Starting phenix.real_space_refine on Fri Oct 11 09:33:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j78_36034/10_2024/8j78_36034_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j78_36034/10_2024/8j78_36034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j78_36034/10_2024/8j78_36034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j78_36034/10_2024/8j78_36034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j78_36034/10_2024/8j78_36034_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j78_36034/10_2024/8j78_36034_trim.cif" } resolution = 3.88 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= 0.043 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: 4 Type Number sf(0) Gaussians S 316 5.16 5 C 34682 2.51 5 N 9680 2.21 5 O 10348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 243 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 55026 Number of models: 1 Model: "" Number of chains: 18 Chain: "F" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "I" Number of atoms: 5065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5065 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 622} Chain breaks: 2 Chain: "J" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4031 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 500} Chain breaks: 1 Chain: "L" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4022 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 499} Chain breaks: 1 Chain: "K" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5098 Classifications: {'peptide': 657} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 629} Chain breaks: 1 Chain: "A" Number of atoms: 4154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4154 Classifications: {'peptide': 541} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 516} Chain: "C" Number of atoms: 5065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 651, 5065 Classifications: {'peptide': 651} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 622} Chain breaks: 2 Chain: "D" Number of atoms: 4031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4031 Classifications: {'peptide': 523} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 500} Chain breaks: 1 Chain: "H" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4022 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 499} Chain breaks: 1 Chain: "B" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5098 Classifications: {'peptide': 657} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 629} Chain breaks: 1 Chain: "E" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5098 Classifications: {'peptide': 657} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 629} Chain breaks: 1 Chain: "G" Number of atoms: 5098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5098 Classifications: {'peptide': 657} Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 629} Chain breaks: 1 Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.73, per 1000 atoms: 0.43 Number of scatterers: 55026 At special positions: 0 Unit cell: (205.307, 255.811, 150.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 316 16.00 O 10348 8.00 N 9680 7.00 C 34682 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: 10.16 Conformation dependent library (CDL) restraints added in 5.4 seconds 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13008 Finding SS restraints... Secondary structure from input PDB file: 266 helices and 73 sheets defined 42.1% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.97 Creating SS restraints... Processing helix chain 'F' and resid 39 through 65 removed outlier: 3.637A pdb=" N LEU F 65 " --> pdb=" O GLU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 78 Processing helix chain 'F' and resid 82 through 91 Processing helix 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 177 through 184 removed outlier: 5.811A pdb=" N ALA F 182 " --> pdb=" O PRO F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 204 removed outlier: 4.292A pdb=" N PHE F 195 " --> pdb=" O PHE F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 227 removed outlier: 3.521A pdb=" N ALA F 225 " --> pdb=" O ALA F 221 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA F 227 " --> pdb=" O VAL F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 252 Processing helix chain 'F' and resid 256 through 261 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 279 through 293 Processing helix chain 'F' and resid 316 through 322 Processing helix chain 'F' and resid 330 through 337 removed outlier: 3.924A pdb=" N VAL F 334 " --> pdb=" O ASP F 330 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG F 337 " --> pdb=" O GLU F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 343 removed outlier: 6.670A pdb=" N GLY F 341 " --> pdb=" O ILE F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 395 Processing helix chain 'F' and resid 416 through 432 removed outlier: 3.888A pdb=" N LYS F 420 " --> pdb=" O GLU F 416 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA F 423 " --> pdb=" O ALA F 419 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS F 424 " --> pdb=" O LYS F 420 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET F 425 " --> pdb=" O ASP F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 446 through 452 removed outlier: 4.110A pdb=" N TYR F 450 " --> pdb=" O GLY F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 458 Processing helix chain 'F' and resid 474 through 494 removed outlier: 3.622A pdb=" N LYS F 487 " --> pdb=" O ALA F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 517 Proline residue: F 508 - end of helix Processing helix chain 'F' and resid 518 through 525 removed outlier: 3.654A pdb=" N ARG F 525 " --> pdb=" O TYR F 521 " (cutoff:3.500A) Processing helix chain 'F' and resid 533 through 535 No H-bonds generated for 'chain 'F' and resid 533 through 535' Processing helix chain 'F' and resid 536 through 549 Processing helix chain 'I' and resid 57 through 72 removed outlier: 3.522A pdb=" N ALA I 61 " --> pdb=" O ARG I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 4.487A pdb=" N ASN I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 92 Processing helix chain 'I' and resid 102 through 106 Processing helix chain 'I' and resid 109 through 120 Processing helix chain 'I' and resid 135 through 145 Processing helix chain 'I' and resid 153 through 162 Processing helix chain 'I' and resid 162 through 174 Processing helix chain 'I' and resid 187 through 199 Processing helix chain 'I' and resid 223 through 233 Processing helix chain 'I' and resid 295 through 313 Processing helix chain 'I' and resid 343 through 352 removed outlier: 4.493A pdb=" N THR I 347 " --> pdb=" O GLU I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 365 Processing helix chain 'I' and resid 443 through 457 Processing helix chain 'I' and resid 466 through 476 Processing helix chain 'I' and resid 476 through 482 Processing helix chain 'I' and resid 487 through 492 Processing helix chain 'I' and resid 492 through 497 Processing helix chain 'I' and resid 504 through 530 removed outlier: 3.621A pdb=" N GLN I 529 " --> pdb=" O THR I 525 " (cutoff:3.500A) Processing helix chain 'I' and resid 535 through 539 Processing helix chain 'I' and resid 634 through 639 Processing helix chain 'I' and resid 639 through 646 removed outlier: 3.890A pdb=" N GLN I 643 " --> pdb=" O SER I 639 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN I 646 " --> pdb=" O SER I 642 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 65 removed outlier: 3.638A pdb=" N LEU J 65 " --> pdb=" O GLU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 78 Processing helix chain 'J' and resid 82 through 91 Processing helix 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 177 through 184 removed outlier: 5.811A pdb=" N ALA J 182 " --> pdb=" O PRO J 179 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 204 removed outlier: 4.290A pdb=" N PHE J 195 " --> pdb=" O PHE J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 220 Processing helix chain 'J' and resid 221 through 227 removed outlier: 3.580A pdb=" N ALA J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) Processing helix chain 'J' and resid 261 through 269 removed outlier: 4.146A pdb=" N LEU J 265 " --> pdb=" O GLY J 261 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 293 Processing helix chain 'J' and resid 316 through 322 Processing helix chain 'J' and resid 330 through 337 removed outlier: 3.924A pdb=" N VAL J 334 " --> pdb=" O ASP J 330 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG J 337 " --> pdb=" O GLU J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 343 removed outlier: 6.672A pdb=" N GLY J 341 " --> pdb=" O ILE J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 395 Processing helix chain 'J' and resid 410 through 416 Processing helix chain 'J' and resid 417 through 432 removed outlier: 3.568A pdb=" N MET J 425 " --> pdb=" O ASP J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 452 removed outlier: 4.108A pdb=" N TYR J 450 " --> pdb=" O GLY J 446 " (cutoff:3.500A) Processing helix chain 'J' and resid 454 through 458 Processing helix chain 'J' and resid 474 through 494 removed outlier: 3.622A pdb=" N LYS J 487 " --> pdb=" O ALA J 483 " (cutoff:3.500A) Processing helix chain 'J' and resid 498 through 517 Proline residue: J 508 - end of helix Processing helix chain 'J' and resid 518 through 525 removed outlier: 3.657A pdb=" N ARG J 525 " --> pdb=" O TYR J 521 " (cutoff:3.500A) Processing helix chain 'J' and resid 533 through 535 No H-bonds generated for 'chain 'J' and resid 533 through 535' Processing helix chain 'J' and resid 536 through 549 Processing helix chain 'L' and resid 39 through 65 removed outlier: 3.637A pdb=" N LEU L 65 " --> pdb=" O GLU L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 78 Processing helix chain 'L' and resid 82 through 91 Processing helix 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 177 through 184 removed outlier: 5.811A pdb=" N ALA L 182 " --> pdb=" O PRO L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 204 removed outlier: 4.291A pdb=" N PHE L 195 " --> pdb=" O PHE L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 227 removed outlier: 3.521A pdb=" N ALA L 225 " --> pdb=" O ALA L 221 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA L 227 " --> pdb=" O VAL L 223 " (cutoff:3.500A) Processing helix chain 'L' and resid 263 through 268 Processing helix chain 'L' and resid 279 through 293 Processing helix chain 'L' and resid 316 through 322 Processing helix chain 'L' and resid 330 through 337 removed outlier: 3.926A pdb=" N VAL L 334 " --> pdb=" O ASP L 330 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG L 337 " --> pdb=" O GLU L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 343 removed outlier: 6.670A pdb=" N GLY L 341 " --> pdb=" O ILE L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 377 through 395 Processing helix chain 'L' and resid 414 through 432 removed outlier: 3.703A pdb=" N ILE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA L 419 " --> pdb=" O ALA L 415 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS L 420 " --> pdb=" O GLU L 416 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP L 421 " --> pdb=" O GLY L 417 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS L 424 " --> pdb=" O LYS L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 446 through 452 removed outlier: 4.109A pdb=" N TYR L 450 " --> pdb=" O GLY L 446 " (cutoff:3.500A) Processing helix chain 'L' and resid 454 through 458 Processing helix chain 'L' and resid 474 through 494 removed outlier: 3.622A pdb=" N LYS L 487 " --> pdb=" O ALA L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 498 through 517 Proline residue: L 508 - end of helix Processing helix chain 'L' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG L 525 " --> pdb=" O TYR L 521 " (cutoff:3.500A) Processing helix chain 'L' and resid 533 through 535 No H-bonds generated for 'chain 'L' and resid 533 through 535' Processing helix chain 'L' and resid 536 through 549 Processing helix chain 'K' and resid 57 through 71 removed outlier: 3.573A pdb=" N ALA K 61 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.506A pdb=" N ARG K 84 " --> pdb=" O GLU K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 92 Processing helix chain 'K' and resid 102 through 106 Processing helix chain 'K' and resid 109 through 120 Processing helix chain 'K' and resid 135 through 145 Processing helix chain 'K' and resid 153 through 162 removed outlier: 3.908A pdb=" N ILE K 162 " --> pdb=" O ARG K 158 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 173 Processing helix chain 'K' and resid 187 through 199 Processing helix chain 'K' and resid 223 through 240 Processing helix chain 'K' and resid 295 through 313 Processing helix chain 'K' and resid 343 through 352 removed outlier: 4.174A pdb=" N THR K 347 " --> pdb=" O GLU K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 364 Processing helix chain 'K' and resid 443 through 458 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 497 removed outlier: 5.562A pdb=" N LYS K 494 " --> pdb=" O PRO K 490 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN K 495 " --> pdb=" O GLN K 491 " (cutoff:3.500A) Processing helix chain 'K' and resid 504 through 529 removed outlier: 3.963A pdb=" N GLN K 529 " --> pdb=" O THR K 525 " (cutoff:3.500A) Processing helix chain 'K' and resid 535 through 539 Processing helix chain 'A' and resid 39 through 65 removed outlier: 3.637A pdb=" N LEU A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 78 Processing helix chain 'A' and resid 82 through 91 Processing helix chain 'A' and resid 114 through 117 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 146 through 164 Processing helix chain 'A' and resid 177 through 184 removed outlier: 5.811A pdb=" N ALA A 182 " --> pdb=" O PRO A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 204 removed outlier: 4.291A pdb=" N PHE A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 removed outlier: 3.521A pdb=" N ALA A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 227 " --> pdb=" O VAL A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 252 Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 279 through 293 Processing helix chain 'A' and resid 316 through 322 Processing helix chain 'A' and resid 330 through 337 removed outlier: 3.924A pdb=" N VAL A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG A 337 " --> pdb=" O GLU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 6.670A pdb=" N GLY A 341 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 395 Processing helix chain 'A' and resid 416 through 432 removed outlier: 3.888A pdb=" N LYS A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET A 425 " --> pdb=" O ASP A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 452 removed outlier: 4.110A pdb=" N TYR A 450 " --> pdb=" O GLY A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 458 Processing helix chain 'A' and resid 474 through 494 removed outlier: 3.622A pdb=" N LYS A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 517 Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 518 through 525 removed outlier: 3.654A pdb=" N ARG A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 535 No H-bonds generated for 'chain 'A' and resid 533 through 535' Processing helix chain 'A' and resid 536 through 549 Processing helix chain 'C' and resid 57 through 72 removed outlier: 3.522A pdb=" N ALA C 61 " --> pdb=" O ARG C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 4.487A pdb=" N ASN C 85 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 Processing helix chain 'C' and resid 102 through 106 Processing helix chain 'C' and resid 109 through 120 Processing helix chain 'C' and resid 135 through 145 Processing helix chain 'C' and resid 153 through 162 Processing helix chain 'C' and resid 162 through 174 Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 223 through 233 Processing helix chain 'C' and resid 295 through 313 Processing helix chain 'C' and resid 343 through 352 removed outlier: 4.493A pdb=" N THR C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 365 Processing helix chain 'C' and resid 443 through 457 Processing helix chain 'C' and resid 466 through 476 Processing helix chain 'C' and resid 476 through 482 Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 492 through 497 Processing helix chain 'C' and resid 504 through 530 removed outlier: 3.621A pdb=" N GLN C 529 " --> pdb=" O THR C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 634 through 639 Processing helix chain 'C' and resid 639 through 646 removed outlier: 3.890A pdb=" N GLN C 643 " --> pdb=" O SER C 639 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN C 646 " --> pdb=" O SER C 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 65 removed outlier: 3.638A pdb=" N LEU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 78 Processing helix chain 'D' and resid 82 through 91 Processing helix 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 177 through 184 removed outlier: 5.811A pdb=" N ALA D 182 " --> pdb=" O PRO D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 204 removed outlier: 4.289A pdb=" N PHE D 195 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 220 Processing helix chain 'D' and resid 221 through 227 removed outlier: 3.580A pdb=" N ALA D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 269 removed outlier: 4.146A pdb=" N LEU D 265 " --> pdb=" O GLY D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 293 Processing helix chain 'D' and resid 316 through 322 Processing helix chain 'D' and resid 330 through 337 removed outlier: 3.924A pdb=" N VAL D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 337 " --> pdb=" O GLU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 removed outlier: 6.671A pdb=" N GLY D 341 " --> pdb=" O ILE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 395 Processing helix chain 'D' and resid 410 through 416 Processing helix chain 'D' and resid 417 through 432 removed outlier: 3.568A pdb=" N MET D 425 " --> pdb=" O ASP D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 452 removed outlier: 4.108A pdb=" N TYR D 450 " --> pdb=" O GLY D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 458 Processing helix chain 'D' and resid 474 through 494 removed outlier: 3.621A pdb=" N LYS D 487 " --> pdb=" O ALA D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 517 Proline residue: D 508 - end of helix Processing helix chain 'D' and resid 518 through 525 removed outlier: 3.657A pdb=" N ARG D 525 " --> pdb=" O TYR D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 535 No H-bonds generated for 'chain 'D' and resid 533 through 535' Processing helix chain 'D' and resid 536 through 549 Processing helix chain 'H' and resid 39 through 65 removed outlier: 3.637A pdb=" N LEU H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 78 Processing helix chain 'H' and resid 82 through 91 Processing helix 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 177 through 184 removed outlier: 5.811A pdb=" N ALA H 182 " --> pdb=" O PRO H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 204 removed outlier: 4.292A pdb=" N PHE H 195 " --> pdb=" O PHE H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 227 removed outlier: 3.521A pdb=" N ALA H 225 " --> pdb=" O ALA H 221 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA H 227 " --> pdb=" O VAL H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 279 through 293 Processing helix chain 'H' and resid 316 through 322 Processing helix chain 'H' and resid 330 through 337 removed outlier: 3.925A pdb=" N VAL H 334 " --> pdb=" O ASP H 330 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG H 337 " --> pdb=" O GLU H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 343 removed outlier: 6.671A pdb=" N GLY H 341 " --> pdb=" O ILE H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 395 Processing helix chain 'H' and resid 414 through 432 removed outlier: 3.703A pdb=" N ILE H 418 " --> pdb=" O GLU H 414 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA H 419 " --> pdb=" O ALA H 415 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS H 420 " --> pdb=" O GLU H 416 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP H 421 " --> pdb=" O GLY H 417 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS H 424 " --> pdb=" O LYS H 420 " (cutoff:3.500A) Processing helix chain 'H' and resid 446 through 452 removed outlier: 4.109A pdb=" N TYR H 450 " --> pdb=" O GLY H 446 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 458 Processing helix chain 'H' and resid 474 through 494 removed outlier: 3.621A pdb=" N LYS H 487 " --> pdb=" O ALA H 483 " (cutoff:3.500A) Processing helix chain 'H' and resid 498 through 517 Proline residue: H 508 - end of helix Processing helix chain 'H' and resid 518 through 525 removed outlier: 3.656A pdb=" N ARG H 525 " --> pdb=" O TYR H 521 " (cutoff:3.500A) Processing helix chain 'H' and resid 533 through 535 No H-bonds generated for 'chain 'H' and resid 533 through 535' Processing helix chain 'H' and resid 536 through 549 Processing helix chain 'B' and resid 57 through 71 removed outlier: 3.573A pdb=" N ALA B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.505A pdb=" N ARG B 84 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 92 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 109 through 120 Processing helix chain 'B' and resid 135 through 145 Processing helix chain 'B' and resid 153 through 162 removed outlier: 3.845A pdb=" N ILE B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 173 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 223 through 240 Processing helix chain 'B' and resid 295 through 313 Processing helix chain 'B' and resid 343 through 352 removed outlier: 4.175A pdb=" N THR B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 443 through 458 Processing helix chain 'B' and resid 466 through 475 Processing helix chain 'B' and resid 476 through 482 Processing helix chain 'B' and resid 487 through 497 removed outlier: 5.562A pdb=" N LYS B 494 " --> pdb=" O PRO B 490 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN B 495 " --> pdb=" O GLN B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 529 removed outlier: 3.963A pdb=" N GLN B 529 " --> pdb=" O THR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 539 Processing helix chain 'E' and resid 57 through 71 removed outlier: 3.573A pdb=" N ALA E 61 " --> pdb=" O ARG E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 removed outlier: 3.505A pdb=" N ARG E 84 " --> pdb=" O GLU E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 102 through 106 Processing helix chain 'E' and resid 109 through 120 Processing helix chain 'E' and resid 135 through 145 Processing helix chain 'E' and resid 153 through 162 removed outlier: 3.807A pdb=" N ILE E 162 " --> pdb=" O ARG E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 173 Processing helix chain 'E' and resid 187 through 199 Processing helix chain 'E' and resid 223 through 240 Processing helix chain 'E' and resid 295 through 313 Processing helix chain 'E' and resid 343 through 352 removed outlier: 4.174A pdb=" N THR E 347 " --> pdb=" O GLU E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 364 Processing helix chain 'E' and resid 443 through 458 Processing helix chain 'E' and resid 466 through 475 Processing helix chain 'E' and resid 476 through 482 Processing helix chain 'E' and resid 487 through 497 removed outlier: 5.561A pdb=" N LYS E 494 " --> pdb=" O PRO E 490 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN E 495 " --> pdb=" O GLN E 491 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 529 removed outlier: 3.963A pdb=" N GLN E 529 " --> pdb=" O THR E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 539 Processing helix chain 'G' and resid 57 through 71 removed outlier: 3.572A pdb=" N ALA G 61 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR G 67 " --> pdb=" O ARG G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 84 removed outlier: 3.506A pdb=" N ARG G 84 " --> pdb=" O GLU G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 92 Processing helix chain 'G' and resid 102 through 106 Processing helix chain 'G' and resid 109 through 120 Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 153 through 162 removed outlier: 3.786A pdb=" N ILE G 162 " --> pdb=" O ARG G 158 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 173 Processing helix chain 'G' and resid 187 through 199 Processing helix chain 'G' and resid 223 through 240 Processing helix chain 'G' and resid 295 through 313 Processing helix chain 'G' and resid 343 through 352 removed outlier: 4.174A pdb=" N THR G 347 " --> pdb=" O GLU G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 364 Processing helix chain 'G' and resid 443 through 458 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 497 removed outlier: 5.561A pdb=" N LYS G 494 " --> pdb=" O PRO G 490 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN G 495 " --> pdb=" O GLN G 491 " (cutoff:3.500A) Processing helix chain 'G' and resid 504 through 529 removed outlier: 3.964A pdb=" N GLN G 529 " --> pdb=" O THR G 525 " (cutoff:3.500A) Processing helix chain 'G' and resid 535 through 539 Processing sheet with id=AA1, first strand: chain 'F' and resid 98 through 100 removed outlier: 4.729A pdb=" N THR F 121 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS F 167 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL F 211 " --> pdb=" O CYS F 167 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N TYR F 169 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN F 230 " --> pdb=" O HIS F 275 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA F 277 " --> pdb=" O ASN F 230 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE F 232 " --> pdb=" O ALA F 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 215 through 216 Processing sheet with id=AA3, first strand: chain 'F' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU F 399 " --> pdb=" O PRO F 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY F 368 " --> pdb=" O LEU F 399 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU F 401 " --> pdb=" O GLY F 368 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL F 370 " --> pdb=" O LEU F 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE F 461 " --> pdb=" O LYS F 436 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 443 through 445 removed outlier: 6.113A pdb=" N SER F 444 " --> pdb=" O SER F 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'I' and resid 148 through 149 removed outlier: 6.939A pdb=" N LYS I 51 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N HIS I 126 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU I 53 " --> pdb=" O HIS I 126 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL I 78 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR G 596 " --> pdb=" O LEU G 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 180 through 181 Processing sheet with id=AA7, first strand: chain 'I' and resid 268 through 275 removed outlier: 3.958A pdb=" N GLN I 259 " --> pdb=" O LEU I 271 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU I 273 " --> pdb=" O GLU I 257 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU I 257 " --> pdb=" O GLU I 273 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASP I 275 " --> pdb=" O HIS I 255 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N HIS I 255 " --> pdb=" O ASP I 275 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG I 254 " --> pdb=" O MET I 325 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU I 335 " --> pdb=" O GLU I 322 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE I 324 " --> pdb=" O PHE I 333 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N PHE I 333 " --> pdb=" O ILE I 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 279 through 280 Processing sheet with id=AA9, first strand: chain 'I' and resid 286 through 289 removed outlier: 3.572A pdb=" N ALA I 435 " --> pdb=" O ILE I 386 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 404 through 406 Processing sheet with id=AB2, first strand: chain 'I' and resid 543 through 544 removed outlier: 3.924A pdb=" N ARG I 544 " --> pdb=" O ILE I 547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE I 547 " --> pdb=" O ARG I 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 148 through 149 removed outlier: 6.982A pdb=" N LYS K 51 " --> pdb=" O ALA K 124 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N HIS K 126 " --> pdb=" O LYS K 51 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU K 53 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL K 78 " --> pdb=" O ILE K 54 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA K 95 " --> pdb=" O ALA I 606 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR I 596 " --> pdb=" O LEU I 611 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 683 through 687 removed outlier: 3.579A pdb=" N MET I 675 " --> pdb=" O ILE I 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU I 674 " --> pdb=" O VAL I 660 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL I 660 " --> pdb=" O LEU I 674 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL I 676 " --> pdb=" O GLU I 658 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 694 through 697 Processing sheet with id=AB6, first strand: chain 'J' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR J 121 " --> pdb=" O LEU J 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS J 167 " --> pdb=" O ILE J 209 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL J 211 " --> pdb=" O CYS J 167 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR J 169 " --> pdb=" O VAL J 211 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN J 230 " --> pdb=" O HIS J 275 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ALA J 277 " --> pdb=" O ASN J 230 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE J 232 " --> pdb=" O ALA J 277 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 345 through 346 removed outlier: 7.655A pdb=" N LEU J 399 " --> pdb=" O PRO J 366 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY J 368 " --> pdb=" O LEU J 399 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU J 401 " --> pdb=" O GLY J 368 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL J 370 " --> pdb=" O LEU J 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE J 461 " --> pdb=" O LYS J 436 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 443 through 445 removed outlier: 6.111A pdb=" N SER J 444 " --> pdb=" O SER J 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'L' and resid 98 through 100 removed outlier: 4.729A pdb=" N THR L 121 " --> pdb=" O LEU L 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS L 167 " --> pdb=" O ILE L 209 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL L 211 " --> pdb=" O CYS L 167 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N TYR L 169 " --> pdb=" O VAL L 211 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN L 230 " --> pdb=" O HIS L 275 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA L 277 " --> pdb=" O ASN L 230 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE L 232 " --> pdb=" O ALA L 277 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 345 through 346 removed outlier: 7.657A pdb=" N LEU L 399 " --> pdb=" O PRO L 366 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY L 368 " --> pdb=" O LEU L 399 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU L 401 " --> pdb=" O GLY L 368 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL L 370 " --> pdb=" O LEU L 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE L 461 " --> pdb=" O LYS L 436 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 443 through 445 removed outlier: 6.114A pdb=" N SER L 444 " --> pdb=" O SER L 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'K' and resid 216 through 218 removed outlier: 3.540A pdb=" N LYS K 205 " --> pdb=" O LEU K 245 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 268 through 270 removed outlier: 5.672A pdb=" N ILE K 324 " --> pdb=" O PHE K 333 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE K 333 " --> pdb=" O ILE K 324 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'K' and resid 268 through 270 removed outlier: 5.521A pdb=" N HIS K 255 " --> pdb=" O CYS K 276 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER K 277 " --> pdb=" O ILE K 286 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE K 286 " --> pdb=" O SER K 277 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN K 279 " --> pdb=" O LYS K 284 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS K 284 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 13.619A pdb=" N GLN K 283 " --> pdb=" O TYR K 387 " (cutoff:3.500A) removed outlier: 10.718A pdb=" N TYR K 387 " --> pdb=" O GLN K 283 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE K 285 " --> pdb=" O ARG K 385 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA K 435 " --> pdb=" O ILE K 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 389 through 390 removed outlier: 3.541A pdb=" N MET K 396 " --> pdb=" O ASP K 390 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 400 through 401 removed outlier: 3.788A pdb=" N GLY K 400 " --> pdb=" O VAL K 426 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 404 through 406 Processing sheet with id=AC9, first strand: chain 'G' and resid 148 through 149 removed outlier: 6.982A pdb=" N LYS G 51 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N HIS G 126 " --> pdb=" O LYS G 51 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU G 53 " --> pdb=" O HIS G 126 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL G 78 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA G 95 " --> pdb=" O ALA K 606 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR K 596 " --> pdb=" O LEU K 611 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 683 through 687 removed outlier: 3.661A pdb=" N MET K 675 " --> pdb=" O ILE K 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU K 674 " --> pdb=" O VAL K 660 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL K 660 " --> pdb=" O LEU K 674 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL K 676 " --> pdb=" O GLU K 658 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 694 through 697 Processing sheet with id=AD3, first strand: chain 'A' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR A 121 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N CYS A 167 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL A 211 " --> pdb=" O CYS A 167 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N TYR A 169 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A 230 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA A 277 " --> pdb=" O ASN A 230 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 232 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AD5, first strand: chain 'A' and resid 345 through 346 removed outlier: 7.655A pdb=" N LEU A 399 " --> pdb=" O PRO A 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY A 368 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU A 401 " --> pdb=" O GLY A 368 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 370 " --> pdb=" O LEU A 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE A 461 " --> pdb=" O LYS A 436 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 443 through 445 removed outlier: 6.113A pdb=" N SER A 444 " --> pdb=" O SER A 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 148 through 149 removed outlier: 6.939A pdb=" N LYS C 51 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N HIS C 126 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU C 53 " --> pdb=" O HIS C 126 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL C 78 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 268 through 275 removed outlier: 3.958A pdb=" N GLN C 259 " --> pdb=" O LEU C 271 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU C 273 " --> pdb=" O GLU C 257 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU C 257 " --> pdb=" O GLU C 273 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASP C 275 " --> pdb=" O HIS C 255 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N HIS C 255 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU C 335 " --> pdb=" O GLU C 322 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ILE C 324 " --> pdb=" O PHE C 333 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N PHE C 333 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 279 through 280 Processing sheet with id=AE1, first strand: chain 'C' and resid 286 through 289 Processing sheet with id=AE2, first strand: chain 'C' and resid 404 through 406 Processing sheet with id=AE3, first strand: chain 'C' and resid 543 through 544 removed outlier: 3.925A pdb=" N ARG C 544 " --> pdb=" O ILE C 547 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE C 547 " --> pdb=" O ARG C 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'E' and resid 148 through 149 removed outlier: 6.983A pdb=" N LYS E 51 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N HIS E 126 " --> pdb=" O LYS E 51 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU E 53 " --> pdb=" O HIS E 126 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL E 78 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 95 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 683 through 687 removed outlier: 3.579A pdb=" N MET C 675 " --> pdb=" O ILE C 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU C 674 " --> pdb=" O VAL C 660 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL C 660 " --> pdb=" O LEU C 674 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL C 676 " --> pdb=" O GLU C 658 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 694 through 697 Processing sheet with id=AE7, first strand: chain 'D' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR D 121 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS D 167 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL D 211 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N TYR D 169 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN D 230 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA D 277 " --> pdb=" O ASN D 230 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE D 232 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 345 through 346 removed outlier: 7.655A pdb=" N LEU D 399 " --> pdb=" O PRO D 366 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY D 368 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU D 401 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL D 370 " --> pdb=" O LEU D 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 461 " --> pdb=" O LYS D 436 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 443 through 445 removed outlier: 6.111A pdb=" N SER D 444 " --> pdb=" O SER D 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'H' and resid 98 through 100 removed outlier: 4.729A pdb=" N THR H 121 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N CYS H 167 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL H 211 " --> pdb=" O CYS H 167 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR H 169 " --> pdb=" O VAL H 211 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN H 230 " --> pdb=" O HIS H 275 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA H 277 " --> pdb=" O ASN H 230 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE H 232 " --> pdb=" O ALA H 277 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU H 399 " --> pdb=" O PRO H 366 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY H 368 " --> pdb=" O LEU H 399 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU H 401 " --> pdb=" O GLY H 368 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL H 370 " --> pdb=" O LEU H 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE H 461 " --> pdb=" O LYS H 436 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 443 through 445 removed outlier: 6.114A pdb=" N SER H 444 " --> pdb=" O SER H 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'B' and resid 148 through 149 removed outlier: 6.982A pdb=" N LYS B 51 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N HIS B 126 " --> pdb=" O LYS B 51 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 53 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 78 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 95 " --> pdb=" O ALA E 606 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR E 596 " --> pdb=" O LEU E 611 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 216 through 218 removed outlier: 3.539A pdb=" N LYS B 205 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 268 through 270 removed outlier: 5.671A pdb=" N ILE B 324 " --> pdb=" O PHE B 333 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE B 333 " --> pdb=" O ILE B 324 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 268 through 270 removed outlier: 5.004A pdb=" N SER B 277 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE B 286 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN B 279 " --> pdb=" O LYS B 284 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LYS B 284 " --> pdb=" O GLN B 279 " (cutoff:3.500A) removed outlier: 13.814A pdb=" N GLN B 283 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 10.541A pdb=" N TYR B 387 " --> pdb=" O GLN B 283 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE B 285 " --> pdb=" O ARG B 385 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 435 " --> pdb=" O ILE B 386 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 389 through 390 removed outlier: 3.540A pdb=" N MET B 396 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 400 through 401 removed outlier: 3.788A pdb=" N GLY B 400 " --> pdb=" O VAL B 426 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 404 through 406 Processing sheet with id=AG2, first strand: chain 'B' and resid 683 through 687 removed outlier: 3.661A pdb=" N MET B 675 " --> pdb=" O ILE B 686 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 674 " --> pdb=" O VAL B 660 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL B 660 " --> pdb=" O LEU B 674 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL B 676 " --> pdb=" O GLU B 658 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 694 through 697 Processing sheet with id=AG4, first strand: chain 'E' and resid 216 through 218 removed outlier: 3.541A pdb=" N LYS E 205 " --> pdb=" O LEU E 245 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 268 through 270 removed outlier: 5.672A pdb=" N ILE E 324 " --> pdb=" O PHE E 333 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE E 333 " --> pdb=" O ILE E 324 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 268 through 270 removed outlier: 5.631A pdb=" N HIS E 255 " --> pdb=" O CYS E 276 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER E 277 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N ILE E 286 " --> pdb=" O SER E 277 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN E 279 " --> pdb=" O LYS E 284 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LYS E 284 " --> pdb=" O GLN E 279 " (cutoff:3.500A) removed outlier: 13.859A pdb=" N GLN E 283 " --> pdb=" O TYR E 387 " (cutoff:3.500A) removed outlier: 10.584A pdb=" N TYR E 387 " --> pdb=" O GLN E 283 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE E 285 " --> pdb=" O ARG E 385 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA E 435 " --> pdb=" O ILE E 386 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 389 through 390 removed outlier: 3.541A pdb=" N MET E 396 " --> pdb=" O ASP E 390 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 400 through 401 removed outlier: 3.788A pdb=" N GLY E 400 " --> pdb=" O VAL E 426 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 404 through 406 Processing sheet with id=AH1, first strand: chain 'E' and resid 683 through 687 removed outlier: 3.661A pdb=" N MET E 675 " --> pdb=" O ILE E 686 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU E 674 " --> pdb=" O VAL E 660 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL E 660 " --> pdb=" O LEU E 674 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL E 676 " --> pdb=" O GLU E 658 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 694 through 697 Processing sheet with id=AH3, first strand: chain 'G' and resid 216 through 218 removed outlier: 3.540A pdb=" N LYS G 205 " --> pdb=" O LEU G 245 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 268 through 270 removed outlier: 5.672A pdb=" N ILE G 324 " --> pdb=" O PHE G 333 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE G 333 " --> pdb=" O ILE G 324 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 268 through 270 removed outlier: 6.414A pdb=" N HIS G 255 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N CYS G 276 " --> pdb=" O HIS G 255 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N SER G 277 " --> pdb=" O ILE G 286 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ILE G 286 " --> pdb=" O SER G 277 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLN G 279 " --> pdb=" O LYS G 284 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS G 284 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE G 285 " --> pdb=" O ARG G 385 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA G 435 " --> pdb=" O ILE G 386 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 389 through 390 removed outlier: 3.540A pdb=" N MET G 396 " --> pdb=" O ASP G 390 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 400 through 401 removed outlier: 3.788A pdb=" N GLY G 400 " --> pdb=" O VAL G 426 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 404 through 406 Processing sheet with id=AH9, first strand: chain 'G' and resid 683 through 687 removed outlier: 3.661A pdb=" N MET G 675 " --> pdb=" O ILE G 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU G 674 " --> pdb=" O VAL G 660 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL G 660 " --> pdb=" O LEU G 674 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL G 676 " --> pdb=" O GLU G 658 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 694 through 697 2716 hydrogen bonds defined for protein. 7470 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: 24.46 Time building geometry restraints manager: 12.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 9438 1.31 - 1.44: 14142 1.44 - 1.57: 31978 1.57 - 1.69: 0 1.69 - 1.82: 530 Bond restraints: 56088 Sorted by residual: bond pdb=" C LYS D 424 " pdb=" N MET D 425 " ideal model delta sigma weight residual 1.335 1.232 0.102 1.36e-02 5.41e+03 5.67e+01 bond pdb=" C LYS J 424 " pdb=" N MET J 425 " ideal model delta sigma weight residual 1.335 1.233 0.102 1.36e-02 5.41e+03 5.61e+01 bond pdb=" C MET D 425 " pdb=" O MET D 425 " ideal model delta sigma weight residual 1.237 1.179 0.057 1.19e-02 7.06e+03 2.32e+01 bond pdb=" C MET A 425 " pdb=" O MET A 425 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.17e-02 7.31e+03 2.27e+01 bond pdb=" C MET F 425 " pdb=" O MET F 425 " ideal model delta sigma weight residual 1.237 1.181 0.055 1.17e-02 7.31e+03 2.23e+01 ... (remaining 56083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 71768 2.79 - 5.57: 3758 5.57 - 8.36: 163 8.36 - 11.15: 31 11.15 - 13.93: 6 Bond angle restraints: 75726 Sorted by residual: angle pdb=" N ASP G 251 " pdb=" CA ASP G 251 " pdb=" C ASP G 251 " ideal model delta sigma weight residual 111.07 122.04 -10.97 1.07e+00 8.73e-01 1.05e+02 angle pdb=" N ASP A 264 " pdb=" CA ASP A 264 " pdb=" C ASP A 264 " ideal model delta sigma weight residual 112.38 99.88 12.50 1.22e+00 6.72e-01 1.05e+02 angle pdb=" N ASP F 264 " pdb=" CA ASP F 264 " pdb=" C ASP F 264 " ideal model delta sigma weight residual 112.38 99.89 12.49 1.22e+00 6.72e-01 1.05e+02 angle pdb=" N ASP H 264 " pdb=" CA ASP H 264 " pdb=" C ASP H 264 " ideal model delta sigma weight residual 112.38 99.93 12.45 1.22e+00 6.72e-01 1.04e+02 angle pdb=" N ASP L 264 " pdb=" CA ASP L 264 " pdb=" C ASP L 264 " ideal model delta sigma weight residual 112.38 99.94 12.44 1.22e+00 6.72e-01 1.04e+02 ... (remaining 75721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 31383 17.52 - 35.05: 1944 35.05 - 52.57: 529 52.57 - 70.09: 140 70.09 - 87.62: 34 Dihedral angle restraints: 34030 sinusoidal: 13698 harmonic: 20332 Sorted by residual: dihedral pdb=" C THR I 486 " pdb=" N THR I 486 " pdb=" CA THR I 486 " pdb=" CB THR I 486 " ideal model delta harmonic sigma weight residual -122.00 -140.62 18.62 0 2.50e+00 1.60e-01 5.55e+01 dihedral pdb=" C THR C 486 " pdb=" N THR C 486 " pdb=" CA THR C 486 " pdb=" CB THR C 486 " ideal model delta harmonic sigma weight residual -122.00 -140.59 18.59 0 2.50e+00 1.60e-01 5.53e+01 dihedral pdb=" N THR I 486 " pdb=" C THR I 486 " pdb=" CA THR I 486 " pdb=" CB THR I 486 " ideal model delta harmonic sigma weight residual 123.40 137.30 -13.90 0 2.50e+00 1.60e-01 3.09e+01 ... (remaining 34027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 7212 0.127 - 0.254: 1051 0.254 - 0.381: 80 0.381 - 0.509: 0 0.509 - 0.636: 3 Chirality restraints: 8346 Sorted by residual: chirality pdb=" CA THR I 486 " pdb=" N THR I 486 " pdb=" C THR I 486 " pdb=" CB THR I 486 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.64 2.00e-01 2.50e+01 1.01e+01 chirality pdb=" CA THR C 486 " pdb=" N THR C 486 " pdb=" C THR C 486 " pdb=" CB THR C 486 " both_signs ideal model delta sigma weight residual False 2.53 1.89 0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CA ARG B 254 " pdb=" N ARG B 254 " pdb=" C ARG B 254 " pdb=" CB ARG B 254 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.76e+00 ... (remaining 8343 not shown) Planarity restraints: 9924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU G 145 " 0.020 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" CD GLU G 145 " -0.067 2.00e-02 2.50e+03 pdb=" OE1 GLU G 145 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU G 145 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 145 " 0.020 2.00e-02 2.50e+03 3.88e-02 1.51e+01 pdb=" CD GLU B 145 " -0.067 2.00e-02 2.50e+03 pdb=" OE1 GLU B 145 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU B 145 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU K 145 " 0.019 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" CD GLU K 145 " -0.067 2.00e-02 2.50e+03 pdb=" OE1 GLU K 145 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU K 145 " 0.024 2.00e-02 2.50e+03 ... (remaining 9921 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 15167 2.82 - 3.34: 50392 3.34 - 3.86: 91698 3.86 - 4.38: 110737 4.38 - 4.90: 182987 Nonbonded interactions: 450981 Sorted by model distance: nonbonded pdb=" CD1 LEU I 340 " pdb=" OE1 GLN I 359 " model vdw 2.301 3.460 nonbonded pdb=" CD1 LEU C 340 " pdb=" OE1 GLN C 359 " model vdw 2.302 3.460 nonbonded pdb=" O ALA J 227 " pdb=" NH2 ARG A 562 " model vdw 2.338 3.120 nonbonded pdb=" NH2 ARG J 562 " pdb=" O ALA A 227 " model vdw 2.366 3.120 nonbonded pdb=" O ALA D 336 " pdb=" OG SER D 342 " model vdw 2.371 3.040 ... (remaining 450976 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 239 or resid 259 through 563)) selection = (chain 'D' and (resid 23 through 239 or resid 259 through 563)) selection = (chain 'F' and (resid 23 through 239 or resid 259 through 563)) selection = chain 'H' selection = (chain 'J' and (resid 23 through 239 or resid 259 through 563)) selection = chain 'L' } ncs_group { reference = (chain 'B' and (resid 47 through 204 or resid 216 through 233 or resid 244 throu \ gh 717 or resid 801)) selection = (chain 'C' and (resid 47 through 365 or resid 380 through 717 or resid 800)) selection = (chain 'E' and (resid 47 through 204 or resid 216 through 233 or resid 244 throu \ gh 717 or resid 801)) selection = (chain 'G' and (resid 47 through 204 or resid 216 through 233 or resid 244 throu \ gh 717 or resid 801)) selection = (chain 'I' and (resid 47 through 365 or resid 380 through 717 or resid 800)) selection = (chain 'K' and (resid 47 through 204 or resid 216 through 233 or resid 244 throu \ gh 717 or resid 801)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 1.540 Check model and map are aligned: 0.310 Set scattering table: 0.370 Process input model: 98.440 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.210 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:2.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5803 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 : 0.009 0.102 56088 Z= 0.602 Angle : 1.275 13.931 75726 Z= 0.912 Chirality : 0.086 0.636 8346 Planarity : 0.006 0.089 9924 Dihedral : 13.179 87.618 21022 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.30 % Favored : 97.63 % Rotamer: Outliers : 1.53 % Allowed : 8.27 % Favored : 90.21 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 4.00 % 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: 1.10 (0.10), residues: 7054 helix: 1.65 (0.10), residues: 2578 sheet: 0.99 (0.14), residues: 1284 loop : -0.08 (0.11), residues: 3192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 440 HIS 0.013 0.002 HIS I 380 PHE 0.047 0.004 PHE B 395 TYR 0.033 0.003 TYR I 200 ARG 0.011 0.001 ARG B 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 988 time to evaluate : 4.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 158 GLU cc_start: 0.7552 (tt0) cc_final: 0.6875 (tt0) REVERT: I 247 GLU cc_start: 0.1467 (OUTLIER) cc_final: 0.1143 (mt-10) REVERT: I 255 HIS cc_start: 0.3027 (t70) cc_final: 0.1543 (t-170) REVERT: J 205 ASN cc_start: 0.7633 (t0) cc_final: 0.6829 (t0) REVERT: L 222 TYR cc_start: 0.7810 (m-80) cc_final: 0.7584 (m-80) REVERT: L 260 LEU cc_start: 0.7687 (tp) cc_final: 0.7379 (pt) REVERT: K 396 MET cc_start: 0.4664 (mtp) cc_final: 0.4399 (tpt) REVERT: K 680 MET cc_start: 0.0796 (mtm) cc_final: -0.2122 (ppp) REVERT: A 158 GLU cc_start: 0.7668 (tt0) cc_final: 0.6929 (tt0) REVERT: C 252 THR cc_start: 0.5064 (OUTLIER) cc_final: 0.4704 (p) REVERT: C 334 MET cc_start: 0.0543 (OUTLIER) cc_final: -0.0309 (tpt) REVERT: D 205 ASN cc_start: 0.7444 (t0) cc_final: 0.6694 (t0) REVERT: B 65 MET cc_start: 0.7655 (mtt) cc_final: 0.7249 (mtm) REVERT: B 175 VAL cc_start: -0.1052 (OUTLIER) cc_final: -0.1308 (t) REVERT: B 403 VAL cc_start: 0.7399 (t) cc_final: 0.7079 (p) REVERT: E 680 MET cc_start: 0.0751 (mtm) cc_final: -0.2355 (ppp) REVERT: G 65 MET cc_start: 0.7601 (mtt) cc_final: 0.7094 (mtm) REVERT: G 160 MET cc_start: -0.0653 (mpp) cc_final: -0.2712 (tmm) REVERT: G 197 ARG cc_start: -0.3583 (OUTLIER) cc_final: -0.4086 (mtm-85) REVERT: G 403 VAL cc_start: 0.7569 (t) cc_final: 0.7212 (p) REVERT: G 611 LEU cc_start: 0.8708 (tp) cc_final: 0.8411 (pp) REVERT: G 662 VAL cc_start: 0.5970 (p) cc_final: 0.5589 (t) outliers start: 89 outliers final: 21 residues processed: 1052 average time/residue: 0.5761 time to fit residues: 975.5781 Evaluate side-chains 536 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 510 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain I residue 91 MET Chi-restraints excluded: chain I residue 246 ILE Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 280 ARG Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 280 ARG Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 197 ARG Chi-restraints excluded: chain G residue 255 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 596 optimal weight: 0.0670 chunk 535 optimal weight: 6.9990 chunk 296 optimal weight: 0.5980 chunk 182 optimal weight: 6.9990 chunk 360 optimal weight: 0.9990 chunk 285 optimal weight: 20.0000 chunk 553 optimal weight: 20.0000 chunk 214 optimal weight: 9.9990 chunk 336 optimal weight: 0.1980 chunk 411 optimal weight: 9.9990 chunk 641 optimal weight: 0.7980 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 389 GLN ** I 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 265 HIS I 329 HIS I 337 ASN I 359 GLN I 380 HIS I 429 HIS I 491 GLN I 531 HIS I 708 HIS J 389 GLN L 198 GLN L 266 HIS L 389 GLN K 74 GLN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 HIS K 283 GLN ** K 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 429 HIS K 457 GLN A 389 GLN C 74 GLN C 265 HIS C 279 GLN C 283 GLN C 337 ASN C 341 GLN C 359 GLN C 429 HIS C 491 GLN C 531 HIS C 684 HIS C 708 HIS D 389 GLN H 198 GLN H 266 HIS H 389 GLN B 255 HIS B 265 HIS B 283 GLN B 429 HIS E 74 GLN ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 HIS E 457 GLN E 493 HIS G 194 HIS G 255 HIS G 265 HIS G 429 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5872 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 56088 Z= 0.198 Angle : 0.650 10.649 75726 Z= 0.344 Chirality : 0.047 0.329 8346 Planarity : 0.004 0.057 9924 Dihedral : 5.445 73.119 7887 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.87 % Allowed : 12.73 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.25 (0.10), residues: 7054 helix: 1.82 (0.10), residues: 2656 sheet: 0.84 (0.13), residues: 1334 loop : 0.02 (0.11), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 276 HIS 0.024 0.001 HIS I 708 PHE 0.022 0.002 PHE E 331 TYR 0.025 0.001 TYR D 145 ARG 0.008 0.001 ARG E 299 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 585 time to evaluate : 5.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 273 SER cc_start: 0.7273 (OUTLIER) cc_final: 0.6740 (p) REVERT: I 247 GLU cc_start: 0.1561 (OUTLIER) cc_final: 0.0349 (mt-10) REVERT: I 256 VAL cc_start: 0.5714 (OUTLIER) cc_final: 0.5504 (p) REVERT: I 331 PHE cc_start: 0.6799 (OUTLIER) cc_final: 0.6558 (p90) REVERT: J 205 ASN cc_start: 0.7669 (t0) cc_final: 0.6990 (t0) REVERT: J 425 MET cc_start: 0.7950 (ttp) cc_final: 0.7643 (ttp) REVERT: J 497 PHE cc_start: 0.4316 (t80) cc_final: 0.3892 (t80) REVERT: L 226 MET cc_start: 0.8348 (mmm) cc_final: 0.8124 (mtp) REVERT: L 260 LEU cc_start: 0.7794 (tp) cc_final: 0.7483 (pt) REVERT: K 274 ARG cc_start: 0.3408 (mtt180) cc_final: 0.3089 (mtt180) REVERT: K 349 MET cc_start: 0.3526 (mmm) cc_final: 0.3314 (tpt) REVERT: K 680 MET cc_start: 0.0899 (mtm) cc_final: -0.2562 (ppp) REVERT: A 158 GLU cc_start: 0.7495 (tt0) cc_final: 0.7285 (tt0) REVERT: A 228 ASP cc_start: 0.7918 (m-30) cc_final: 0.7337 (m-30) REVERT: A 273 SER cc_start: 0.7229 (OUTLIER) cc_final: 0.6604 (p) REVERT: C 160 MET cc_start: 0.3429 (tmm) cc_final: 0.3039 (ttp) REVERT: C 325 MET cc_start: 0.4155 (tmm) cc_final: 0.3837 (tmm) REVERT: C 329 HIS cc_start: 0.6245 (m-70) cc_final: 0.6031 (m-70) REVERT: C 331 PHE cc_start: 0.6930 (OUTLIER) cc_final: 0.6691 (p90) REVERT: D 205 ASN cc_start: 0.7637 (t0) cc_final: 0.7241 (t0) REVERT: D 497 PHE cc_start: 0.4083 (t80) cc_final: 0.3532 (t80) REVERT: H 226 MET cc_start: 0.8305 (mmm) cc_final: 0.8087 (mmm) REVERT: B 160 MET cc_start: 0.0898 (mpp) cc_final: -0.1927 (tpt) REVERT: B 349 MET cc_start: 0.3483 (mmm) cc_final: 0.3030 (mmp) REVERT: B 675 MET cc_start: 0.0023 (mmm) cc_final: -0.0672 (mmt) REVERT: E 167 LYS cc_start: 0.3020 (mmtt) cc_final: 0.2600 (mmtt) REVERT: E 274 ARG cc_start: 0.3342 (mtt180) cc_final: 0.3077 (mtt180) REVERT: E 680 MET cc_start: 0.0696 (mtm) cc_final: -0.1143 (ptt) REVERT: G 396 MET cc_start: 0.2375 (ttp) cc_final: 0.2133 (ttt) REVERT: G 675 MET cc_start: 0.0276 (mmm) cc_final: -0.0693 (mmm) outliers start: 109 outliers final: 43 residues processed: 662 average time/residue: 0.5793 time to fit residues: 633.2540 Evaluate side-chains 488 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 439 time to evaluate : 5.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 499 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 256 VAL Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 331 PHE Chi-restraints excluded: chain I residue 333 PHE Chi-restraints excluded: chain I residue 484 VAL Chi-restraints excluded: chain I residue 595 CYS Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain K residue 62 CYS Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 255 HIS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 595 CYS Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 618 ILE Chi-restraints excluded: chain B residue 623 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 197 ARG Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain G residue 385 ARG Chi-restraints excluded: chain G residue 418 THR Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 579 GLU Chi-restraints excluded: chain G residue 618 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 356 optimal weight: 30.0000 chunk 198 optimal weight: 7.9990 chunk 533 optimal weight: 8.9990 chunk 436 optimal weight: 2.9990 chunk 176 optimal weight: 10.0000 chunk 642 optimal weight: 20.0000 chunk 693 optimal weight: 8.9990 chunk 572 optimal weight: 50.0000 chunk 636 optimal weight: 20.0000 chunk 218 optimal weight: 10.0000 chunk 515 optimal weight: 30.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 198 GLN F 389 GLN I 255 HIS ** I 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 531 HIS ** I 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 107 GLN J 389 GLN J 433 GLN L 275 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 492 HIS K 546 ASN A 107 GLN A 198 GLN A 389 GLN ** C 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 459 ASN D 107 GLN D 275 HIS D 389 GLN D 449 ASN H 107 GLN H 275 HIS ** B 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 HIS ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS ** E 492 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 ASN E 684 HIS ** G 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 531 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6194 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 56088 Z= 0.428 Angle : 0.801 12.316 75726 Z= 0.416 Chirality : 0.050 0.385 8346 Planarity : 0.006 0.064 9924 Dihedral : 5.475 59.049 7850 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.73 % Allowed : 13.17 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.53 (0.10), residues: 7054 helix: 1.14 (0.10), residues: 2648 sheet: 0.56 (0.13), residues: 1334 loop : -0.35 (0.11), residues: 3072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 440 HIS 0.012 0.002 HIS E 684 PHE 0.034 0.003 PHE J 497 TYR 0.028 0.002 TYR B 387 ARG 0.013 0.001 ARG I 280 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 444 time to evaluate : 4.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: F 488 ASP cc_start: 0.8102 (m-30) cc_final: 0.7751 (m-30) REVERT: I 48 ASN cc_start: 0.7173 (OUTLIER) cc_final: 0.6966 (t0) REVERT: I 160 MET cc_start: 0.2661 (ttm) cc_final: 0.2363 (ttp) REVERT: I 272 PHE cc_start: 0.5211 (m-80) cc_final: 0.4961 (m-10) REVERT: I 334 MET cc_start: 0.2137 (ttt) cc_final: -0.0008 (ptp) REVERT: K 65 MET cc_start: 0.6542 (ttm) cc_final: 0.5485 (ttm) REVERT: K 274 ARG cc_start: 0.3496 (mtt180) cc_final: 0.2889 (mtt180) REVERT: K 421 ARG cc_start: 0.7647 (mtm110) cc_final: 0.7433 (mtm-85) REVERT: K 680 MET cc_start: 0.1004 (mtm) cc_final: -0.0650 (ptt) REVERT: A 158 GLU cc_start: 0.7438 (tt0) cc_final: 0.7222 (tt0) REVERT: A 228 ASP cc_start: 0.8747 (m-30) cc_final: 0.8455 (m-30) REVERT: C 160 MET cc_start: 0.3330 (tmm) cc_final: 0.3053 (ttp) REVERT: B 65 MET cc_start: 0.7555 (mtm) cc_final: 0.7265 (mtp) REVERT: B 249 PHE cc_start: 0.5414 (m-80) cc_final: 0.4856 (m-10) REVERT: B 675 MET cc_start: 0.0226 (mmm) cc_final: -0.0166 (mmt) REVERT: E 65 MET cc_start: 0.6615 (ttm) cc_final: 0.6051 (ttm) REVERT: E 167 LYS cc_start: 0.3162 (mmtt) cc_final: 0.2831 (mmtt) REVERT: E 274 ARG cc_start: 0.3999 (mtt180) cc_final: 0.3486 (mtt180) REVERT: E 680 MET cc_start: 0.0959 (mtm) cc_final: -0.0184 (ptt) REVERT: G 65 MET cc_start: 0.7480 (mtm) cc_final: 0.7262 (mtp) REVERT: G 160 MET cc_start: 0.0901 (mpp) cc_final: -0.1516 (tpt) REVERT: G 197 ARG cc_start: -0.3127 (OUTLIER) cc_final: -0.4054 (mmp80) REVERT: G 396 MET cc_start: 0.3579 (ttp) cc_final: 0.3351 (ttt) REVERT: G 675 MET cc_start: 0.0296 (mmm) cc_final: -0.0252 (mmt) outliers start: 159 outliers final: 83 residues processed: 571 average time/residue: 0.5404 time to fit residues: 514.7122 Evaluate side-chains 473 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 388 time to evaluate : 4.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 499 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 333 PHE Chi-restraints excluded: chain I residue 464 HIS Chi-restraints excluded: chain I residue 595 CYS Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain I residue 668 VAL Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 216 CYS Chi-restraints excluded: chain L residue 223 VAL Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain L residue 302 VAL Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 438 VAL Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 255 HIS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 464 HIS Chi-restraints excluded: chain C residue 595 CYS Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 301 ASP Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain H residue 170 LEU Chi-restraints excluded: chain H residue 216 CYS Chi-restraints excluded: chain H residue 223 VAL Chi-restraints excluded: chain H residue 273 SER Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 302 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 623 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 668 VAL Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 329 HIS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 708 HIS Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 197 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 255 HIS Chi-restraints excluded: chain G residue 276 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain G residue 386 ILE Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 579 GLU Chi-restraints excluded: chain G residue 662 VAL Chi-restraints excluded: chain G residue 668 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 634 optimal weight: 0.6980 chunk 482 optimal weight: 8.9990 chunk 333 optimal weight: 6.9990 chunk 71 optimal weight: 50.0000 chunk 306 optimal weight: 5.9990 chunk 431 optimal weight: 1.9990 chunk 644 optimal weight: 20.0000 chunk 682 optimal weight: 8.9990 chunk 336 optimal weight: 4.9990 chunk 610 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 341 GLN J 107 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 330 ASN K 404 HIS K 531 HIS A 107 GLN C 459 ASN D 107 GLN D 433 GLN H 107 GLN B 85 ASN B 88 HIS B 394 ASN E 88 HIS ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 ASN E 404 HIS E 492 HIS G 85 ASN G 88 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6134 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 56088 Z= 0.199 Angle : 0.583 11.664 75726 Z= 0.302 Chirality : 0.045 0.269 8346 Planarity : 0.004 0.047 9924 Dihedral : 4.987 58.930 7850 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.87 % Allowed : 14.27 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.89 (0.10), residues: 7054 helix: 1.65 (0.10), residues: 2642 sheet: 0.67 (0.13), residues: 1284 loop : -0.30 (0.11), residues: 3128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 276 HIS 0.009 0.001 HIS C 255 PHE 0.015 0.001 PHE G 224 TYR 0.021 0.001 TYR C 270 ARG 0.008 0.000 ARG K 299 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 432 time to evaluate : 4.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 201 MET cc_start: 0.7812 (mmm) cc_final: 0.7540 (mmm) REVERT: F 273 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.7630 (p) REVERT: I 48 ASN cc_start: 0.7149 (OUTLIER) cc_final: 0.6948 (t0) REVERT: I 334 MET cc_start: 0.1776 (ttt) cc_final: -0.0176 (ptm) REVERT: I 349 MET cc_start: -0.0935 (ttt) cc_final: -0.2254 (mtt) REVERT: L 408 MET cc_start: 0.5921 (pmm) cc_final: 0.5340 (pmm) REVERT: K 65 MET cc_start: 0.6422 (ttm) cc_final: 0.5605 (ttm) REVERT: K 215 MET cc_start: 0.0334 (mmt) cc_final: -0.0006 (mmp) REVERT: K 274 ARG cc_start: 0.3275 (mtt180) cc_final: 0.2855 (mtm-85) REVERT: K 463 LEU cc_start: 0.4904 (OUTLIER) cc_final: 0.4619 (pp) REVERT: K 680 MET cc_start: 0.0915 (mtm) cc_final: -0.0638 (ptt) REVERT: A 158 GLU cc_start: 0.7687 (tt0) cc_final: 0.7385 (tt0) REVERT: A 161 MET cc_start: 0.8413 (tmm) cc_final: 0.8183 (tmm) REVERT: C 160 MET cc_start: 0.3074 (tmm) cc_final: 0.2811 (ttm) REVERT: C 216 ARG cc_start: 0.0748 (OUTLIER) cc_final: -0.0420 (mpt-90) REVERT: C 349 MET cc_start: -0.0072 (ttt) cc_final: -0.1269 (mtt) REVERT: D 555 LYS cc_start: 0.8934 (tppt) cc_final: 0.8658 (tptt) REVERT: H 408 MET cc_start: 0.5747 (pmm) cc_final: 0.5259 (pmm) REVERT: H 452 MET cc_start: 0.8569 (mmm) cc_final: 0.8366 (mmm) REVERT: B 65 MET cc_start: 0.7354 (mtm) cc_final: 0.6970 (mtp) REVERT: B 249 PHE cc_start: 0.5681 (m-80) cc_final: 0.5204 (m-10) REVERT: B 513 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8604 (mm) REVERT: B 675 MET cc_start: 0.0244 (mmm) cc_final: -0.0170 (mmt) REVERT: E 167 LYS cc_start: 0.3096 (mmtt) cc_final: 0.2667 (mmtt) REVERT: E 274 ARG cc_start: 0.3691 (mtt180) cc_final: 0.3322 (mtt180) REVERT: E 680 MET cc_start: 0.0277 (mtm) cc_final: -0.0490 (ptt) REVERT: E 682 MET cc_start: -0.3931 (ttt) cc_final: -0.4298 (ttp) REVERT: G 65 MET cc_start: 0.7501 (mtm) cc_final: 0.7203 (mtp) REVERT: G 197 ARG cc_start: -0.3206 (OUTLIER) cc_final: -0.4029 (mmp80) REVERT: G 675 MET cc_start: 0.0657 (mmm) cc_final: 0.0102 (mmt) outliers start: 109 outliers final: 61 residues processed: 514 average time/residue: 0.5258 time to fit residues: 452.4831 Evaluate side-chains 443 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 376 time to evaluate : 4.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 499 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 333 PHE Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain L residue 216 CYS Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 329 HIS Chi-restraints excluded: chain K residue 394 ASN Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 618 ILE Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 216 ARG Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 255 HIS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain H residue 216 CYS Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 329 HIS Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 708 HIS Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 197 ARG Chi-restraints excluded: chain G residue 255 HIS Chi-restraints excluded: chain G residue 276 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 472 ASN Chi-restraints excluded: chain G residue 579 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 568 optimal weight: 30.0000 chunk 387 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 508 optimal weight: 0.5980 chunk 281 optimal weight: 0.5980 chunk 582 optimal weight: 1.9990 chunk 471 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 348 optimal weight: 0.2980 chunk 612 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 344 HIS I 616 ASN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 275 HIS D 433 GLN ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.4538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 56088 Z= 0.153 Angle : 0.566 15.483 75726 Z= 0.288 Chirality : 0.044 0.390 8346 Planarity : 0.004 0.048 9924 Dihedral : 4.740 59.795 7850 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.80 % Allowed : 14.12 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.02 (0.10), residues: 7054 helix: 1.82 (0.10), residues: 2648 sheet: 0.71 (0.13), residues: 1338 loop : -0.31 (0.11), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 276 HIS 0.011 0.001 HIS C 255 PHE 0.019 0.001 PHE B 149 TYR 0.019 0.001 TYR B 387 ARG 0.011 0.000 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 415 time to evaluate : 4.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 273 SER cc_start: 0.8390 (OUTLIER) cc_final: 0.7577 (p) REVERT: I 334 MET cc_start: 0.1935 (ttt) cc_final: -0.0099 (ptp) REVERT: L 408 MET cc_start: 0.5630 (pmm) cc_final: 0.5123 (pmm) REVERT: L 452 MET cc_start: 0.8666 (mmm) cc_final: 0.8212 (mmm) REVERT: K 65 MET cc_start: 0.6480 (ttm) cc_final: 0.5657 (ttm) REVERT: K 215 MET cc_start: 0.0307 (mmt) cc_final: 0.0030 (mmp) REVERT: K 274 ARG cc_start: 0.3444 (mtt180) cc_final: 0.2957 (mtt180) REVERT: K 463 LEU cc_start: 0.4814 (OUTLIER) cc_final: 0.4610 (pp) REVERT: K 680 MET cc_start: 0.0646 (mtm) cc_final: -0.0844 (ptt) REVERT: A 273 SER cc_start: 0.8420 (OUTLIER) cc_final: 0.7725 (p) REVERT: C 349 MET cc_start: -0.0672 (ttt) cc_final: -0.1706 (mtp) REVERT: H 213 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8099 (tpp) REVERT: H 408 MET cc_start: 0.5544 (pmm) cc_final: 0.5095 (pmm) REVERT: B 65 MET cc_start: 0.7395 (mtt) cc_final: 0.7107 (mtp) REVERT: B 160 MET cc_start: 0.1065 (mpp) cc_final: -0.1840 (tpt) REVERT: B 249 PHE cc_start: 0.5409 (m-80) cc_final: 0.4969 (m-10) REVERT: B 675 MET cc_start: 0.0202 (mmm) cc_final: -0.0093 (mmt) REVERT: E 65 MET cc_start: 0.6485 (ttm) cc_final: 0.5544 (ttm) REVERT: E 167 LYS cc_start: 0.3003 (mmtt) cc_final: 0.2779 (mmtt) REVERT: E 274 ARG cc_start: 0.3687 (mtt180) cc_final: 0.3340 (mtm-85) REVERT: E 680 MET cc_start: 0.0908 (mtm) cc_final: -0.0538 (ptt) REVERT: G 65 MET cc_start: 0.7601 (mtm) cc_final: 0.7216 (mtp) REVERT: G 66 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7424 (tpp80) REVERT: G 170 MET cc_start: 0.0517 (mmm) cc_final: -0.0041 (mmp) REVERT: G 197 ARG cc_start: -0.3389 (OUTLIER) cc_final: -0.4173 (mmp80) REVERT: G 675 MET cc_start: 0.0547 (mmm) cc_final: -0.0019 (mmt) outliers start: 105 outliers final: 72 residues processed: 492 average time/residue: 0.5307 time to fit residues: 442.4966 Evaluate side-chains 459 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 381 time to evaluate : 4.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 499 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 333 PHE Chi-restraints excluded: chain I residue 407 THR Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain I residue 631 ILE Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain L residue 216 CYS Chi-restraints excluded: chain L residue 229 GLU Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 438 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 618 ILE Chi-restraints excluded: chain K residue 712 VAL Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 255 HIS Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain H residue 213 MET Chi-restraints excluded: chain H residue 216 CYS Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 273 SER Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 556 THR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain E residue 138 PHE Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 197 ARG Chi-restraints excluded: chain G residue 255 HIS Chi-restraints excluded: chain G residue 276 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 472 ASN Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 579 GLU Chi-restraints excluded: chain G residue 623 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 229 optimal weight: 6.9990 chunk 614 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 chunk 400 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 683 optimal weight: 20.0000 chunk 567 optimal weight: 3.9990 chunk 316 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 225 optimal weight: 20.0000 chunk 358 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 281 HIS ** I 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 283 GLN I 344 HIS I 616 ASN L 111 ASN L 153 GLN ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 259 GLN A 281 HIS ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN H 111 ASN ** H 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 56088 Z= 0.292 Angle : 0.629 14.421 75726 Z= 0.322 Chirality : 0.045 0.311 8346 Planarity : 0.004 0.079 9924 Dihedral : 4.799 59.500 7845 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.21 % Allowed : 14.60 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 0.86 (0.10), residues: 7054 helix: 1.70 (0.10), residues: 2646 sheet: 0.63 (0.14), residues: 1320 loop : -0.41 (0.11), residues: 3088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 276 HIS 0.008 0.001 HIS D 62 PHE 0.023 0.002 PHE J 497 TYR 0.019 0.001 TYR C 96 ARG 0.009 0.001 ARG I 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 395 time to evaluate : 4.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 273 SER cc_start: 0.8808 (OUTLIER) cc_final: 0.8067 (p) REVERT: I 334 MET cc_start: 0.2393 (ttt) cc_final: 0.0329 (ptm) REVERT: I 349 MET cc_start: -0.0355 (ttt) cc_final: -0.2001 (mtt) REVERT: J 555 LYS cc_start: 0.8829 (tppt) cc_final: 0.8431 (tptt) REVERT: L 408 MET cc_start: 0.6028 (pmm) cc_final: 0.5432 (pmm) REVERT: K 65 MET cc_start: 0.6601 (ttm) cc_final: 0.5651 (mmm) REVERT: K 215 MET cc_start: 0.0517 (mmt) cc_final: 0.0307 (mmp) REVERT: K 274 ARG cc_start: 0.3734 (mtt180) cc_final: 0.3014 (mtt180) REVERT: K 463 LEU cc_start: 0.5046 (OUTLIER) cc_final: 0.4507 (pp) REVERT: K 680 MET cc_start: 0.0243 (mtm) cc_final: -0.0770 (ptt) REVERT: A 273 SER cc_start: 0.8730 (OUTLIER) cc_final: 0.7976 (p) REVERT: D 555 LYS cc_start: 0.8808 (tppt) cc_final: 0.8604 (tppt) REVERT: H 408 MET cc_start: 0.5829 (pmm) cc_final: 0.5317 (pmm) REVERT: B 65 MET cc_start: 0.7317 (mtt) cc_final: 0.6714 (mtp) REVERT: B 249 PHE cc_start: 0.5765 (m-80) cc_final: 0.5172 (m-10) REVERT: B 513 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8713 (mm) REVERT: B 675 MET cc_start: 0.0444 (mmm) cc_final: 0.0001 (mmt) REVERT: E 65 MET cc_start: 0.6336 (ttm) cc_final: 0.6090 (ttp) REVERT: E 167 LYS cc_start: 0.3057 (mmtt) cc_final: 0.2817 (mmtt) REVERT: E 274 ARG cc_start: 0.3863 (mtt180) cc_final: 0.3402 (mtm-85) REVERT: E 680 MET cc_start: 0.0276 (mtm) cc_final: -0.0019 (ptt) REVERT: G 65 MET cc_start: 0.7618 (mtm) cc_final: 0.7184 (mtp) REVERT: G 66 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7557 (tpp80) REVERT: G 170 MET cc_start: 0.0454 (OUTLIER) cc_final: -0.0143 (mmp) REVERT: G 197 ARG cc_start: -0.3039 (OUTLIER) cc_final: -0.4195 (mmp80) REVERT: G 675 MET cc_start: 0.0606 (mmm) cc_final: -0.0046 (mmt) outliers start: 129 outliers final: 87 residues processed: 489 average time/residue: 0.5203 time to fit residues: 431.4580 Evaluate side-chains 469 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 375 time to evaluate : 4.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 331 VAL Chi-restraints excluded: chain F residue 499 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 333 PHE Chi-restraints excluded: chain I residue 407 THR Chi-restraints excluded: chain I residue 595 CYS Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain I residue 694 VAL Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 145 TYR Chi-restraints excluded: chain L residue 216 CYS Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain L residue 299 LYS Chi-restraints excluded: chain L residue 426 VAL Chi-restraints excluded: chain L residue 449 ASN Chi-restraints excluded: chain K residue 136 MET Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 438 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 576 MET Chi-restraints excluded: chain K residue 618 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 255 HIS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 595 CYS Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 145 TYR Chi-restraints excluded: chain H residue 216 CYS Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 265 HIS Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 329 HIS Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 708 HIS Chi-restraints excluded: chain G residue 66 ARG Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 197 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 255 HIS Chi-restraints excluded: chain G residue 270 TYR Chi-restraints excluded: chain G residue 276 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 472 ASN Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 579 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 658 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 389 optimal weight: 0.6980 chunk 498 optimal weight: 7.9990 chunk 386 optimal weight: 2.9990 chunk 575 optimal weight: 0.0670 chunk 381 optimal weight: 20.0000 chunk 680 optimal weight: 20.0000 chunk 425 optimal weight: 0.9990 chunk 414 optimal weight: 6.9990 chunk 314 optimal weight: 0.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 102 GLN ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6142 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 56088 Z= 0.150 Angle : 0.560 14.370 75726 Z= 0.284 Chirality : 0.044 0.311 8346 Planarity : 0.004 0.048 9924 Dihedral : 4.556 58.920 7844 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.80 % Allowed : 15.18 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.00 (0.10), residues: 7054 helix: 1.89 (0.10), residues: 2656 sheet: 0.63 (0.14), residues: 1322 loop : -0.37 (0.11), residues: 3076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 276 HIS 0.007 0.001 HIS C 255 PHE 0.013 0.001 PHE J 497 TYR 0.016 0.001 TYR G 387 ARG 0.006 0.000 ARG K 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 401 time to evaluate : 4.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 273 SER cc_start: 0.8666 (OUTLIER) cc_final: 0.7923 (p) REVERT: I 65 MET cc_start: 0.3349 (ttp) cc_final: 0.3142 (ttm) REVERT: I 91 MET cc_start: 0.3890 (ptp) cc_final: 0.3381 (ptp) REVERT: I 334 MET cc_start: 0.2223 (ttt) cc_final: 0.0158 (ptp) REVERT: I 349 MET cc_start: -0.0082 (ttt) cc_final: -0.2188 (mtt) REVERT: I 520 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7799 (tppt) REVERT: J 49 MET cc_start: 0.8502 (tpp) cc_final: 0.8224 (tpp) REVERT: J 213 MET cc_start: 0.8138 (tmm) cc_final: 0.7916 (tmm) REVERT: L 408 MET cc_start: 0.5868 (pmm) cc_final: 0.5313 (pmm) REVERT: K 65 MET cc_start: 0.6200 (ttm) cc_final: 0.5544 (mmm) REVERT: K 110 MET cc_start: 0.2016 (tpp) cc_final: 0.1813 (tpp) REVERT: K 215 MET cc_start: 0.0494 (mmt) cc_final: 0.0247 (mmp) REVERT: K 274 ARG cc_start: 0.3528 (mtt180) cc_final: 0.2843 (mtm-85) REVERT: K 463 LEU cc_start: 0.4916 (OUTLIER) cc_final: 0.4444 (pp) REVERT: K 680 MET cc_start: 0.0175 (mtm) cc_final: -0.0929 (ptt) REVERT: A 110 ASP cc_start: 0.8911 (OUTLIER) cc_final: 0.8614 (p0) REVERT: A 273 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.7823 (p) REVERT: C 349 MET cc_start: -0.0746 (ttt) cc_final: -0.2157 (mtt) REVERT: C 407 THR cc_start: 0.5724 (OUTLIER) cc_final: 0.5416 (t) REVERT: C 520 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8000 (tppt) REVERT: H 408 MET cc_start: 0.5746 (pmm) cc_final: 0.5232 (pmm) REVERT: H 452 MET cc_start: 0.8666 (mmm) cc_final: 0.8380 (mtp) REVERT: B 65 MET cc_start: 0.7378 (mtt) cc_final: 0.6768 (mtp) REVERT: B 160 MET cc_start: 0.0953 (mpp) cc_final: -0.1085 (mmt) REVERT: B 170 MET cc_start: 0.0530 (OUTLIER) cc_final: 0.0068 (mmp) REVERT: B 249 PHE cc_start: 0.5620 (m-80) cc_final: 0.5064 (m-10) REVERT: B 513 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8667 (mm) REVERT: B 675 MET cc_start: 0.0229 (mmm) cc_final: -0.0107 (mmt) REVERT: E 65 MET cc_start: 0.6414 (ttm) cc_final: 0.5759 (ttm) REVERT: E 167 LYS cc_start: 0.2915 (mmtt) cc_final: 0.2688 (mmtt) REVERT: G 65 MET cc_start: 0.7672 (mtm) cc_final: 0.7074 (mtp) REVERT: G 160 MET cc_start: 0.0429 (mpp) cc_final: -0.1847 (mmt) REVERT: G 170 MET cc_start: 0.0508 (OUTLIER) cc_final: -0.0144 (mmp) REVERT: G 197 ARG cc_start: -0.3054 (OUTLIER) cc_final: -0.4122 (mmp80) REVERT: G 675 MET cc_start: 0.0667 (mmm) cc_final: 0.0061 (mmt) outliers start: 105 outliers final: 81 residues processed: 473 average time/residue: 0.5184 time to fit residues: 417.3140 Evaluate side-chains 475 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 383 time to evaluate : 4.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 110 ASP Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 240 PHE Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 499 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 331 PHE Chi-restraints excluded: chain I residue 333 PHE Chi-restraints excluded: chain I residue 520 LYS Chi-restraints excluded: chain I residue 588 ASN Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain I residue 694 VAL Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain L residue 145 TYR Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 229 GLU Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain K residue 136 MET Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 278 VAL Chi-restraints excluded: chain K residue 438 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 618 ILE Chi-restraints excluded: chain A residue 110 ASP Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 255 HIS Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 PHE Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 520 LYS Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain H residue 229 GLU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 449 ASN Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 402 LEU Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain E residue 265 HIS Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain G residue 148 ILE Chi-restraints excluded: chain G residue 170 MET Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 197 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 255 HIS Chi-restraints excluded: chain G residue 276 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 330 ASN Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 472 ASN Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 576 MET Chi-restraints excluded: chain G residue 579 GLU Chi-restraints excluded: chain G residue 623 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 420 optimal weight: 1.9990 chunk 271 optimal weight: 20.0000 chunk 406 optimal weight: 5.9990 chunk 204 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 131 optimal weight: 0.7980 chunk 432 optimal weight: 1.9990 chunk 463 optimal weight: 2.9990 chunk 336 optimal weight: 0.9980 chunk 63 optimal weight: 20.0000 chunk 534 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 264 HIS A 198 GLN ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6133 moved from start: 0.5204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 56088 Z= 0.146 Angle : 0.556 15.219 75726 Z= 0.280 Chirality : 0.044 0.384 8346 Planarity : 0.004 0.049 9924 Dihedral : 4.409 59.412 7844 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.70 % Allowed : 15.40 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.09 (0.10), residues: 7054 helix: 1.99 (0.10), residues: 2654 sheet: 0.64 (0.14), residues: 1316 loop : -0.32 (0.11), residues: 3084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP L 276 HIS 0.006 0.001 HIS C 255 PHE 0.023 0.001 PHE I 323 TYR 0.017 0.001 TYR B 453 ARG 0.006 0.000 ARG J 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 404 time to evaluate : 4.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 273 SER cc_start: 0.8710 (OUTLIER) cc_final: 0.7987 (p) REVERT: I 65 MET cc_start: 0.3242 (ttp) cc_final: 0.3025 (ttm) REVERT: I 91 MET cc_start: 0.3817 (ptp) cc_final: 0.3283 (ptp) REVERT: I 334 MET cc_start: 0.2201 (ttt) cc_final: 0.0182 (ptp) REVERT: I 520 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8028 (tppt) REVERT: J 49 MET cc_start: 0.8503 (tpp) cc_final: 0.8246 (tpp) REVERT: J 213 MET cc_start: 0.7909 (tmm) cc_final: 0.7641 (tmm) REVERT: J 490 ARG cc_start: 0.8549 (mtp-110) cc_final: 0.8269 (mtp-110) REVERT: J 555 LYS cc_start: 0.8777 (tptt) cc_final: 0.8514 (tppt) REVERT: L 408 MET cc_start: 0.5888 (pmm) cc_final: 0.5324 (pmm) REVERT: K 65 MET cc_start: 0.6383 (ttm) cc_final: 0.5739 (ttm) REVERT: K 215 MET cc_start: 0.0429 (mmt) cc_final: 0.0204 (mmp) REVERT: K 463 LEU cc_start: 0.4779 (OUTLIER) cc_final: 0.4302 (pp) REVERT: K 680 MET cc_start: 0.0330 (mtm) cc_final: -0.0188 (ptt) REVERT: A 273 SER cc_start: 0.8637 (OUTLIER) cc_final: 0.7895 (p) REVERT: C 349 MET cc_start: -0.0468 (ttt) cc_final: -0.1979 (mtt) REVERT: C 407 THR cc_start: 0.5735 (OUTLIER) cc_final: 0.5448 (t) REVERT: D 555 LYS cc_start: 0.8691 (tppt) cc_final: 0.8270 (tptt) REVERT: H 408 MET cc_start: 0.5641 (pmm) cc_final: 0.5225 (pmm) REVERT: B 65 MET cc_start: 0.7283 (mtt) cc_final: 0.6317 (ttm) REVERT: B 160 MET cc_start: 0.0796 (mpp) cc_final: -0.1051 (mmt) REVERT: B 170 MET cc_start: 0.0348 (OUTLIER) cc_final: 0.0029 (mmp) REVERT: B 675 MET cc_start: 0.0228 (mmm) cc_final: -0.0124 (mmt) REVERT: E 65 MET cc_start: 0.6340 (ttm) cc_final: 0.5766 (ttm) REVERT: E 167 LYS cc_start: 0.2930 (mmtt) cc_final: 0.2720 (mmtt) REVERT: E 274 ARG cc_start: 0.3713 (mtt180) cc_final: 0.3072 (mtm180) REVERT: E 680 MET cc_start: 0.0846 (ptt) cc_final: 0.0522 (ppp) REVERT: G 65 MET cc_start: 0.7787 (mtm) cc_final: 0.7428 (mtp) REVERT: G 91 MET cc_start: 0.5920 (ptm) cc_final: 0.5536 (ptm) REVERT: G 160 MET cc_start: 0.0194 (mpp) cc_final: -0.1714 (mmt) REVERT: G 197 ARG cc_start: -0.3074 (OUTLIER) cc_final: -0.4185 (mmp80) REVERT: G 675 MET cc_start: 0.0739 (mmm) cc_final: 0.0175 (mmt) outliers start: 99 outliers final: 73 residues processed: 471 average time/residue: 0.5921 time to fit residues: 472.4951 Evaluate side-chains 465 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 385 time to evaluate : 4.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 499 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 331 PHE Chi-restraints excluded: chain I residue 333 PHE Chi-restraints excluded: chain I residue 520 LYS Chi-restraints excluded: chain I residue 588 ASN Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain I residue 631 ILE Chi-restraints excluded: chain I residue 694 VAL Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain L residue 145 TYR Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain K residue 136 MET Chi-restraints excluded: chain K residue 175 VAL Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 438 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 618 ILE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 255 HIS Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 449 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 330 ASN Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain E residue 265 HIS Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 197 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 255 HIS Chi-restraints excluded: chain G residue 276 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 472 ASN Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 576 MET Chi-restraints excluded: chain G residue 579 GLU Chi-restraints excluded: chain G residue 623 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 618 optimal weight: 6.9990 chunk 651 optimal weight: 3.9990 chunk 594 optimal weight: 9.9990 chunk 634 optimal weight: 10.0000 chunk 381 optimal weight: 0.7980 chunk 276 optimal weight: 5.9990 chunk 497 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 573 optimal weight: 0.0980 chunk 599 optimal weight: 6.9990 chunk 631 optimal weight: 0.9980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 HIS H 275 HIS ** E 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.5363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 56088 Z= 0.174 Angle : 0.562 13.357 75726 Z= 0.284 Chirality : 0.044 0.252 8346 Planarity : 0.004 0.055 9924 Dihedral : 4.397 59.400 7844 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.63 % Allowed : 15.80 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.07 (0.10), residues: 7054 helix: 2.00 (0.10), residues: 2656 sheet: 0.56 (0.14), residues: 1338 loop : -0.33 (0.11), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP L 276 HIS 0.005 0.001 HIS F 266 PHE 0.022 0.001 PHE I 323 TYR 0.014 0.001 TYR G 387 ARG 0.009 0.000 ARG K 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 398 time to evaluate : 4.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: F 273 SER cc_start: 0.8714 (OUTLIER) cc_final: 0.7979 (p) REVERT: I 65 MET cc_start: 0.3233 (ttp) cc_final: 0.2991 (ttm) REVERT: I 91 MET cc_start: 0.3760 (ptp) cc_final: 0.3123 (ptp) REVERT: I 274 ARG cc_start: 0.4566 (mtt180) cc_final: 0.3190 (tpt-90) REVERT: I 349 MET cc_start: -0.0779 (ttt) cc_final: -0.1164 (mtp) REVERT: I 520 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8066 (tppt) REVERT: L 408 MET cc_start: 0.5830 (pmm) cc_final: 0.5326 (pmm) REVERT: K 65 MET cc_start: 0.6436 (ttm) cc_final: 0.5804 (ttm) REVERT: K 215 MET cc_start: 0.0290 (mmt) cc_final: 0.0086 (mmp) REVERT: K 325 MET cc_start: 0.1742 (mmm) cc_final: 0.1400 (mmm) REVERT: K 463 LEU cc_start: 0.4904 (OUTLIER) cc_final: 0.4419 (pp) REVERT: K 680 MET cc_start: 0.0369 (mtm) cc_final: -0.0192 (ptt) REVERT: A 273 SER cc_start: 0.8629 (OUTLIER) cc_final: 0.7916 (p) REVERT: C 334 MET cc_start: 0.3365 (OUTLIER) cc_final: 0.3124 (mpp) REVERT: C 349 MET cc_start: -0.0299 (ttt) cc_final: -0.1843 (mtm) REVERT: C 407 THR cc_start: 0.5760 (OUTLIER) cc_final: 0.5446 (t) REVERT: C 520 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8117 (tppt) REVERT: D 555 LYS cc_start: 0.8734 (tppt) cc_final: 0.8488 (tptt) REVERT: H 408 MET cc_start: 0.5787 (pmm) cc_final: 0.5319 (pmm) REVERT: B 65 MET cc_start: 0.7318 (mtt) cc_final: 0.6444 (mtp) REVERT: B 160 MET cc_start: 0.0627 (mpp) cc_final: -0.1378 (mmt) REVERT: B 170 MET cc_start: 0.0247 (OUTLIER) cc_final: 0.0018 (mmp) REVERT: B 675 MET cc_start: 0.0424 (mmm) cc_final: 0.0017 (mmt) REVERT: E 65 MET cc_start: 0.6472 (ttm) cc_final: 0.5804 (ttm) REVERT: E 167 LYS cc_start: 0.2926 (mmtt) cc_final: 0.2562 (mmtt) REVERT: E 274 ARG cc_start: 0.3789 (mtt180) cc_final: 0.3183 (mtm180) REVERT: E 682 MET cc_start: -0.3874 (tmm) cc_final: -0.4087 (tmm) REVERT: G 65 MET cc_start: 0.7715 (mtm) cc_final: 0.7448 (mtp) REVERT: G 110 MET cc_start: 0.6244 (mtp) cc_final: 0.5941 (mtt) REVERT: G 160 MET cc_start: 0.0828 (mpp) cc_final: -0.1049 (mmt) REVERT: G 197 ARG cc_start: -0.3210 (OUTLIER) cc_final: -0.4231 (mmp80) REVERT: G 675 MET cc_start: 0.0765 (mmm) cc_final: 0.0212 (mmt) outliers start: 95 outliers final: 77 residues processed: 461 average time/residue: 0.5227 time to fit residues: 405.8778 Evaluate side-chains 474 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 388 time to evaluate : 4.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 499 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 333 PHE Chi-restraints excluded: chain I residue 520 LYS Chi-restraints excluded: chain I residue 588 ASN Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain I residue 631 ILE Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 694 VAL Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain K residue 136 MET Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 438 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 618 ILE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 255 HIS Chi-restraints excluded: chain C residue 256 VAL Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 520 LYS Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 449 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain E residue 265 HIS Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 197 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 255 HIS Chi-restraints excluded: chain G residue 276 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 472 ASN Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 576 MET Chi-restraints excluded: chain G residue 579 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 416 optimal weight: 0.3980 chunk 670 optimal weight: 9.9990 chunk 409 optimal weight: 9.9990 chunk 318 optimal weight: 4.9990 chunk 466 optimal weight: 10.0000 chunk 703 optimal weight: 6.9990 chunk 647 optimal weight: 0.0270 chunk 560 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 432 optimal weight: 4.9990 chunk 343 optimal weight: 0.9990 overall best weight: 2.0844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 329 HIS ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 HIS ** G 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6153 moved from start: 0.5467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 56088 Z= 0.166 Angle : 0.571 13.818 75726 Z= 0.287 Chirality : 0.044 0.260 8346 Planarity : 0.004 0.056 9924 Dihedral : 4.369 58.813 7844 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.53 % Allowed : 15.85 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.03 (0.10), residues: 7054 helix: 1.95 (0.10), residues: 2688 sheet: 0.54 (0.14), residues: 1318 loop : -0.36 (0.11), residues: 3048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 276 HIS 0.008 0.001 HIS C 255 PHE 0.023 0.001 PHE J 497 TYR 0.017 0.001 TYR G 453 ARG 0.007 0.000 ARG B 421 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14108 Ramachandran restraints generated. 7054 Oldfield, 0 Emsley, 7054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 393 time to evaluate : 4.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: F 273 SER cc_start: 0.8720 (OUTLIER) cc_final: 0.8005 (p) REVERT: I 65 MET cc_start: 0.3243 (ttp) cc_final: 0.2999 (ttm) REVERT: I 91 MET cc_start: 0.3740 (ptp) cc_final: 0.3090 (ptp) REVERT: I 160 MET cc_start: 0.2961 (tpp) cc_final: 0.2687 (tpp) REVERT: I 274 ARG cc_start: 0.4388 (mtt180) cc_final: 0.3756 (mpt-90) REVERT: I 349 MET cc_start: -0.0572 (ttt) cc_final: -0.1673 (mtt) REVERT: I 417 GLU cc_start: 0.3490 (OUTLIER) cc_final: 0.3203 (mt-10) REVERT: I 520 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8082 (tppt) REVERT: L 408 MET cc_start: 0.5949 (pmm) cc_final: 0.5382 (pmm) REVERT: K 65 MET cc_start: 0.6415 (ttm) cc_final: 0.5798 (ttm) REVERT: K 215 MET cc_start: 0.0271 (mmt) cc_final: -0.0007 (mmp) REVERT: K 325 MET cc_start: 0.1758 (mmm) cc_final: 0.1425 (mmm) REVERT: K 463 LEU cc_start: 0.4942 (OUTLIER) cc_final: 0.4447 (pp) REVERT: K 680 MET cc_start: 0.0419 (mtm) cc_final: -0.0236 (ptt) REVERT: A 273 SER cc_start: 0.8705 (OUTLIER) cc_final: 0.7982 (p) REVERT: C 255 HIS cc_start: 0.5088 (t-90) cc_final: 0.4025 (t-170) REVERT: C 349 MET cc_start: -0.0465 (ttt) cc_final: -0.1988 (mtm) REVERT: C 407 THR cc_start: 0.5638 (OUTLIER) cc_final: 0.5312 (t) REVERT: C 520 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8099 (tppt) REVERT: D 555 LYS cc_start: 0.8792 (tppt) cc_final: 0.8513 (tptt) REVERT: H 408 MET cc_start: 0.5817 (pmm) cc_final: 0.5354 (pmm) REVERT: B 65 MET cc_start: 0.7624 (mtt) cc_final: 0.7315 (mtp) REVERT: B 87 MET cc_start: 0.4565 (tmm) cc_final: 0.4090 (tmm) REVERT: B 160 MET cc_start: 0.0306 (mpp) cc_final: -0.1653 (mmt) REVERT: B 170 MET cc_start: 0.0200 (OUTLIER) cc_final: -0.0017 (mmp) REVERT: B 675 MET cc_start: 0.0457 (mmm) cc_final: 0.0164 (mmt) REVERT: E 65 MET cc_start: 0.6591 (ttm) cc_final: 0.5896 (ttm) REVERT: E 274 ARG cc_start: 0.3728 (mtt180) cc_final: 0.3247 (mtm180) REVERT: E 682 MET cc_start: -0.3944 (tmm) cc_final: -0.4257 (tmm) REVERT: G 65 MET cc_start: 0.7783 (mtm) cc_final: 0.7529 (mtp) REVERT: G 87 MET cc_start: 0.4792 (tmm) cc_final: 0.4581 (tmm) REVERT: G 110 MET cc_start: 0.6241 (mtp) cc_final: 0.5932 (mtt) REVERT: G 160 MET cc_start: 0.0440 (mpp) cc_final: -0.1062 (mmt) REVERT: G 197 ARG cc_start: -0.3206 (OUTLIER) cc_final: -0.4243 (mmp80) REVERT: G 675 MET cc_start: 0.0742 (mmm) cc_final: 0.0366 (mmt) outliers start: 89 outliers final: 76 residues processed: 456 average time/residue: 0.5407 time to fit residues: 413.8694 Evaluate side-chains 468 residues out of total 5830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 383 time to evaluate : 4.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 132 MET Chi-restraints excluded: chain F residue 273 SER Chi-restraints excluded: chain F residue 294 LEU Chi-restraints excluded: chain F residue 300 LEU Chi-restraints excluded: chain F residue 499 SER Chi-restraints excluded: chain F residue 549 LEU Chi-restraints excluded: chain I residue 245 LEU Chi-restraints excluded: chain I residue 247 GLU Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 333 PHE Chi-restraints excluded: chain I residue 417 GLU Chi-restraints excluded: chain I residue 520 LYS Chi-restraints excluded: chain I residue 588 ASN Chi-restraints excluded: chain I residue 611 LEU Chi-restraints excluded: chain I residue 631 ILE Chi-restraints excluded: chain I residue 663 LYS Chi-restraints excluded: chain I residue 694 VAL Chi-restraints excluded: chain J residue 74 LEU Chi-restraints excluded: chain J residue 165 LEU Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 510 ILE Chi-restraints excluded: chain L residue 294 LEU Chi-restraints excluded: chain K residue 136 MET Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 265 HIS Chi-restraints excluded: chain K residue 438 VAL Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 618 ILE Chi-restraints excluded: chain A residue 132 MET Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain C residue 48 ASN Chi-restraints excluded: chain C residue 51 LYS Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 247 GLU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 407 THR Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 520 LYS Chi-restraints excluded: chain C residue 588 ASN Chi-restraints excluded: chain C residue 668 VAL Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 165 LEU Chi-restraints excluded: chain D residue 300 LEU Chi-restraints excluded: chain D residue 482 LEU Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 449 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 218 VAL Chi-restraints excluded: chain B residue 255 HIS Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 276 CYS Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 387 TYR Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 472 ASN Chi-restraints excluded: chain B residue 576 MET Chi-restraints excluded: chain B residue 579 GLU Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain E residue 265 HIS Chi-restraints excluded: chain E residue 280 ARG Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain G residue 177 VAL Chi-restraints excluded: chain G residue 197 ARG Chi-restraints excluded: chain G residue 218 VAL Chi-restraints excluded: chain G residue 255 HIS Chi-restraints excluded: chain G residue 276 CYS Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 347 THR Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 472 ASN Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain G residue 576 MET Chi-restraints excluded: chain G residue 579 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 706 random chunks: chunk 444 optimal weight: 2.9990 chunk 596 optimal weight: 0.0870 chunk 171 optimal weight: 20.0000 chunk 516 optimal weight: 10.0000 chunk 82 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 560 optimal weight: 2.9990 chunk 234 optimal weight: 20.0000 chunk 576 optimal weight: 50.0000 chunk 71 optimal weight: 9.9990 chunk 103 optimal weight: 0.1980 overall best weight: 2.4564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.159094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.125463 restraints weight = 307506.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.125974 restraints weight = 182929.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.125470 restraints weight = 123230.291| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 56088 Z= 0.176 Angle : 0.570 13.795 75726 Z= 0.287 Chirality : 0.044 0.248 8346 Planarity : 0.004 0.085 9924 Dihedral : 4.356 57.499 7843 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.58 % Allowed : 15.83 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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: 1.03 (0.10), residues: 7054 helix: 1.97 (0.10), residues: 2688 sheet: 0.54 (0.14), residues: 1314 loop : -0.38 (0.11), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 276 HIS 0.006 0.001 HIS G 684 PHE 0.024 0.001 PHE D 497 TYR 0.015 0.001 TYR G 387 ARG 0.009 0.000 ARG J 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10078.51 seconds wall clock time: 179 minutes 10.73 seconds (10750.73 seconds total)