_start: 0.6815 (t70) cc_final: 0.6568 (p0) REVERT: K 493 HIS cc_start: 0.2879 (OUTLIER) cc_final: 0.2294 (p-80) REVERT: K 672 ASP cc_start: 0.3766 (OUTLIER) cc_final: 0.2507 (m-30) REVERT: K 678 ILE cc_start: 0.6304 (OUTLIER) cc_final: 0.5811 (pt) REVERT: L 278 LEU cc_start: 0.8629 (mp) cc_final: 0.8412 (mt) REVERT: L 292 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7687 (ttp80) REVERT: L 376 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8391 (tp) REVERT: L 563 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7103 (mmm) outliers start: 183 outliers final: 67 residues processed: 570 average time/residue: 1.7362 time to fit residues: 1215.1718 Evaluate side-chains 521 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 424 time to evaluate : 5.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 599 LYS Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 189 ASP 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 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 255 VAL Chi-restraints excluded: chain D residue 425 MET Chi-restraints excluded: chain D residue 485 ILE Chi-restraints excluded: chain D residue 509 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 653 MET Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain E residue 709 THR Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 178 LEU Chi-restraints excluded: chain F residue 297 GLN Chi-restraints excluded: chain F residue 346 GLU Chi-restraints excluded: chain F residue 509 ILE Chi-restraints excluded: chain F residue 515 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 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 111 ASN 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 425 MET Chi-restraints excluded: chain H residue 509 ILE 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 104 GLN Chi-restraints excluded: chain I residue 258 VAL Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 331 PHE 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 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 672 ASP 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 J residue 555 LYS 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 428 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 493 HIS 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 672 ASP Chi-restraints excluded: chain K residue 678 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 292 ARG 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 376 LEU Chi-restraints excluded: chain L residue 378 SER Chi-restraints excluded: chain L residue 563 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 458 optimal weight: 0.7980 chunk 312 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 409 optimal weight: 0.8980 chunk 226 optimal weight: 5.9990 chunk 469 optimal weight: 3.9990 chunk 380 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 493 optimal weight: 0.8980 chunk 138 optimal weight: 0.3980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 E 684 HIS G 380 HIS G 492 HIS H 489 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 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** K 459 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 45182 Z= 0.190 Angle : 0.586 9.962 61069 Z= 0.307 Chirality : 0.045 0.300 6745 Planarity : 0.004 0.054 7927 Dihedral : 7.992 76.633 6613 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.64 % Favored : 96.35 % Rotamer: Outliers : 3.23 % Allowed : 16.26 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.11), residues: 5664 helix: 1.07 (0.12), residues: 2028 sheet: 0.04 (0.14), residues: 1148 loop : -1.24 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 276 HIS 0.011 0.001 HIS K 344 PHE 0.025 0.001 PHE I 333 TYR 0.019 0.001 TYR A 619 ARG 0.009 0.000 ARG D 292 *********************** 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 624 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 474 time to evaluate : 5.535 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 528 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7602 (mm) REVERT: A 577 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.6707 (tp-100) REVERT: A 599 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7221 (tttt) REVERT: B 43 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7632 (mp10) REVERT: B 183 ASP cc_start: 0.7596 (m-30) cc_final: 0.7375 (m-30) REVERT: B 189 ASP cc_start: 0.7351 (OUTLIER) cc_final: 0.7081 (t0) REVERT: B 204 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8818 (mttm) REVERT: B 269 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7633 (mttt) REVERT: C 687 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5415 (mttt) REVERT: C 713 GLU cc_start: 0.5212 (mp0) cc_final: 0.4817 (mp0) REVERT: D 425 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7663 (tpt) REVERT: E 613 ILE cc_start: 0.7037 (mt) cc_final: 0.6510 (pp) REVERT: F 130 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7084 (mt-10) REVERT: G 84 ARG cc_start: 0.6326 (ttm110) cc_final: 0.5553 (mtt-85) REVERT: G 160 MET cc_start: 0.5419 (tmm) cc_final: 0.5041 (tpp) REVERT: G 304 GLU cc_start: 0.6081 (OUTLIER) cc_final: 0.5591 (mp0) REVERT: G 336 MET cc_start: 0.4333 (OUTLIER) cc_final: 0.3647 (ptp) REVERT: G 349 MET cc_start: 0.5927 (mmm) cc_final: 0.5482 (mtt) REVERT: G 402 LEU cc_start: 0.7580 (mp) cc_final: 0.7245 (mp) REVERT: G 672 ASP cc_start: 0.3734 (OUTLIER) cc_final: 0.3356 (m-30) REVERT: G 675 MET cc_start: 0.5059 (ttm) cc_final: 0.4526 (ttm) REVERT: H 188 ARG cc_start: 0.7631 (ttp-110) cc_final: 0.7295 (ttt-90) REVERT: H 213 MET cc_start: 0.8737 (mtt) cc_final: 0.8313 (mtt) REVERT: H 411 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7450 (ttm-80) REVERT: H 473 MET cc_start: 0.8813 (ptp) cc_final: 0.8561 (ptp) REVERT: I 74 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6261 (mt0) REVERT: I 110 MET cc_start: 0.4661 (mmm) cc_final: 0.4388 (mmm) REVERT: I 163 LYS cc_start: 0.5018 (mmtt) cc_final: 0.4334 (mtmt) REVERT: I 433 MET cc_start: 0.7137 (ttt) cc_final: 0.6819 (tpt) REVERT: I 458 TYR cc_start: 0.6918 (t80) cc_final: 0.6519 (t80) REVERT: I 559 LYS cc_start: 0.8124 (OUTLIER) cc_final: 0.7385 (mmtt) REVERT: I 653 MET cc_start: 0.7124 (OUTLIER) cc_final: 0.6334 (mtp) REVERT: I 713 GLU cc_start: 0.7270 (tp30) cc_final: 0.6681 (mt-10) REVERT: J 258 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.6094 (tt0) REVERT: J 476 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6514 (mp0) REVERT: K 84 ARG cc_start: 0.6541 (OUTLIER) cc_final: 0.5732 (ttt90) REVERT: K 135 ASN cc_start: 0.6759 (OUTLIER) cc_final: 0.6412 (t0) REVERT: K 160 MET cc_start: 0.2682 (mpt) cc_final: 0.2285 (mmm) REVERT: K 270 TYR cc_start: 0.6669 (p90) cc_final: 0.6267 (p90) REVERT: K 295 LYS cc_start: 0.4311 (mmtt) cc_final: 0.3895 (mtpp) REVERT: K 341 GLN cc_start: 0.4502 (OUTLIER) cc_final: 0.4175 (pt0) REVERT: K 354 ASP cc_start: 0.6433 (t0) cc_final: 0.5959 (t0) REVERT: K 383 GLU cc_start: 0.6998 (tt0) cc_final: 0.6757 (tt0) REVERT: K 396 MET cc_start: 0.4649 (ttm) cc_final: 0.4238 (ppp) REVERT: K 431 ASP cc_start: 0.6846 (t70) cc_final: 0.6541 (t70) REVERT: L 213 MET cc_start: 0.8645 (mtt) cc_final: 0.8338 (mtt) REVERT: L 278 LEU cc_start: 0.8586 (mp) cc_final: 0.8382 (mt) REVERT: L 292 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7618 (ttp80) outliers start: 150 outliers final: 51 residues processed: 573 average time/residue: 1.6933 time to fit residues: 1195.9432 Evaluate side-chains 499 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 425 time to evaluate : 4.957 ------------------------------------------------------------------------------- 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 599 LYS Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 682 MET 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 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 633 VAL Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 509 ILE 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 336 MET 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 61 GLU Chi-restraints excluded: chain H residue 111 ASN 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 I residue 74 GLN Chi-restraints excluded: chain I residue 177 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 677 MET Chi-restraints excluded: chain I residue 684 HIS Chi-restraints excluded: chain I residue 712 VAL Chi-restraints excluded: chain J residue 258 GLU Chi-restraints excluded: chain J residue 421 ASP Chi-restraints excluded: chain J residue 476 GLU Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 341 GLN 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 709 THR Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain L residue 292 ARG Chi-restraints excluded: chain L residue 328 SER Chi-restraints excluded: chain L residue 353 ASP Chi-restraints excluded: chain L residue 375 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 185 optimal weight: 0.7980 chunk 495 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 322 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 550 optimal weight: 1.9990 chunk 457 optimal weight: 10.0000 chunk 254 optimal weight: 7.9990 chunk 45 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 289 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 GLN ** C 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN H 230 ASN ** 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 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 45182 Z= 0.234 Angle : 0.604 9.989 61069 Z= 0.315 Chirality : 0.045 0.296 6745 Planarity : 0.004 0.055 7927 Dihedral : 7.885 75.232 6610 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 3.29 % Allowed : 16.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.11), residues: 5664 helix: 1.16 (0.12), residues: 2031 sheet: -0.04 (0.14), residues: 1155 loop : -1.14 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 276 HIS 0.008 0.001 HIS G 492 PHE 0.026 0.001 PHE K 333 TYR 0.016 0.001 TYR J 457 ARG 0.007 0.000 ARG D 292 *********************** 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 607 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 454 time to evaluate : 5.573 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 577 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.6703 (tp-100) REVERT: A 599 LYS cc_start: 0.7548 (OUTLIER) cc_final: 0.7221 (tttt) REVERT: B 189 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7126 (t0) REVERT: B 204 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8650 (mttp) REVERT: B 269 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7613 (mttt) REVERT: C 677 MET cc_start: 0.5180 (ttm) cc_final: 0.4902 (ttm) REVERT: C 687 LYS cc_start: 0.5757 (OUTLIER) cc_final: 0.5405 (mttt) REVERT: C 713 GLU cc_start: 0.5368 (mp0) cc_final: 0.4879 (mp0) REVERT: D 425 MET cc_start: 0.8003 (OUTLIER) cc_final: 0.7696 (tpt) REVERT: E 613 ILE cc_start: 0.7187 (mt) cc_final: 0.6589 (pp) REVERT: F 130 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7125 (mt-10) REVERT: F 240 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.8099 (p90) REVERT: F 346 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7012 (tp30) REVERT: F 515 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6945 (tt0) REVERT: F 557 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6927 (t70) REVERT: G 160 MET cc_start: 0.5876 (tmm) cc_final: 0.5521 (tpp) REVERT: G 304 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5608 (mp0) REVERT: G 349 MET cc_start: 0.6021 (mmm) cc_final: 0.5575 (mtt) REVERT: G 672 ASP cc_start: 0.3882 (OUTLIER) cc_final: 0.3385 (m-30) REVERT: G 675 MET cc_start: 0.5128 (ttm) cc_final: 0.4621 (ttm) REVERT: H 213 MET cc_start: 0.8754 (mtt) cc_final: 0.8325 (mtt) REVERT: H 411 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.7409 (ttm-80) REVERT: H 473 MET cc_start: 0.8807 (ptp) cc_final: 0.8576 (ptp) REVERT: I 74 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.6212 (mt0) REVERT: I 104 GLN cc_start: 0.5697 (OUTLIER) cc_final: 0.5380 (mp10) REVERT: I 110 MET cc_start: 0.4836 (mmm) cc_final: 0.4572 (mmm) REVERT: I 163 LYS cc_start: 0.4915 (mmtt) cc_final: 0.4294 (mtmt) REVERT: I 328 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7782 (ptpt) REVERT: I 396 MET cc_start: 0.4011 (tmm) cc_final: 0.3490 (tmm) REVERT: I 559 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7343 (mmtt) REVERT: I 653 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.6261 (mtp) REVERT: I 713 GLU cc_start: 0.7361 (tp30) cc_final: 0.6816 (mt-10) REVERT: J 213 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7512 (mtt) REVERT: J 258 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.6156 (tt0) REVERT: J 476 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.6567 (mp0) REVERT: K 135 ASN cc_start: 0.6788 (OUTLIER) cc_final: 0.6436 (t0) REVERT: K 160 MET cc_start: 0.2739 (mpt) cc_final: 0.2276 (mmm) REVERT: K 270 TYR cc_start: 0.6665 (p90) cc_final: 0.6223 (p90) REVERT: K 295 LYS cc_start: 0.4204 (mmtt) cc_final: 0.3858 (mtpp) REVERT: K 301 LYS cc_start: 0.7349 (mmmm) cc_final: 0.6632 (tmtm) REVERT: K 333 PHE cc_start: 0.5425 (t80) cc_final: 0.4719 (t80) REVERT: K 341 GLN cc_start: 0.4629 (OUTLIER) cc_final: 0.4356 (pt0) REVERT: K 354 ASP cc_start: 0.6480 (t0) cc_final: 0.5959 (t0) REVERT: K 383 GLU cc_start: 0.6939 (tt0) cc_final: 0.6624 (tt0) REVERT: K 396 MET cc_start: 0.4643 (ttm) cc_final: 0.4214 (ppp) REVERT: K 431 ASP cc_start: 0.6890 (t70) cc_final: 0.6626 (t70) REVERT: K 433 MET cc_start: 0.6174 (tmm) cc_final: 0.5165 (ttp) REVERT: L 278 LEU cc_start: 0.8604 (mp) cc_final: 0.8386 (mt) REVERT: L 292 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7691 (ttp80) outliers start: 153 outliers final: 69 residues processed: 552 average time/residue: 1.6787 time to fit residues: 1141.9997 Evaluate side-chains 521 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 426 time to evaluate : 4.724 ------------------------------------------------------------------------------- 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 612 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 189 ASP 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 582 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 630 ASP 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 178 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 378 SER 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 63 ILE 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 346 GLU Chi-restraints excluded: chain F residue 509 ILE Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 557 ASP 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 61 GLU Chi-restraints excluded: chain H residue 111 ASN Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 315 ASP 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 104 GLN Chi-restraints excluded: chain I residue 177 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 334 MET 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 677 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 213 MET Chi-restraints excluded: chain J residue 234 ARG Chi-restraints excluded: chain J residue 258 GLU 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 133 SER Chi-restraints excluded: chain K residue 135 ASN Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 341 GLN 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 553 MET Chi-restraints excluded: chain K residue 627 ILE Chi-restraints excluded: chain K residue 682 MET Chi-restraints excluded: chain K residue 709 THR Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain L residue 292 ARG Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 328 SER Chi-restraints excluded: chain L residue 375 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 530 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 313 optimal weight: 3.9990 chunk 402 optimal weight: 10.0000 chunk 311 optimal weight: 0.4980 chunk 463 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 548 optimal weight: 3.9990 chunk 343 optimal weight: 2.9990 chunk 334 optimal weight: 1.9990 chunk 253 optimal weight: 9.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- 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 I 341 GLN ** 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 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 45182 Z= 0.367 Angle : 0.658 9.948 61069 Z= 0.343 Chirality : 0.048 0.335 6745 Planarity : 0.005 0.058 7927 Dihedral : 7.952 75.954 6610 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.33 % Favored : 95.64 % Rotamer: Outliers : 3.38 % Allowed : 17.40 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.11), residues: 5664 helix: 0.94 (0.12), residues: 2044 sheet: -0.03 (0.14), residues: 1143 loop : -1.18 (0.12), residues: 2477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP J 276 HIS 0.010 0.001 HIS K 492 PHE 0.023 0.002 PHE K 333 TYR 0.022 0.002 TYR J 457 ARG 0.006 0.001 ARG J 234 *********************** 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 614 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 457 time to evaluate : 5.557 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 528 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.7963 (tt) REVERT: A 577 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.6805 (tp-100) REVERT: A 599 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7290 (tttt) REVERT: B 43 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7701 (mp10) REVERT: B 204 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8677 (mttp) REVERT: B 269 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7628 (mttt) REVERT: C 614 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7342 (tm) REVERT: C 677 MET cc_start: 0.5519 (ttm) cc_final: 0.5160 (ttm) REVERT: C 687 LYS cc_start: 0.5872 (OUTLIER) cc_final: 0.5418 (mttt) REVERT: C 713 GLU cc_start: 0.5307 (mp0) cc_final: 0.4890 (mp0) REVERT: F 130 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: F 240 PHE cc_start: 0.8423 (OUTLIER) cc_final: 0.7950 (p90) REVERT: F 346 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7027 (tp30) REVERT: F 515 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6929 (tt0) REVERT: F 557 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6962 (t70) REVERT: G 84 ARG cc_start: 0.6444 (ttm110) cc_final: 0.5927 (mtt-85) REVERT: G 160 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5783 (tpp) REVERT: G 311 LYS cc_start: 0.5644 (mttt) cc_final: 0.5318 (mmpt) REVERT: G 672 ASP cc_start: 0.4063 (OUTLIER) cc_final: 0.3437 (m-30) REVERT: G 675 MET cc_start: 0.4912 (ttm) cc_final: 0.4475 (ttm) REVERT: H 213 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8340 (mtt) REVERT: H 411 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7251 (ttm-80) REVERT: I 74 GLN cc_start: 0.7529 (OUTLIER) cc_final: 0.6279 (mt0) REVERT: I 104 GLN cc_start: 0.5737 (OUTLIER) cc_final: 0.5394 (mp10) REVERT: I 110 MET cc_start: 0.4923 (mmm) cc_final: 0.4618 (mmm) REVERT: I 163 LYS cc_start: 0.5000 (mmtt) cc_final: 0.4328 (mtmm) REVERT: I 328 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7809 (ptpt) REVERT: I 559 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.8010 (tmmt) REVERT: I 653 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6312 (mtp) REVERT: I 713 GLU cc_start: 0.7297 (tp30) cc_final: 0.6742 (mt-10) REVERT: J 213 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7594 (mtt) REVERT: J 240 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7319 (p90) REVERT: J 258 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6290 (tt0) REVERT: J 473 MET cc_start: 0.8713 (ptp) cc_final: 0.8442 (ptm) REVERT: J 476 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.6597 (mp0) REVERT: K 84 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.5959 (ttt90) REVERT: K 135 ASN cc_start: 0.6762 (OUTLIER) cc_final: 0.6409 (t0) REVERT: K 160 MET cc_start: 0.2904 (mpt) cc_final: 0.2093 (mmm) REVERT: K 270 TYR cc_start: 0.6716 (p90) cc_final: 0.6307 (p90) REVERT: K 301 LYS cc_start: 0.7460 (mmmm) cc_final: 0.6707 (tmtm) REVERT: K 333 PHE cc_start: 0.5524 (t80) cc_final: 0.4869 (t80) REVERT: K 354 ASP cc_start: 0.6584 (t0) cc_final: 0.6052 (t0) REVERT: K 383 GLU cc_start: 0.7138 (tt0) cc_final: 0.6822 (tt0) REVERT: K 396 MET cc_start: 0.4460 (ttm) cc_final: 0.3921 (mtp) REVERT: K 431 ASP cc_start: 0.6735 (t70) cc_final: 0.6508 (t70) REVERT: K 433 MET cc_start: 0.6366 (tmm) cc_final: 0.5386 (ttp) REVERT: L 292 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7736 (ttp80) outliers start: 157 outliers final: 69 residues processed: 556 average time/residue: 1.6861 time to fit residues: 1151.9424 Evaluate side-chains 532 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 434 time to evaluate : 5.129 ------------------------------------------------------------------------------- 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 599 LYS Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 255 VAL 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 582 THR Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain D residue 178 LEU 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 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 63 ILE 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 346 GLU Chi-restraints excluded: chain F residue 509 ILE Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain F residue 557 ASP Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 160 MET 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 33 THR Chi-restraints excluded: chain H residue 49 MET Chi-restraints excluded: chain H residue 61 GLU Chi-restraints excluded: chain H residue 111 ASN 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 104 GLN Chi-restraints excluded: chain I residue 177 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 328 LYS Chi-restraints excluded: chain I residue 334 MET Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 522 MET 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 114 VAL Chi-restraints excluded: chain J residue 213 MET Chi-restraints excluded: chain J residue 240 PHE Chi-restraints excluded: chain J residue 258 GLU 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 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 682 MET Chi-restraints excluded: chain K residue 709 THR Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain L residue 292 ARG Chi-restraints excluded: chain L residue 301 ASP Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 328 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 339 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 chunk 327 optimal weight: 0.0980 chunk 165 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 348 optimal weight: 3.9990 chunk 373 optimal weight: 1.9990 chunk 271 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 431 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN B 136 ASN D 433 GLN E 529 GLN ** G 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 341 GLN ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 457 GLN I 616 ASN ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 45182 Z= 0.210 Angle : 0.600 10.166 61069 Z= 0.313 Chirality : 0.045 0.299 6745 Planarity : 0.004 0.057 7927 Dihedral : 7.766 76.265 6610 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 2.92 % Allowed : 18.06 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 5664 helix: 1.18 (0.12), residues: 2037 sheet: -0.02 (0.14), residues: 1157 loop : -1.11 (0.13), residues: 2470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 276 HIS 0.011 0.001 HIS K 492 PHE 0.023 0.001 PHE K 333 TYR 0.015 0.001 TYR J 318 ARG 0.005 0.000 ARG J 234 *********************** 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 593 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 457 time to evaluate : 5.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 528 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7897 (tt) REVERT: A 543 ARG cc_start: 0.8838 (mmm-85) cc_final: 0.8441 (mmt90) REVERT: A 577 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.6731 (tp-100) REVERT: A 599 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7345 (tttt) REVERT: B 43 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7635 (mp10) REVERT: B 204 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8621 (mttp) REVERT: B 269 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7610 (mttt) REVERT: C 614 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7221 (tm) REVERT: C 658 GLU cc_start: 0.6560 (tp30) cc_final: 0.5970 (mt-10) REVERT: C 677 MET cc_start: 0.5561 (ttm) cc_final: 0.5199 (ttm) REVERT: C 687 LYS cc_start: 0.5857 (OUTLIER) cc_final: 0.5414 (mttt) REVERT: C 713 GLU cc_start: 0.5284 (mp0) cc_final: 0.4863 (mp0) REVERT: F 130 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: F 240 PHE cc_start: 0.8364 (OUTLIER) cc_final: 0.7908 (p90) REVERT: F 515 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6901 (tt0) REVERT: G 84 ARG cc_start: 0.6441 (ttm110) cc_final: 0.5929 (mtt-85) REVERT: G 311 LYS cc_start: 0.5630 (mttt) cc_final: 0.5319 (mmpt) REVERT: G 349 MET cc_start: 0.6325 (mmm) cc_final: 0.6059 (mtt) REVERT: G 402 LEU cc_start: 0.7660 (mp) cc_final: 0.7363 (mp) REVERT: G 672 ASP cc_start: 0.3987 (OUTLIER) cc_final: 0.3470 (m-30) REVERT: G 675 MET cc_start: 0.5255 (ttm) cc_final: 0.4832 (ttm) REVERT: H 213 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8357 (mtt) REVERT: H 297 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7029 (tm-30) REVERT: H 510 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8194 (pp) REVERT: I 74 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6152 (mt0) REVERT: I 110 MET cc_start: 0.4776 (mmm) cc_final: 0.4504 (mmm) REVERT: I 163 LYS cc_start: 0.4781 (mmtt) cc_final: 0.4353 (mtmm) REVERT: I 328 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7780 (ptpt) REVERT: I 713 GLU cc_start: 0.7358 (tp30) cc_final: 0.6768 (mt-10) REVERT: J 473 MET cc_start: 0.8675 (ptp) cc_final: 0.8317 (ptm) REVERT: J 476 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6522 (mp0) REVERT: K 84 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.5966 (ttt90) REVERT: K 135 ASN cc_start: 0.6715 (OUTLIER) cc_final: 0.6405 (t0) REVERT: K 160 MET cc_start: 0.2874 (mpt) cc_final: 0.2088 (mmm) REVERT: K 270 TYR cc_start: 0.6677 (p90) cc_final: 0.6342 (p90) REVERT: K 301 LYS cc_start: 0.7375 (mmmm) cc_final: 0.6734 (tmtm) REVERT: K 333 PHE cc_start: 0.5322 (t80) cc_final: 0.4772 (t80) REVERT: K 354 ASP cc_start: 0.6628 (t0) cc_final: 0.6061 (t0) REVERT: K 383 GLU cc_start: 0.7151 (tt0) cc_final: 0.6827 (tt0) REVERT: K 396 MET cc_start: 0.4241 (ttm) cc_final: 0.3907 (ppp) REVERT: K 431 ASP cc_start: 0.6750 (t70) cc_final: 0.6424 (t70) REVERT: K 433 MET cc_start: 0.6484 (tmm) cc_final: 0.5449 (ttp) REVERT: K 458 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.5859 (m-80) REVERT: L 278 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8334 (mt) outliers start: 136 outliers final: 65 residues processed: 549 average time/residue: 1.6927 time to fit residues: 1145.1575 Evaluate side-chains 520 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 433 time to evaluate : 5.060 ------------------------------------------------------------------------------- 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 599 LYS Chi-restraints excluded: chain A residue 601 SER 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 43 GLN Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 404 ILE 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 654 THR Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 63 ILE 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 509 ILE Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 531 ILE Chi-restraints excluded: chain G residue 75 THR 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 61 GLU 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 510 ILE Chi-restraints excluded: chain I residue 74 GLN Chi-restraints excluded: chain I residue 177 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 341 GLN Chi-restraints excluded: chain I residue 414 THR Chi-restraints excluded: chain I residue 556 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 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 420 VAL Chi-restraints excluded: chain K residue 458 TYR Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 473 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 278 LEU 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 404 ILE Chi-restraints excluded: chain L residue 510 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 498 optimal weight: 2.9990 chunk 525 optimal weight: 1.9990 chunk 479 optimal weight: 1.9990 chunk 511 optimal weight: 7.9990 chunk 307 optimal weight: 4.9990 chunk 222 optimal weight: 0.7980 chunk 401 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 461 optimal weight: 4.9990 chunk 483 optimal weight: 9.9990 chunk 509 optimal weight: 6.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN ** G 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 230 ASN H 389 GLN ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 457 GLN I 616 ASN ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 HIS ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 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 : 0.006 0.058 45182 Z= 0.406 Angle : 0.695 10.585 61069 Z= 0.360 Chirality : 0.048 0.296 6745 Planarity : 0.005 0.059 7927 Dihedral : 7.907 76.323 6609 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 2.69 % Allowed : 18.58 % Favored : 78.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.11), residues: 5664 helix: 0.90 (0.12), residues: 2047 sheet: -0.09 (0.14), residues: 1157 loop : -1.16 (0.12), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 358 HIS 0.010 0.001 HIS K 492 PHE 0.022 0.002 PHE K 333 TYR 0.025 0.002 TYR J 457 ARG 0.007 0.001 ARG H 469 *********************** 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 561 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 436 time to evaluate : 5.476 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 528 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7913 (tt) REVERT: A 577 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.6865 (tp-100) REVERT: A 599 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7462 (tptp) REVERT: B 43 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7677 (mp10) REVERT: B 204 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8673 (mttp) REVERT: B 269 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7674 (mttt) REVERT: C 614 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.7310 (tm) REVERT: C 658 GLU cc_start: 0.6573 (tp30) cc_final: 0.6010 (mt-10) REVERT: C 677 MET cc_start: 0.5598 (ttm) cc_final: 0.5242 (ttm) REVERT: C 687 LYS cc_start: 0.5882 (OUTLIER) cc_final: 0.5148 (ttpt) REVERT: C 713 GLU cc_start: 0.5244 (mp0) cc_final: 0.4786 (mp0) REVERT: F 130 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: F 240 PHE cc_start: 0.8463 (OUTLIER) cc_final: 0.7955 (p90) REVERT: F 297 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: F 515 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.6906 (tt0) REVERT: F 557 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.7002 (t70) REVERT: G 311 LYS cc_start: 0.5754 (mttt) cc_final: 0.5520 (mmpt) REVERT: G 334 MET cc_start: 0.2241 (mpt) cc_final: 0.1918 (pp-130) REVERT: G 349 MET cc_start: 0.6466 (mmm) cc_final: 0.6200 (mtt) REVERT: G 672 ASP cc_start: 0.4106 (OUTLIER) cc_final: 0.3425 (m-30) REVERT: H 213 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8384 (mtt) REVERT: H 510 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8240 (pp) REVERT: I 74 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.6252 (mt0) REVERT: I 110 MET cc_start: 0.4976 (mmm) cc_final: 0.4716 (mmm) REVERT: I 163 LYS cc_start: 0.4720 (mmtt) cc_final: 0.4285 (mtmm) REVERT: I 328 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7900 (ptpt) REVERT: I 331 PHE cc_start: 0.6520 (OUTLIER) cc_final: 0.5587 (p90) REVERT: I 334 MET cc_start: 0.4260 (mmm) cc_final: 0.4026 (mtp) REVERT: I 653 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.5609 (ptm) REVERT: I 713 GLU cc_start: 0.7157 (tp30) cc_final: 0.6549 (mt-10) REVERT: J 213 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7533 (mtt) REVERT: J 473 MET cc_start: 0.8681 (ptp) cc_final: 0.8330 (ptm) REVERT: J 476 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6593 (mp0) REVERT: K 84 ARG cc_start: 0.6770 (OUTLIER) cc_final: 0.5903 (ttt90) REVERT: K 135 ASN cc_start: 0.6773 (OUTLIER) cc_final: 0.6424 (t0) REVERT: K 270 TYR cc_start: 0.6600 (p90) cc_final: 0.6199 (p90) REVERT: K 301 LYS cc_start: 0.7439 (mmmm) cc_final: 0.6708 (tmtm) REVERT: K 333 PHE cc_start: 0.5452 (t80) cc_final: 0.4766 (t80) REVERT: K 354 ASP cc_start: 0.6743 (t0) cc_final: 0.6191 (t0) REVERT: K 383 GLU cc_start: 0.7274 (tt0) cc_final: 0.6968 (tt0) REVERT: K 396 MET cc_start: 0.4263 (ttm) cc_final: 0.3704 (mtp) REVERT: K 431 ASP cc_start: 0.6741 (t70) cc_final: 0.6426 (t70) REVERT: K 433 MET cc_start: 0.6563 (tmm) cc_final: 0.5571 (ttp) REVERT: K 458 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.5762 (m-80) REVERT: K 680 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.4967 (ttt) REVERT: L 278 LEU cc_start: 0.8650 (mp) cc_final: 0.8418 (mt) REVERT: L 292 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7745 (ttp80) outliers start: 125 outliers final: 66 residues processed: 519 average time/residue: 1.7643 time to fit residues: 1138.8402 Evaluate side-chains 520 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 427 time to evaluate : 5.123 ------------------------------------------------------------------------------- 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 599 LYS Chi-restraints excluded: chain A residue 601 SER 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 43 GLN Chi-restraints excluded: chain B residue 49 MET Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 614 LEU Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 687 LYS Chi-restraints excluded: chain D residue 49 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 255 VAL 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 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 654 THR Chi-restraints excluded: chain E residue 685 THR Chi-restraints excluded: chain F residue 63 ILE 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 297 GLN Chi-restraints excluded: chain F residue 509 ILE Chi-restraints excluded: chain F residue 515 GLU Chi-restraints excluded: chain F residue 557 ASP Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 297 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 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 177 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 331 PHE Chi-restraints excluded: chain I residue 414 THR 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 63 ILE Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 201 MET Chi-restraints excluded: chain J residue 213 MET 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 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 680 MET Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain L residue 292 ARG 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 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 569 random chunks: chunk 335 optimal weight: 0.3980 chunk 540 optimal weight: 0.5980 chunk 329 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 375 optimal weight: 0.9980 chunk 566 optimal weight: 0.9990 chunk 521 optimal weight: 0.7980 chunk 451 optimal weight: 0.1980 chunk 46 optimal weight: 1.9990 chunk 348 optimal weight: 0.0020 chunk 276 optimal weight: 0.3980 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 75 HIS ** I 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 457 GLN J 24 HIS ** K 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 45182 Z= 0.155 Angle : 0.592 10.770 61069 Z= 0.307 Chirality : 0.044 0.299 6745 Planarity : 0.004 0.057 7927 Dihedral : 7.629 76.480 6609 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 1.98 % Allowed : 19.20 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.11), residues: 5664 helix: 1.33 (0.12), residues: 2043 sheet: -0.06 (0.14), residues: 1172 loop : -1.08 (0.13), residues: 2449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 276 HIS 0.011 0.001 HIS F 190 PHE 0.024 0.001 PHE K 323 TYR 0.017 0.001 TYR J 318 ARG 0.007 0.000 ARG H 327 ********************** 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 552 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 460 time to evaluate : 6.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7456 (tttt) REVERT: B 43 GLN cc_start: 0.7886 (OUTLIER) cc_final: 0.7571 (mp10) REVERT: B 189 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7120 (t0) REVERT: B 204 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8846 (mttm) REVERT: B 269 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7659 (mttt) REVERT: C 653 MET cc_start: 0.5076 (mmm) cc_final: 0.4701 (mtp) REVERT: C 658 GLU cc_start: 0.6393 (tp30) cc_final: 0.6051 (mt-10) REVERT: C 677 MET cc_start: 0.5773 (ttm) cc_final: 0.5505 (ttm) REVERT: C 687 LYS cc_start: 0.5713 (OUTLIER) cc_final: 0.5381 (mttt) REVERT: C 713 GLU cc_start: 0.5280 (mp0) cc_final: 0.4866 (mp0) REVERT: D 425 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7622 (tpt) REVERT: E 653 MET cc_start: 0.1812 (ttp) cc_final: 0.0813 (mtm) REVERT: F 130 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7174 (mt-10) REVERT: F 240 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7782 (p90) REVERT: G 84 ARG cc_start: 0.6511 (ttm110) cc_final: 0.6019 (mtt-85) REVERT: G 334 MET cc_start: 0.2955 (mpt) cc_final: 0.2504 (pp-130) REVERT: G 349 MET cc_start: 0.6459 (mmm) cc_final: 0.6123 (mtt) REVERT: G 402 LEU cc_start: 0.7530 (mp) cc_final: 0.7317 (mp) REVERT: G 672 ASP cc_start: 0.4014 (OUTLIER) cc_final: 0.3587 (m-30) REVERT: G 675 MET cc_start: 0.4967 (ttm) cc_final: 0.4564 (ttm) REVERT: H 213 MET cc_start: 0.8775 (mtt) cc_final: 0.8367 (mtt) REVERT: H 510 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8168 (pp) REVERT: I 74 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6321 (mt0) REVERT: I 110 MET cc_start: 0.4785 (mmm) cc_final: 0.4550 (mmm) REVERT: I 163 LYS cc_start: 0.4760 (mmtt) cc_final: 0.4319 (mtmm) REVERT: I 328 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7850 (ptpt) REVERT: I 653 MET cc_start: 0.5804 (OUTLIER) cc_final: 0.5480 (ptm) REVERT: I 713 GLU cc_start: 0.7347 (tp30) cc_final: 0.6548 (mt-10) REVERT: J 473 MET cc_start: 0.8529 (ptp) cc_final: 0.8176 (ptm) REVERT: J 476 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6495 (mp0) REVERT: K 84 ARG cc_start: 0.6724 (OUTLIER) cc_final: 0.5881 (ttt90) REVERT: K 135 ASN cc_start: 0.6606 (OUTLIER) cc_final: 0.6337 (t0) REVERT: K 160 MET cc_start: 0.3180 (OUTLIER) cc_final: 0.1531 (mmm) REVERT: K 270 TYR cc_start: 0.6692 (p90) cc_final: 0.6387 (p90) REVERT: K 301 LYS cc_start: 0.7396 (mmmm) cc_final: 0.6738 (tmtm) REVERT: K 333 PHE cc_start: 0.5486 (t80) cc_final: 0.4852 (t80) REVERT: K 354 ASP cc_start: 0.6634 (t0) cc_final: 0.6070 (t0) REVERT: K 383 GLU cc_start: 0.7160 (tt0) cc_final: 0.6836 (tt0) REVERT: K 396 MET cc_start: 0.4532 (ttm) cc_final: 0.4207 (mtp) REVERT: K 431 ASP cc_start: 0.6764 (t70) cc_final: 0.6415 (t70) REVERT: K 433 MET cc_start: 0.6500 (tmm) cc_final: 0.5657 (ttp) REVERT: K 458 TYR cc_start: 0.7139 (OUTLIER) cc_final: 0.5771 (m-80) REVERT: K 712 VAL cc_start: 0.4463 (OUTLIER) cc_final: 0.4140 (p) REVERT: L 278 LEU cc_start: 0.8478 (mp) cc_final: 0.8245 (mt) outliers start: 92 outliers final: 42 residues processed: 523 average time/residue: 1.6777 time to fit residues: 1078.5479 Evaluate side-chains 493 residues out of total 4650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 431 time to evaluate : 5.557 ------------------------------------------------------------------------------- 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 612 ILE Chi-restraints excluded: chain A residue 633 VAL Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 189 ASP Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain C residue 519 GLU Chi-restraints excluded: chain C residue 582 THR Chi-restraints excluded: chain C residue 617 THR Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 687 LYS 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 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 E residue 654 THR Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain G residue 75 THR 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 684 HIS Chi-restraints excluded: chain H residue 61 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 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 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 135 ASN Chi-restraints excluded: chain K residue 160 MET Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 347 THR 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 627 ILE Chi-restraints excluded: chain K residue 712 VAL 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 358 optimal weight: 10.0000 chunk 480 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 416 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 452 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 464 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 GLN D 433 GLN D 449 ASN F 230 ASN ** G 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 492 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 230 ASN J 372 ASN ** K 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.185768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.124845 restraints weight = 57307.711| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.75 r_work: 0.3216 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 45182 Z= 0.216 Angle : 0.612 10.006 61069 Z= 0.316 Chirality : 0.045 0.297 6745 Planarity : 0.004 0.058 7927 Dihedral : 7.588 75.120 6609 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.75 % Rotamer: Outliers : 1.83 % Allowed : 19.59 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.22 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.11), residues: 5664 helix: 1.34 (0.12), residues: 2037 sheet: -0.04 (0.14), residues: 1167 loop : -1.04 (0.13), residues: 2460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 276 HIS 0.012 0.001 HIS G 380 PHE 0.020 0.001 PHE K 333 TYR 0.017 0.001 TYR G 79 ARG 0.007 0.000 ARG H 469 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18329.79 seconds wall clock time: 332 minutes 1.65 seconds (19921.65 seconds total)