Starting phenix.real_space_refine on Fri Oct 11 11:21:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jak_36128/10_2024/8jak_36128_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jak_36128/10_2024/8jak_36128.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jak_36128/10_2024/8jak_36128.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jak_36128/10_2024/8jak_36128.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jak_36128/10_2024/8jak_36128_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jak_36128/10_2024/8jak_36128_neut.cif" } resolution = 2.52 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= 0.056 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 318 5.16 5 C 35088 2.51 5 N 9786 2.21 5 O 10476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 245 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: 55668 Number of models: 1 Model: "" Number of chains: 18 Chain: "E" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4055 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 503} Chain breaks: 1 Chain: "A" Number of atoms: 5208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5208 Classifications: {'peptide': 671} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 642} Chain: "C" Number of atoms: 5208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5208 Classifications: {'peptide': 671} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 642} Chain: "G" Number of atoms: 5208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5208 Classifications: {'peptide': 671} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 642} Chain: "F" Number of atoms: 5208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5208 Classifications: {'peptide': 671} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 642} Chain: "I" Number of atoms: 5208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5208 Classifications: {'peptide': 671} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 642} Chain: "K" Number of atoms: 5208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5208 Classifications: {'peptide': 671} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 642} Chain: "B" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4055 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 503} Chain breaks: 1 Chain: "D" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4055 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 503} Chain breaks: 1 Chain: "H" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4055 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 503} Chain breaks: 1 Chain: "J" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4055 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 503} Chain breaks: 1 Chain: "L" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4055 Classifications: {'peptide': 526} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 503} Chain breaks: 1 Chain: "A" 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: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'BTI': 1} Classifications: {'undetermined': 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} Time building chain proxies: 27.18, per 1000 atoms: 0.49 Number of scatterers: 55668 At special positions: 0 Unit cell: (161.391, 153.706, 225.07, 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 318 16.00 O 10476 8.00 N 9786 7.00 C 35088 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: 10.08 Conformation dependent library (CDL) restraints added in 5.5 seconds 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13152 Finding SS restraints... Secondary structure from input PDB file: 253 helices and 78 sheets defined 40.8% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.02 Creating SS restraints... Processing helix chain 'E' and resid 39 through 65 removed outlier: 3.636A pdb=" N LEU E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 78 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 114 through 117 Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 146 through 164 Processing helix chain 'E' and resid 177 through 184 removed outlier: 5.811A pdb=" N ALA E 182 " --> pdb=" O PRO E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 204 removed outlier: 4.290A pdb=" N PHE E 195 " --> pdb=" O PHE E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 227 removed outlier: 3.522A pdb=" N ALA E 225 " --> pdb=" O ALA E 221 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 227 " --> pdb=" O VAL E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 268 Processing helix chain 'E' and resid 279 through 293 Processing helix chain 'E' and resid 316 through 322 Processing helix chain 'E' and resid 330 through 337 removed outlier: 3.926A pdb=" N VAL E 334 " --> pdb=" O ASP E 330 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG E 337 " --> pdb=" O GLU E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 removed outlier: 6.673A pdb=" N GLY E 341 " --> pdb=" O ILE E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 395 Processing helix chain 'E' and resid 414 through 432 removed outlier: 4.205A pdb=" N ILE E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS E 420 " --> pdb=" O GLU E 416 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP E 421 " --> pdb=" O GLY E 417 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA E 423 " --> pdb=" O ALA E 419 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS E 424 " --> pdb=" O LYS E 420 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET E 425 " --> pdb=" O ASP E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 446 through 452 removed outlier: 4.111A pdb=" N TYR E 450 " --> pdb=" O GLY E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 458 Processing helix chain 'E' and resid 474 through 494 Processing helix chain 'E' and resid 498 through 518 Proline residue: E 508 - end of helix removed outlier: 3.526A pdb=" N ASN E 518 " --> pdb=" O GLU E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 525 removed outlier: 3.647A pdb=" N ARG E 525 " --> pdb=" O TYR E 521 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 535 No H-bonds generated for 'chain 'E' and resid 533 through 535' Processing helix chain 'E' and resid 536 through 549 Processing helix chain 'A' and resid 57 through 71 removed outlier: 3.571A pdb=" N ALA A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 84 removed outlier: 3.505A pdb=" N ARG A 84 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 102 through 106 Processing helix chain 'A' and resid 109 through 120 Processing helix chain 'A' and resid 135 through 145 Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.853A pdb=" N ILE A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 173 Processing helix chain 'A' and resid 187 through 199 Processing helix chain 'A' and resid 223 through 240 Processing helix chain 'A' and resid 295 through 313 Processing helix chain 'A' and resid 343 through 352 removed outlier: 4.174A pdb=" N THR A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 443 through 458 Processing helix chain 'A' and resid 466 through 475 Processing helix chain 'A' and resid 476 through 482 Processing helix chain 'A' and resid 487 through 497 removed outlier: 5.354A pdb=" N LYS A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLN A 495 " --> pdb=" O GLN A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 529 removed outlier: 3.963A pdb=" N GLN A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 539 Processing helix chain 'A' and resid 635 through 639 removed outlier: 3.603A pdb=" N SER A 639 " --> pdb=" O TYR A 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 71 removed outlier: 3.571A pdb=" N ALA C 61 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 67 " --> pdb=" O ARG C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 84 removed outlier: 3.505A pdb=" N ARG C 84 " --> pdb=" O GLU C 81 " (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 removed outlier: 3.852A pdb=" N ILE C 162 " --> pdb=" O ARG C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 173 Processing helix chain 'C' and resid 187 through 199 Processing helix chain 'C' and resid 223 through 240 Processing helix chain 'C' and resid 295 through 313 Processing helix chain 'C' and resid 343 through 352 removed outlier: 4.174A pdb=" N THR C 347 " --> pdb=" O GLU C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 364 Processing helix chain 'C' and resid 443 through 458 Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 482 Processing helix chain 'C' and resid 487 through 497 removed outlier: 5.554A pdb=" N LYS C 494 " --> pdb=" O PRO C 490 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLN C 495 " --> pdb=" O GLN C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 529 removed outlier: 3.964A 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 'G' and resid 57 through 71 removed outlier: 3.571A pdb=" N ALA G 61 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 3.544A 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: 3.853A 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: 5.316A pdb=" N LYS G 494 " --> pdb=" O PRO G 490 " (cutoff:3.500A) removed outlier: 6.434A 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 helix chain 'F' and resid 57 through 71 removed outlier: 3.571A pdb=" N ALA F 61 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.505A pdb=" N ARG F 84 " --> pdb=" O GLU F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 92 Processing helix chain 'F' and resid 102 through 106 Processing helix chain 'F' and resid 109 through 120 Processing helix chain 'F' and resid 135 through 145 Processing helix chain 'F' and resid 153 through 162 removed outlier: 3.852A pdb=" N ILE F 162 " --> pdb=" O ARG F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 173 Processing helix chain 'F' and resid 187 through 199 Processing helix chain 'F' and resid 223 through 240 Processing helix chain 'F' and resid 295 through 313 Processing helix chain 'F' and resid 343 through 352 removed outlier: 4.175A pdb=" N THR F 347 " --> pdb=" O GLU F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 364 Processing helix chain 'F' and resid 443 through 458 Processing helix chain 'F' and resid 466 through 475 Processing helix chain 'F' and resid 476 through 482 Processing helix chain 'F' and resid 487 through 497 removed outlier: 5.339A pdb=" N LYS F 494 " --> pdb=" O PRO F 490 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN F 495 " --> pdb=" O GLN F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 504 through 529 removed outlier: 3.963A pdb=" N GLN F 529 " --> pdb=" O THR F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 539 Processing helix chain 'I' and resid 57 through 71 removed outlier: 3.571A pdb=" N ALA I 61 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR I 67 " --> pdb=" O ARG I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.504A pdb=" N ARG I 84 " --> pdb=" O GLU I 81 " (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 removed outlier: 3.853A pdb=" N ILE I 162 " --> pdb=" O ARG I 158 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 173 Processing helix chain 'I' and resid 187 through 199 Processing helix chain 'I' and resid 223 through 240 Processing helix chain 'I' and resid 295 through 313 Processing helix chain 'I' and resid 343 through 352 removed outlier: 4.173A pdb=" N THR I 347 " --> pdb=" O GLU I 343 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 364 Processing helix chain 'I' and resid 443 through 458 Processing helix chain 'I' and resid 466 through 475 Processing helix chain 'I' and resid 476 through 482 Processing helix chain 'I' and resid 487 through 497 removed outlier: 5.379A pdb=" N LYS I 494 " --> pdb=" O PRO I 490 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN I 495 " --> pdb=" O GLN I 491 " (cutoff:3.500A) Processing helix chain 'I' and resid 504 through 529 removed outlier: 3.963A 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 'K' and resid 57 through 71 removed outlier: 3.571A 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: 3.505A 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: 3.853A 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: 5.315A pdb=" N LYS K 494 " --> pdb=" O PRO K 490 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLN K 495 " --> pdb=" O GLN K 491 " (cutoff:3.500A) Processing helix chain 'K' and resid 504 through 529 removed outlier: 3.964A 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 'B' and resid 39 through 65 removed outlier: 3.636A pdb=" N LEU B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 114 through 117 Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 146 through 164 Processing helix chain 'B' and resid 177 through 184 removed outlier: 5.810A pdb=" N ALA B 182 " --> pdb=" O PRO B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 204 removed outlier: 4.290A pdb=" N PHE B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.521A pdb=" N ALA B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA B 227 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 279 through 293 Processing helix chain 'B' and resid 316 through 322 Processing helix chain 'B' and resid 330 through 337 removed outlier: 3.925A pdb=" N VAL B 334 " --> pdb=" O ASP B 330 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 337 " --> pdb=" O GLU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 removed outlier: 6.672A pdb=" N GLY B 341 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 395 Processing helix chain 'B' and resid 414 through 432 removed outlier: 4.205A pdb=" N ILE B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET B 425 " --> pdb=" O ASP B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 452 removed outlier: 4.111A pdb=" N TYR B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 458 Processing helix chain 'B' and resid 474 through 494 Processing helix chain 'B' and resid 498 through 518 Proline residue: B 508 - end of helix removed outlier: 3.526A pdb=" N ASN B 518 " --> pdb=" O GLU B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 525 removed outlier: 3.647A pdb=" N ARG B 525 " --> pdb=" O TYR B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 535 No H-bonds generated for 'chain 'B' and resid 533 through 535' Processing helix chain 'B' and resid 536 through 549 Processing helix chain 'D' and resid 39 through 65 removed outlier: 3.636A 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 221 through 227 removed outlier: 3.522A pdb=" N ALA D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA D 227 " --> pdb=" O VAL D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 268 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: 3.926A pdb=" N VAL D 334 " --> pdb=" O ASP D 330 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG D 337 " --> pdb=" O GLU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 343 removed outlier: 6.672A 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 414 through 432 removed outlier: 4.205A pdb=" N ILE D 418 " --> pdb=" O GLU D 414 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP D 421 " --> pdb=" O GLY D 417 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS D 424 " --> pdb=" O LYS D 420 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET D 425 " --> pdb=" O ASP D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 452 removed outlier: 4.111A 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 Processing helix chain 'D' and resid 498 through 518 Proline residue: D 508 - end of helix removed outlier: 3.526A pdb=" N ASN D 518 " --> pdb=" O GLU D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 525 removed outlier: 3.647A 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: 3.636A 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: 4.290A pdb=" N PHE H 195 " --> pdb=" O PHE H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 227 removed outlier: 3.522A 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: 3.926A pdb=" N VAL H 334 " --> pdb=" O ASP H 330 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG H 337 " --> pdb=" O GLU H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 343 removed outlier: 6.672A 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: 4.205A pdb=" N ILE H 418 " --> pdb=" O GLU H 414 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS H 420 " --> pdb=" O GLU H 416 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP H 421 " --> pdb=" O GLY H 417 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA H 423 " --> pdb=" O ALA H 419 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS H 424 " --> pdb=" O LYS H 420 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET H 425 " --> pdb=" O ASP H 421 " (cutoff:3.500A) Processing helix chain 'H' and resid 446 through 452 removed outlier: 4.111A 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 Processing helix chain 'H' and resid 498 through 518 Proline residue: H 508 - end of helix removed outlier: 3.525A pdb=" N ASN H 518 " --> pdb=" O GLU H 514 " (cutoff:3.500A) Processing helix chain 'H' and resid 518 through 525 removed outlier: 3.647A 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 'J' and resid 39 through 65 removed outlier: 3.637A 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: 4.291A pdb=" N PHE J 195 " --> pdb=" O PHE J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 227 removed outlier: 3.522A pdb=" N ALA J 225 " --> pdb=" O ALA J 221 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA J 227 " --> pdb=" O VAL J 223 " (cutoff:3.500A) Processing helix chain 'J' and resid 263 through 268 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: 3.925A pdb=" N VAL J 334 " --> pdb=" O ASP J 330 " (cutoff:3.500A) removed outlier: 3.541A 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 414 through 432 removed outlier: 4.206A pdb=" N ILE J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS J 420 " --> pdb=" O GLU J 416 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP J 421 " --> pdb=" O GLY J 417 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA J 423 " --> pdb=" O ALA J 419 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS J 424 " --> pdb=" O LYS J 420 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET J 425 " --> pdb=" O ASP J 421 " (cutoff:3.500A) Processing helix chain 'J' and resid 446 through 452 removed outlier: 4.111A 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 Processing helix chain 'J' and resid 498 through 518 Proline residue: J 508 - end of helix removed outlier: 3.526A pdb=" N ASN J 518 " --> pdb=" O GLU J 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 518 through 525 removed outlier: 3.647A 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: 4.290A pdb=" N PHE L 195 " --> pdb=" O PHE L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 221 through 227 removed outlier: 3.522A 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: 3.925A pdb=" N VAL L 334 " --> pdb=" O ASP L 330 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG L 337 " --> pdb=" O GLU L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 343 removed outlier: 6.673A 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: 4.206A pdb=" N ILE L 418 " --> pdb=" O GLU L 414 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS L 420 " --> pdb=" O GLU L 416 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASP L 421 " --> pdb=" O GLY L 417 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA L 423 " --> pdb=" O ALA L 419 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LYS L 424 " --> pdb=" O LYS L 420 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET L 425 " --> pdb=" O ASP L 421 " (cutoff:3.500A) Processing helix chain 'L' and resid 446 through 452 removed outlier: 4.110A 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 Processing helix chain 'L' and resid 498 through 518 Proline residue: L 508 - end of helix removed outlier: 3.526A pdb=" N ASN L 518 " --> pdb=" O GLU L 514 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 525 removed outlier: 3.647A 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 sheet with id=AA1, first strand: chain 'E' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR E 121 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS E 167 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL E 211 " --> pdb=" O CYS E 167 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N TYR E 169 " --> pdb=" O VAL E 211 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN E 230 " --> pdb=" O HIS E 275 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ALA E 277 " --> pdb=" O ASN E 230 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE E 232 " --> pdb=" O ALA E 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 215 through 216 Processing sheet with id=AA3, first strand: chain 'E' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU E 399 " --> pdb=" O PRO E 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY E 368 " --> pdb=" O LEU E 399 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU E 401 " --> pdb=" O GLY E 368 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL E 370 " --> pdb=" O LEU E 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE E 461 " --> pdb=" O LYS E 436 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 443 through 445 Processing sheet with id=AA5, first strand: chain 'A' and resid 148 through 149 removed outlier: 6.982A pdb=" N LYS A 51 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS A 126 " --> pdb=" O LYS A 51 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 53 " --> pdb=" O HIS A 126 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 78 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 95 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 216 through 218 removed outlier: 3.541A pdb=" N LYS A 205 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 268 through 270 removed outlier: 5.670A pdb=" N ILE A 324 " --> pdb=" O PHE A 333 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE A 333 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 268 through 270 removed outlier: 5.329A pdb=" N HIS A 255 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER A 277 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE A 286 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN A 279 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS A 284 " --> pdb=" O GLN A 279 " (cutoff:3.500A) removed outlier: 13.693A pdb=" N GLN A 283 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 10.649A pdb=" N TYR A 387 " --> pdb=" O GLN A 283 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE A 285 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS A 380 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TRP A 440 " --> pdb=" O HIS A 380 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE A 382 " --> pdb=" O VAL A 438 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL A 438 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA A 384 " --> pdb=" O LYS A 436 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS A 436 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE A 386 " --> pdb=" O ILE A 434 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 390 removed outlier: 3.541A pdb=" N MET A 396 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 400 through 401 removed outlier: 3.787A pdb=" N GLY A 400 " --> pdb=" O VAL A 426 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 404 through 406 Processing sheet with id=AB3, first strand: chain 'G' and resid 148 through 149 removed outlier: 6.981A pdb=" N LYS G 51 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 7.846A 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: 3.929A pdb=" N VAL G 78 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA G 95 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 683 through 687 removed outlier: 3.661A pdb=" N MET A 675 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU A 674 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL A 660 " --> pdb=" O LEU A 674 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL A 676 " --> pdb=" O GLU A 658 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 694 through 697 Processing sheet with id=AB6, first strand: chain 'C' and resid 148 through 149 removed outlier: 6.982A pdb=" N LYS C 51 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N HIS C 126 " --> pdb=" O LYS C 51 " (cutoff:3.500A) removed outlier: 6.548A 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: 3.606A pdb=" N ALA C 95 " --> pdb=" O ALA G 606 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR G 596 " --> pdb=" O LEU G 611 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 216 through 218 removed outlier: 3.540A pdb=" N LYS C 205 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 268 through 270 removed outlier: 5.670A pdb=" N ILE C 324 " --> pdb=" O PHE C 333 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE C 333 " --> pdb=" O ILE C 324 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 268 through 270 removed outlier: 5.361A pdb=" N HIS C 255 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER C 277 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE C 286 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN C 279 " --> pdb=" O LYS C 284 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS C 284 " --> pdb=" O GLN C 279 " (cutoff:3.500A) removed outlier: 13.693A pdb=" N GLN C 283 " --> pdb=" O TYR C 387 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N TYR C 387 " --> pdb=" O GLN C 283 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE C 285 " --> pdb=" O ARG C 385 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N HIS C 380 " --> pdb=" O TRP C 440 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N TRP C 440 " --> pdb=" O HIS C 380 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE C 382 " --> pdb=" O VAL C 438 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL C 438 " --> pdb=" O PHE C 382 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA C 384 " --> pdb=" O LYS C 436 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N LYS C 436 " --> pdb=" O ALA C 384 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE C 386 " --> pdb=" O ILE C 434 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 389 through 390 removed outlier: 3.541A pdb=" N MET C 396 " --> pdb=" O ASP C 390 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 400 through 401 removed outlier: 3.787A pdb=" N GLY C 400 " --> pdb=" O VAL C 426 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 404 through 406 Processing sheet with id=AC4, first strand: chain 'C' and resid 683 through 687 removed outlier: 3.661A pdb=" N MET C 675 " --> pdb=" O ILE C 686 " (cutoff:3.500A) removed outlier: 7.801A 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: 6.392A pdb=" N VAL C 676 " --> pdb=" O GLU C 658 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 694 through 697 Processing sheet with id=AC6, first strand: chain 'G' and resid 216 through 218 removed outlier: 3.541A pdb=" N LYS G 205 " --> pdb=" O LEU G 245 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 268 through 270 removed outlier: 5.670A pdb=" N ILE G 324 " --> pdb=" O PHE G 333 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE G 333 " --> pdb=" O ILE G 324 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 268 through 270 removed outlier: 5.417A pdb=" N HIS G 255 " --> pdb=" O CYS G 276 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS G 276 " --> pdb=" O HIS G 255 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER G 277 " --> pdb=" O ILE G 286 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE G 286 " --> pdb=" O SER G 277 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLN G 279 " --> pdb=" O LYS G 284 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS G 284 " --> pdb=" O GLN G 279 " (cutoff:3.500A) removed outlier: 13.694A pdb=" N GLN G 283 " --> pdb=" O TYR G 387 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N TYR G 387 " --> pdb=" O GLN G 283 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE G 285 " --> pdb=" O ARG G 385 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N HIS G 380 " --> pdb=" O TRP G 440 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP G 440 " --> pdb=" O HIS G 380 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE G 382 " --> pdb=" O VAL G 438 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL G 438 " --> pdb=" O PHE G 382 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA G 384 " --> pdb=" O LYS G 436 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS G 436 " --> pdb=" O ALA G 384 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE G 386 " --> pdb=" O ILE G 434 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 389 through 390 removed outlier: 3.541A pdb=" N MET G 396 " --> pdb=" O ASP G 390 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 400 through 401 removed outlier: 3.787A pdb=" N GLY G 400 " --> pdb=" O VAL G 426 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 404 through 406 Processing sheet with id=AD3, first strand: chain 'G' and resid 683 through 687 removed outlier: 3.662A 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=AD4, first strand: chain 'G' and resid 694 through 697 Processing sheet with id=AD5, first strand: chain 'F' and resid 148 through 149 removed outlier: 6.981A pdb=" N LYS F 51 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS F 126 " --> pdb=" O LYS F 51 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU F 53 " --> pdb=" O HIS F 126 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL F 78 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA F 95 " --> pdb=" O ALA I 606 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR I 596 " --> pdb=" O LEU I 611 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 216 through 218 removed outlier: 3.541A pdb=" N LYS F 205 " --> pdb=" O LEU F 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 268 through 270 removed outlier: 5.670A pdb=" N ILE F 324 " --> pdb=" O PHE F 333 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE F 333 " --> pdb=" O ILE F 324 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 268 through 270 removed outlier: 5.004A pdb=" N SER F 277 " --> pdb=" O ILE F 286 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE F 286 " --> pdb=" O SER F 277 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN F 279 " --> pdb=" O LYS F 284 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS F 284 " --> pdb=" O GLN F 279 " (cutoff:3.500A) removed outlier: 13.693A pdb=" N GLN F 283 " --> pdb=" O TYR F 387 " (cutoff:3.500A) removed outlier: 10.649A pdb=" N TYR F 387 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE F 285 " --> pdb=" O ARG F 385 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N HIS F 380 " --> pdb=" O TRP F 440 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP F 440 " --> pdb=" O HIS F 380 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE F 382 " --> pdb=" O VAL F 438 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VAL F 438 " --> pdb=" O PHE F 382 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA F 384 " --> pdb=" O LYS F 436 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS F 436 " --> pdb=" O ALA F 384 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE F 386 " --> pdb=" O ILE F 434 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 389 through 390 removed outlier: 3.541A pdb=" N MET F 396 " --> pdb=" O ASP F 390 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 400 through 401 removed outlier: 3.787A pdb=" N GLY F 400 " --> pdb=" O VAL F 426 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 404 through 406 Processing sheet with id=AE3, first strand: chain 'K' and resid 148 through 149 removed outlier: 6.981A pdb=" N LYS K 51 " --> pdb=" O ALA K 124 " (cutoff:3.500A) removed outlier: 7.846A 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: 3.929A pdb=" N VAL K 78 " --> pdb=" O ILE K 54 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA K 95 " --> pdb=" O ALA F 606 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR F 596 " --> pdb=" O LEU F 611 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 683 through 687 removed outlier: 3.662A pdb=" N MET F 675 " --> pdb=" O ILE F 686 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU F 674 " --> pdb=" O VAL F 660 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL F 660 " --> pdb=" O LEU F 674 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL F 676 " --> pdb=" O GLU F 658 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 694 through 697 Processing sheet with id=AE6, first strand: chain 'I' and resid 148 through 149 removed outlier: 6.981A pdb=" N LYS I 51 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N HIS I 126 " --> pdb=" O LYS I 51 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU I 53 " --> pdb=" O HIS I 126 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL I 78 " --> pdb=" O ILE I 54 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA I 95 " --> pdb=" O ALA K 606 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N THR K 596 " --> pdb=" O LEU K 611 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 216 through 218 removed outlier: 3.540A pdb=" N LYS I 205 " --> pdb=" O LEU I 245 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 268 through 270 removed outlier: 5.669A pdb=" N ILE I 324 " --> pdb=" O PHE I 333 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE I 333 " --> pdb=" O ILE I 324 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 268 through 270 removed outlier: 5.815A pdb=" N HIS I 255 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N SER I 277 " --> pdb=" O ILE I 286 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE I 286 " --> pdb=" O SER I 277 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN I 279 " --> pdb=" O LYS I 284 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS I 284 " --> pdb=" O GLN I 279 " (cutoff:3.500A) removed outlier: 13.694A pdb=" N GLN I 283 " --> pdb=" O TYR I 387 " (cutoff:3.500A) removed outlier: 10.648A pdb=" N TYR I 387 " --> pdb=" O GLN I 283 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE I 285 " --> pdb=" O ARG I 385 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N HIS I 380 " --> pdb=" O TRP I 440 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP I 440 " --> pdb=" O HIS I 380 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE I 382 " --> pdb=" O VAL I 438 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL I 438 " --> pdb=" O PHE I 382 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ALA I 384 " --> pdb=" O LYS I 436 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS I 436 " --> pdb=" O ALA I 384 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE I 386 " --> pdb=" O ILE I 434 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 389 through 390 removed outlier: 3.541A pdb=" N MET I 396 " --> pdb=" O ASP I 390 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 400 through 401 removed outlier: 3.787A pdb=" N GLY I 400 " --> pdb=" O VAL I 426 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 404 through 406 Processing sheet with id=AF4, first strand: chain 'I' and resid 683 through 687 removed outlier: 3.662A 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: 4.746A pdb=" N VAL I 660 " --> pdb=" O LEU I 674 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL I 676 " --> pdb=" O GLU I 658 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 694 through 697 Processing sheet with id=AF6, 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=AF7, first strand: chain 'K' and resid 268 through 270 removed outlier: 5.670A 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=AF8, first strand: chain 'K' and resid 268 through 270 removed outlier: 5.005A pdb=" N SER K 277 " --> pdb=" O ILE K 286 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE K 286 " --> pdb=" O SER K 277 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN K 279 " --> pdb=" O LYS K 284 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LYS K 284 " --> pdb=" O GLN K 279 " (cutoff:3.500A) removed outlier: 13.694A pdb=" N GLN K 283 " --> pdb=" O TYR K 387 " (cutoff:3.500A) removed outlier: 10.649A 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: 6.483A pdb=" N HIS K 380 " --> pdb=" O TRP K 440 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP K 440 " --> pdb=" O HIS K 380 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE K 382 " --> pdb=" O VAL K 438 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL K 438 " --> pdb=" O PHE K 382 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA K 384 " --> pdb=" O LYS K 436 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS K 436 " --> pdb=" O ALA K 384 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE K 386 " --> pdb=" O ILE K 434 " (cutoff:3.500A) Processing sheet with id=AF9, 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=AG1, first strand: chain 'K' and resid 400 through 401 removed outlier: 3.787A pdb=" N GLY K 400 " --> pdb=" O VAL K 426 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 404 through 406 Processing sheet with id=AG3, first strand: chain 'K' and resid 683 through 687 removed outlier: 3.662A 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: 4.746A pdb=" N VAL K 660 " --> pdb=" O LEU K 674 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N VAL K 676 " --> pdb=" O GLU K 658 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 694 through 697 Processing sheet with id=AG5, first strand: chain 'B' and resid 98 through 100 removed outlier: 4.731A pdb=" N THR B 121 " --> pdb=" O LEU B 100 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N CYS B 167 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 211 " --> pdb=" O CYS B 167 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR B 169 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN B 230 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ALA B 277 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 232 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 215 through 216 Processing sheet with id=AG7, first strand: chain 'B' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU B 399 " --> pdb=" O PRO B 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY B 368 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU B 401 " --> pdb=" O GLY B 368 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 370 " --> pdb=" O LEU B 401 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE B 461 " --> pdb=" O LYS B 436 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 443 through 445 Processing sheet with id=AG9, 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: 6.158A pdb=" N CYS D 167 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL D 211 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYR D 169 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.858A 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: 6.531A pdb=" N ILE D 232 " --> pdb=" O ALA D 277 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 215 through 216 Processing sheet with id=AH2, first strand: chain 'D' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU D 399 " --> pdb=" O PRO D 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY D 368 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU D 401 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 6.790A 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=AH3, first strand: chain 'D' and resid 443 through 445 Processing sheet with id=AH4, first strand: chain 'H' and resid 98 through 100 removed outlier: 4.730A pdb=" N THR H 121 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS H 167 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 7.591A 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: 6.858A pdb=" N ASN H 230 " --> pdb=" O HIS H 275 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ALA H 277 " --> pdb=" O ASN H 230 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE H 232 " --> pdb=" O ALA H 277 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'H' and resid 215 through 216 Processing sheet with id=AH6, 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: 6.216A pdb=" N GLY H 368 " --> pdb=" O LEU H 399 " (cutoff:3.500A) removed outlier: 7.680A 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=AH7, first strand: chain 'H' and resid 443 through 445 Processing sheet with id=AH8, 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: 6.160A pdb=" N CYS J 167 " --> pdb=" O ILE J 209 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL J 211 " --> pdb=" O CYS J 167 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N TYR J 169 " --> pdb=" O VAL J 211 " (cutoff:3.500A) removed outlier: 6.857A 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: 6.530A pdb=" N ILE J 232 " --> pdb=" O ALA J 277 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 215 through 216 Processing sheet with id=AI1, first strand: chain 'J' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU J 399 " --> pdb=" O PRO J 366 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY J 368 " --> pdb=" O LEU J 399 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LEU J 401 " --> pdb=" O GLY J 368 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL J 370 " --> pdb=" O LEU J 401 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE J 461 " --> pdb=" O LYS J 436 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'J' and resid 443 through 445 Processing sheet with id=AI3, first strand: chain 'L' and resid 98 through 100 removed outlier: 4.730A 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: 7.591A pdb=" N VAL L 211 " --> pdb=" O CYS L 167 " (cutoff:3.500A) removed outlier: 6.197A 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: 7.914A pdb=" N ALA L 277 " --> pdb=" O ASN L 230 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE L 232 " --> pdb=" O ALA L 277 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 215 through 216 Processing sheet with id=AI5, first strand: chain 'L' and resid 345 through 346 removed outlier: 7.656A pdb=" N LEU L 399 " --> pdb=" O PRO L 366 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N GLY L 368 " --> pdb=" O LEU L 399 " (cutoff:3.500A) removed outlier: 7.681A 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: 3.697A pdb=" N PHE L 461 " --> pdb=" O LYS L 436 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'L' and resid 443 through 445 2692 hydrogen bonds defined for protein. 7392 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: 22.14 Time building geometry restraints manager: 12.09 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: 9715 1.31 - 1.44: 14212 1.44 - 1.57: 32280 1.57 - 1.70: 1 1.70 - 1.83: 534 Bond restraints: 56742 Sorted by residual: bond pdb=" CA THR I 252 " pdb=" CB THR I 252 " ideal model delta sigma weight residual 1.522 1.570 -0.048 7.00e-03 2.04e+04 4.67e+01 bond pdb=" C MET J 425 " pdb=" O MET J 425 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.19e-02 7.06e+03 2.21e+01 bond pdb=" C MET H 425 " pdb=" O MET H 425 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.19e-02 7.06e+03 2.21e+01 bond pdb=" C MET D 425 " pdb=" O MET D 425 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.19e-02 7.06e+03 2.20e+01 bond pdb=" C MET E 425 " pdb=" O MET E 425 " ideal model delta sigma weight residual 1.237 1.181 0.056 1.19e-02 7.06e+03 2.20e+01 ... (remaining 56737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 70881 2.50 - 5.00: 5445 5.00 - 7.50: 225 7.50 - 10.00: 36 10.00 - 12.50: 15 Bond angle restraints: 76602 Sorted by residual: angle pdb=" N ASP J 264 " pdb=" CA ASP J 264 " pdb=" C ASP J 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 E 264 " pdb=" CA ASP E 264 " pdb=" C ASP E 264 " ideal model delta sigma weight residual 112.38 99.94 12.44 1.22e+00 6.72e-01 1.04e+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 99.96 12.42 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 99.96 12.42 1.22e+00 6.72e-01 1.04e+02 angle pdb=" N ASP D 264 " pdb=" CA ASP D 264 " pdb=" C ASP D 264 " ideal model delta sigma weight residual 112.38 99.96 12.42 1.22e+00 6.72e-01 1.04e+02 ... (remaining 76597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 31487 16.43 - 32.86: 2080 32.86 - 49.29: 613 49.29 - 65.72: 206 65.72 - 82.15: 54 Dihedral angle restraints: 34440 sinusoidal: 13878 harmonic: 20562 Sorted by residual: dihedral pdb=" C THR I 252 " pdb=" N THR I 252 " pdb=" CA THR I 252 " pdb=" CB THR I 252 " ideal model delta harmonic sigma weight residual -122.00 -137.50 15.50 0 2.50e+00 1.60e-01 3.84e+01 dihedral pdb=" CA TYR A 200 " pdb=" C TYR A 200 " pdb=" N PRO A 201 " pdb=" CA PRO A 201 " ideal model delta harmonic sigma weight residual 0.00 29.57 -29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" N ARG K 254 " pdb=" C ARG K 254 " pdb=" CA ARG K 254 " pdb=" CB ARG K 254 " ideal model delta harmonic sigma weight residual 122.80 136.57 -13.77 0 2.50e+00 1.60e-01 3.03e+01 ... (remaining 34437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 7210 0.119 - 0.238: 1117 0.238 - 0.357: 106 0.357 - 0.476: 1 0.476 - 0.595: 2 Chirality restraints: 8436 Sorted by residual: chirality pdb=" CA ARG K 254 " pdb=" N ARG K 254 " pdb=" C ARG K 254 " pdb=" CB ARG K 254 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.85e+00 chirality pdb=" CA THR I 252 " pdb=" N THR I 252 " pdb=" C THR I 252 " pdb=" CB THR I 252 " both_signs ideal model delta sigma weight residual False 2.53 2.00 0.53 2.00e-01 2.50e+01 6.91e+00 chirality pdb=" CA ARG F 254 " pdb=" N ARG F 254 " pdb=" C ARG F 254 " pdb=" CB ARG F 254 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 8433 not shown) Planarity restraints: 10044 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR G 387 " -0.057 2.00e-02 2.50e+03 4.33e-02 3.76e+01 pdb=" CG TYR G 387 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR G 387 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR G 387 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR G 387 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR G 387 " 0.042 2.00e-02 2.50e+03 pdb=" CZ TYR G 387 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR G 387 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 387 " -0.057 2.00e-02 2.50e+03 4.32e-02 3.74e+01 pdb=" CG TYR K 387 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR K 387 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR K 387 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR K 387 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR K 387 " 0.042 2.00e-02 2.50e+03 pdb=" CZ TYR K 387 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR K 387 " -0.080 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 387 " -0.057 2.00e-02 2.50e+03 4.32e-02 3.74e+01 pdb=" CG TYR C 387 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR C 387 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR C 387 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR C 387 " 0.047 2.00e-02 2.50e+03 pdb=" CE2 TYR C 387 " 0.042 2.00e-02 2.50e+03 pdb=" CZ TYR C 387 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR C 387 " -0.080 2.00e-02 2.50e+03 ... (remaining 10041 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 11896 2.80 - 3.33: 52400 3.33 - 3.85: 91125 3.85 - 4.38: 112762 4.38 - 4.90: 186072 Nonbonded interactions: 454255 Sorted by model distance: nonbonded pdb=" CE MET H 563 " pdb=" CE MET L 563 " model vdw 2.277 3.880 nonbonded pdb=" CE MET B 563 " pdb=" CE MET J 563 " model vdw 2.280 3.880 nonbonded pdb=" CE MET E 563 " pdb=" CE MET D 563 " model vdw 2.282 3.880 nonbonded pdb=" O ALA L 336 " pdb=" OG SER L 342 " model vdw 2.371 3.040 nonbonded pdb=" O ALA J 336 " pdb=" OG SER J 342 " model vdw 2.371 3.040 ... (remaining 454250 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'E' selection = chain 'H' selection = chain 'J' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 1.880 Check model and map are aligned: 0.320 Set scattering table: 0.390 Process input model: 99.470 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 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 0.058 56742 Z= 0.629 Angle : 1.266 12.497 76602 Z= 0.893 Chirality : 0.083 0.595 8436 Planarity : 0.007 0.090 10044 Dihedral : 13.296 82.150 21288 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.46 % Favored : 97.52 % Rotamer: Outliers : 1.85 % Allowed : 7.93 % Favored : 90.22 % Cbeta Deviations : 0.23 % 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: 7146 helix: 1.74 (0.10), residues: 2634 sheet: 0.80 (0.14), residues: 1278 loop : -0.08 (0.11), residues: 3234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP I 440 HIS 0.010 0.002 HIS G 485 PHE 0.047 0.004 PHE G 395 TYR 0.080 0.003 TYR G 387 ARG 0.013 0.001 ARG K 280 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 765 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 656 time to evaluate : 4.707 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: A 453 TYR cc_start: 0.6274 (t80) cc_final: 0.5922 (t80) REVERT: A 675 MET cc_start: -0.1840 (mtt) cc_final: -0.2649 (ptm) REVERT: C 251 ASP cc_start: 0.0085 (OUTLIER) cc_final: -0.0810 (p0) REVERT: C 453 TYR cc_start: 0.6260 (t80) cc_final: 0.5758 (t80) REVERT: C 675 MET cc_start: -0.2016 (mtt) cc_final: -0.2727 (ptm) REVERT: G 65 MET cc_start: 0.8351 (mtt) cc_final: 0.8089 (mtp) REVERT: G 675 MET cc_start: -0.2017 (mtt) cc_final: -0.2828 (ptm) REVERT: F 453 TYR cc_start: 0.6290 (t80) cc_final: 0.5845 (t80) REVERT: F 675 MET cc_start: -0.2076 (mtt) cc_final: -0.2552 (ptm) REVERT: I 65 MET cc_start: 0.8356 (mtt) cc_final: 0.8090 (mtp) REVERT: I 522 MET cc_start: 0.8935 (tpp) cc_final: 0.8728 (tpp) REVERT: I 675 MET cc_start: -0.1822 (mtt) cc_final: -0.2720 (ptm) REVERT: K 453 TYR cc_start: 0.6225 (t80) cc_final: 0.5894 (t80) REVERT: K 675 MET cc_start: -0.1904 (mtt) cc_final: -0.2953 (ptm) REVERT: B 409 VAL cc_start: 0.5962 (OUTLIER) cc_final: 0.5725 (p) REVERT: H 409 VAL cc_start: 0.6021 (OUTLIER) cc_final: 0.5763 (p) REVERT: H 506 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8573 (mttm) REVERT: J 409 VAL cc_start: 0.6037 (OUTLIER) cc_final: 0.5775 (p) REVERT: J 506 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8585 (mttm) REVERT: L 409 VAL cc_start: 0.5961 (OUTLIER) cc_final: 0.5753 (p) outliers start: 109 outliers final: 6 residues processed: 761 average time/residue: 1.4599 time to fit residues: 1384.4121 Evaluate side-chains 441 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 428 time to evaluate : 4.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 493 HIS Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain K residue 377 LEU Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain H residue 409 VAL Chi-restraints excluded: chain H residue 492 ARG Chi-restraints excluded: chain H residue 506 LYS Chi-restraints excluded: chain J residue 409 VAL Chi-restraints excluded: chain J residue 506 LYS Chi-restraints excluded: chain L residue 409 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 602 optimal weight: 0.9990 chunk 541 optimal weight: 2.9990 chunk 300 optimal weight: 4.9990 chunk 184 optimal weight: 8.9990 chunk 365 optimal weight: 0.5980 chunk 289 optimal weight: 10.0000 chunk 559 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 340 optimal weight: 0.0000 chunk 416 optimal weight: 10.0000 chunk 648 optimal weight: 0.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN A 259 GLN A 265 HIS A 329 HIS A 429 HIS ** A 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 HIS C 259 GLN C 429 HIS C 457 GLN C 684 HIS G 194 HIS G 255 HIS G 259 GLN G 329 HIS G 337 ASN G 429 HIS G 457 GLN G 684 HIS F 194 HIS F 255 HIS F 259 GLN F 429 HIS F 457 GLN F 684 HIS I 194 HIS I 259 GLN I 283 GLN I 329 HIS I 337 ASN I 429 HIS I 457 GLN I 684 HIS K 194 HIS K 259 GLN K 265 HIS K 329 HIS K 429 HIS ** K 684 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN D 389 GLN H 389 GLN J 389 GLN L 389 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 56742 Z= 0.197 Angle : 0.609 8.835 76602 Z= 0.324 Chirality : 0.046 0.297 8436 Planarity : 0.004 0.079 10044 Dihedral : 4.750 52.818 7946 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.73 % Rotamer: Outliers : 2.56 % Allowed : 11.75 % Favored : 85.69 % 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: 1.40 (0.10), residues: 7146 helix: 2.22 (0.10), residues: 2622 sheet: 0.80 (0.13), residues: 1320 loop : -0.05 (0.11), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 276 HIS 0.017 0.001 HIS B 266 PHE 0.021 0.001 PHE K 323 TYR 0.030 0.001 TYR K 453 ARG 0.009 0.000 ARG A 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 459 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 486 THR cc_start: 0.8735 (m) cc_final: 0.8485 (t) REVERT: A 500 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6931 (ptm-80) REVERT: A 675 MET cc_start: -0.1857 (mtt) cc_final: -0.2627 (ptm) REVERT: A 682 MET cc_start: -0.0501 (ptm) cc_final: -0.0748 (ptt) REVERT: C 251 ASP cc_start: -0.0510 (OUTLIER) cc_final: -0.1393 (p0) REVERT: C 675 MET cc_start: -0.2041 (mtt) cc_final: -0.2452 (ptm) REVERT: G 416 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8841 (mp) REVERT: G 495 GLN cc_start: 0.6355 (OUTLIER) cc_final: 0.5720 (pm20) REVERT: G 675 MET cc_start: -0.1748 (mtt) cc_final: -0.2611 (ptm) REVERT: F 675 MET cc_start: -0.2149 (mtt) cc_final: -0.2570 (ptm) REVERT: I 416 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8821 (mp) REVERT: I 522 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8735 (tpp) REVERT: I 675 MET cc_start: -0.1666 (mtt) cc_final: -0.2546 (ptm) REVERT: K 675 MET cc_start: -0.2003 (mtt) cc_final: -0.2767 (ptm) REVERT: K 682 MET cc_start: -0.0551 (ptm) cc_final: -0.0862 (ptt) REVERT: B 408 MET cc_start: 0.7129 (mpm) cc_final: 0.6746 (ppp) REVERT: D 486 THR cc_start: 0.8741 (m) cc_final: 0.8494 (t) REVERT: H 408 MET cc_start: 0.7222 (mpm) cc_final: 0.6803 (ppp) REVERT: H 482 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9019 (mm) REVERT: H 486 THR cc_start: 0.8589 (m) cc_final: 0.8354 (t) REVERT: J 408 MET cc_start: 0.7230 (mpm) cc_final: 0.6799 (ppp) REVERT: J 482 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9028 (mm) REVERT: J 486 THR cc_start: 0.8571 (m) cc_final: 0.8317 (t) REVERT: L 408 MET cc_start: 0.7802 (mpp) cc_final: 0.6861 (ppp) outliers start: 151 outliers final: 35 residues processed: 556 average time/residue: 1.3792 time to fit residues: 969.3420 Evaluate side-chains 413 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 370 time to evaluate : 4.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 70 LYS Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 500 ARG Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 707 ARG Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 282 HIS Chi-restraints excluded: chain G residue 416 ILE Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 495 GLN Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain F residue 707 ARG Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 416 ILE Chi-restraints excluded: chain I residue 451 LEU Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 522 MET Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 70 LYS Chi-restraints excluded: chain K residue 451 LEU Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 707 ARG Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain L residue 240 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 360 optimal weight: 4.9990 chunk 201 optimal weight: 40.0000 chunk 539 optimal weight: 4.9990 chunk 441 optimal weight: 10.0000 chunk 178 optimal weight: 10.0000 chunk 649 optimal weight: 0.9990 chunk 701 optimal weight: 0.9980 chunk 578 optimal weight: 5.9990 chunk 644 optimal weight: 6.9990 chunk 221 optimal weight: 0.9980 chunk 521 optimal weight: 8.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN A 194 HIS A 329 HIS A 684 HIS G 329 HIS F 495 GLN I 329 HIS K 329 HIS K 684 HIS ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 389 GLN H 389 GLN J 389 GLN L 389 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 56742 Z= 0.267 Angle : 0.583 9.326 76602 Z= 0.310 Chirality : 0.046 0.247 8436 Planarity : 0.004 0.055 10044 Dihedral : 4.542 50.667 7923 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.70 % Allowed : 12.38 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.10), residues: 7146 helix: 2.16 (0.10), residues: 2622 sheet: 0.89 (0.13), residues: 1272 loop : -0.18 (0.11), residues: 3252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 276 HIS 0.017 0.001 HIS A 255 PHE 0.023 0.002 PHE F 331 TYR 0.020 0.001 TYR E 457 ARG 0.017 0.001 ARG H 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 392 time to evaluate : 4.809 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: A 675 MET cc_start: -0.1963 (mtt) cc_final: -0.2695 (ptm) REVERT: C 457 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: C 675 MET cc_start: -0.1807 (mtt) cc_final: -0.2426 (ptm) REVERT: G 675 MET cc_start: -0.1844 (mtt) cc_final: -0.2585 (ptm) REVERT: F 170 MET cc_start: 0.4330 (OUTLIER) cc_final: 0.3901 (mmt) REVERT: F 495 GLN cc_start: 0.6335 (OUTLIER) cc_final: 0.5632 (pm20) REVERT: F 675 MET cc_start: -0.1760 (mtt) cc_final: -0.2449 (ptm) REVERT: I 334 MET cc_start: 0.6154 (tmt) cc_final: 0.5533 (ppp) REVERT: I 453 TYR cc_start: 0.7280 (t80) cc_final: 0.6526 (t80) REVERT: I 522 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8807 (tpp) REVERT: I 675 MET cc_start: -0.1894 (mtt) cc_final: -0.2617 (ptm) REVERT: K 675 MET cc_start: -0.2216 (mtt) cc_final: -0.2945 (ptm) REVERT: B 408 MET cc_start: 0.6976 (mpm) cc_final: 0.6471 (ppp) REVERT: H 408 MET cc_start: 0.7516 (mpm) cc_final: 0.6796 (ppp) REVERT: H 482 LEU cc_start: 0.9356 (mm) cc_final: 0.9061 (mm) REVERT: J 408 MET cc_start: 0.7505 (mpm) cc_final: 0.6807 (ppp) REVERT: J 482 LEU cc_start: 0.9356 (mm) cc_final: 0.9064 (mm) REVERT: L 408 MET cc_start: 0.7821 (mpp) cc_final: 0.6864 (ppp) outliers start: 159 outliers final: 50 residues processed: 481 average time/residue: 1.4717 time to fit residues: 887.2030 Evaluate side-chains 412 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 358 time to evaluate : 4.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 497 PHE Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 707 ARG Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain F residue 495 GLN Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 451 LEU Chi-restraints excluded: chain I residue 522 MET Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 402 LEU Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 451 LEU Chi-restraints excluded: chain K residue 463 LEU Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 707 ARG Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 497 PHE Chi-restraints excluded: chain H residue 216 CYS Chi-restraints excluded: chain H residue 497 PHE Chi-restraints excluded: chain J residue 216 CYS Chi-restraints excluded: chain J residue 497 PHE Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain L residue 273 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 641 optimal weight: 5.9990 chunk 488 optimal weight: 7.9990 chunk 337 optimal weight: 0.5980 chunk 71 optimal weight: 8.9990 chunk 309 optimal weight: 7.9990 chunk 436 optimal weight: 3.9990 chunk 651 optimal weight: 3.9990 chunk 690 optimal weight: 7.9990 chunk 340 optimal weight: 5.9990 chunk 617 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS G 329 HIS G 457 GLN F 464 HIS F 495 GLN I 329 HIS K 329 HIS ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 153 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 56742 Z= 0.367 Angle : 0.611 9.354 76602 Z= 0.325 Chirality : 0.047 0.218 8436 Planarity : 0.004 0.051 10044 Dihedral : 4.567 28.553 7921 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.55 % Favored : 97.44 % Rotamer: Outliers : 2.87 % Allowed : 12.68 % Favored : 84.45 % 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: 1.16 (0.10), residues: 7146 helix: 2.07 (0.10), residues: 2610 sheet: 1.04 (0.13), residues: 1206 loop : -0.37 (0.10), residues: 3330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 276 HIS 0.014 0.001 HIS A 255 PHE 0.024 0.002 PHE B 497 TYR 0.026 0.002 TYR I 453 ARG 0.021 0.001 ARG F 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 381 time to evaluate : 4.809 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: E 408 MET cc_start: 0.7405 (mpp) cc_final: 0.6569 (pp-130) REVERT: A 433 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8154 (ttp) REVERT: A 675 MET cc_start: -0.1893 (mtt) cc_final: -0.2847 (ptm) REVERT: A 682 MET cc_start: -0.1170 (ptm) cc_final: -0.2348 (ttt) REVERT: C 215 MET cc_start: 0.4294 (tmm) cc_final: 0.3433 (mmm) REVERT: C 251 ASP cc_start: -0.0048 (OUTLIER) cc_final: -0.1261 (p0) REVERT: C 334 MET cc_start: 0.6371 (tmt) cc_final: 0.5540 (ppp) REVERT: C 457 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7806 (mt0) REVERT: C 529 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8534 (pp30) REVERT: C 675 MET cc_start: -0.1849 (mtt) cc_final: -0.2780 (tmt) REVERT: C 682 MET cc_start: -0.1293 (ptt) cc_final: -0.1508 (ptt) REVERT: G 302 LEU cc_start: 0.5043 (OUTLIER) cc_final: 0.4785 (tt) REVERT: G 322 GLU cc_start: 0.5633 (OUTLIER) cc_final: 0.5431 (tp30) REVERT: G 675 MET cc_start: -0.1799 (mtt) cc_final: -0.2754 (ptm) REVERT: F 170 MET cc_start: 0.4134 (OUTLIER) cc_final: 0.3842 (mmt) REVERT: F 334 MET cc_start: 0.6134 (tmt) cc_final: 0.5270 (ppp) REVERT: F 529 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8535 (pp30) REVERT: F 675 MET cc_start: -0.1575 (mtt) cc_final: -0.2656 (tmt) REVERT: I 302 LEU cc_start: 0.5033 (OUTLIER) cc_final: 0.4772 (tt) REVERT: I 334 MET cc_start: 0.6184 (tmt) cc_final: 0.5925 (tmt) REVERT: I 522 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8835 (tpp) REVERT: I 675 MET cc_start: -0.1625 (mtt) cc_final: -0.2626 (ptm) REVERT: K 334 MET cc_start: 0.5889 (tmt) cc_final: 0.5608 (tmt) REVERT: K 675 MET cc_start: -0.2123 (mtt) cc_final: -0.3048 (ptm) REVERT: K 680 MET cc_start: 0.0655 (mtt) cc_final: 0.0399 (mpt) REVERT: D 408 MET cc_start: 0.7404 (mpp) cc_final: 0.6565 (pp-130) REVERT: H 161 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8812 (ttp) REVERT: H 408 MET cc_start: 0.7415 (mpm) cc_final: 0.6714 (ppp) REVERT: H 482 LEU cc_start: 0.9354 (mm) cc_final: 0.9029 (mm) REVERT: J 161 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8813 (ttp) REVERT: J 408 MET cc_start: 0.7422 (mpm) cc_final: 0.6709 (ppp) REVERT: J 482 LEU cc_start: 0.9351 (mm) cc_final: 0.9033 (mm) REVERT: L 408 MET cc_start: 0.7833 (mpp) cc_final: 0.6937 (ppp) outliers start: 169 outliers final: 66 residues processed: 484 average time/residue: 1.5127 time to fit residues: 911.2686 Evaluate side-chains 422 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 344 time to evaluate : 4.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 497 PHE Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 638 SER Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 110 MET Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 322 GLU Chi-restraints excluded: chain G residue 396 MET Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 638 SER Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 464 HIS Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 529 GLN Chi-restraints excluded: chain F residue 638 SER Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 402 LEU Chi-restraints excluded: chain I residue 451 LEU Chi-restraints excluded: chain I residue 522 MET Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 451 LEU Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 638 SER Chi-restraints excluded: chain K residue 707 ARG Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 497 PHE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 497 PHE Chi-restraints excluded: chain H residue 161 MET Chi-restraints excluded: chain H residue 240 PHE Chi-restraints excluded: chain H residue 273 SER Chi-restraints excluded: chain H residue 497 PHE Chi-restraints excluded: chain H residue 510 ILE Chi-restraints excluded: chain J residue 161 MET Chi-restraints excluded: chain J residue 240 PHE Chi-restraints excluded: chain J residue 497 PHE Chi-restraints excluded: chain J residue 510 ILE Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 497 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 574 optimal weight: 2.9990 chunk 391 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 513 optimal weight: 4.9990 chunk 284 optimal weight: 7.9990 chunk 588 optimal weight: 0.8980 chunk 477 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 352 optimal weight: 20.0000 chunk 619 optimal weight: 3.9990 chunk 174 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 153 GLN E 208 GLN ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 GLN G 329 HIS I 329 HIS I 457 GLN K 329 HIS ** K 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN D 153 GLN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 153 GLN L 153 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 56742 Z= 0.278 Angle : 0.572 12.383 76602 Z= 0.301 Chirality : 0.045 0.227 8436 Planarity : 0.004 0.051 10044 Dihedral : 4.419 26.016 7921 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.31 % Allowed : 13.82 % Favored : 83.88 % 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: 1.20 (0.10), residues: 7146 helix: 2.16 (0.10), residues: 2616 sheet: 1.10 (0.13), residues: 1230 loop : -0.44 (0.10), residues: 3300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 276 HIS 0.024 0.001 HIS F 464 PHE 0.014 0.001 PHE B 497 TYR 0.021 0.001 TYR I 453 ARG 0.011 0.000 ARG K 361 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 375 time to evaluate : 4.617 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: E 408 MET cc_start: 0.7354 (mpp) cc_final: 0.6588 (pp-130) REVERT: A 433 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.7961 (ttp) REVERT: A 675 MET cc_start: -0.1824 (mtt) cc_final: -0.2881 (ptm) REVERT: A 682 MET cc_start: -0.0838 (ptm) cc_final: -0.2172 (ttt) REVERT: C 215 MET cc_start: 0.4334 (tmm) cc_final: 0.3498 (mmm) REVERT: C 251 ASP cc_start: -0.0313 (OUTLIER) cc_final: -0.1385 (p0) REVERT: C 361 ARG cc_start: 0.8194 (mtp85) cc_final: 0.7993 (mtp180) REVERT: C 675 MET cc_start: -0.1766 (mtt) cc_final: -0.2733 (tmt) REVERT: G 302 LEU cc_start: 0.4957 (OUTLIER) cc_final: 0.4683 (tt) REVERT: G 464 HIS cc_start: 0.6678 (m-70) cc_final: 0.6467 (m90) REVERT: G 675 MET cc_start: -0.1832 (mtt) cc_final: -0.2894 (ptm) REVERT: F 334 MET cc_start: 0.6174 (tmt) cc_final: 0.5809 (tmt) REVERT: F 457 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8065 (mt0) REVERT: F 675 MET cc_start: -0.1785 (mtt) cc_final: -0.2757 (tmt) REVERT: I 215 MET cc_start: 0.5474 (tpp) cc_final: 0.5120 (tpp) REVERT: I 302 LEU cc_start: 0.4953 (OUTLIER) cc_final: 0.4676 (tt) REVERT: I 334 MET cc_start: 0.6190 (tmt) cc_final: 0.5886 (tmt) REVERT: I 457 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: I 464 HIS cc_start: 0.6682 (m-70) cc_final: 0.6465 (m90) REVERT: I 522 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8803 (tpp) REVERT: I 675 MET cc_start: -0.1824 (mtt) cc_final: -0.2878 (ptm) REVERT: K 675 MET cc_start: -0.2003 (mtt) cc_final: -0.2995 (ptm) REVERT: K 680 MET cc_start: 0.0733 (mtt) cc_final: -0.0264 (mpt) REVERT: B 130 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8832 (mp0) REVERT: B 408 MET cc_start: 0.7258 (mpm) cc_final: 0.6494 (ppp) REVERT: D 408 MET cc_start: 0.7354 (mpp) cc_final: 0.6587 (pp-130) REVERT: H 482 LEU cc_start: 0.9344 (mm) cc_final: 0.9039 (mm) REVERT: J 482 LEU cc_start: 0.9340 (mm) cc_final: 0.9041 (mm) REVERT: L 130 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8840 (mp0) REVERT: L 408 MET cc_start: 0.7822 (mpp) cc_final: 0.6918 (ppp) outliers start: 136 outliers final: 56 residues processed: 454 average time/residue: 1.4373 time to fit residues: 823.4774 Evaluate side-chains 415 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 350 time to evaluate : 4.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 497 PHE Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 93 ASP Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 349 MET Chi-restraints excluded: chain G residue 451 LEU Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 529 GLN Chi-restraints excluded: chain F residue 70 LYS Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 457 GLN Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 465 THR Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 93 ASP Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 457 GLN Chi-restraints excluded: chain I residue 522 MET Chi-restraints excluded: chain I residue 529 GLN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 497 PHE Chi-restraints excluded: chain H residue 240 PHE Chi-restraints excluded: chain H residue 497 PHE Chi-restraints excluded: chain H residue 510 ILE Chi-restraints excluded: chain J residue 240 PHE Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 497 PHE Chi-restraints excluded: chain J residue 510 ILE Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 315 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 232 optimal weight: 6.9990 chunk 621 optimal weight: 4.9990 chunk 136 optimal weight: 50.0000 chunk 405 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 chunk 690 optimal weight: 8.9990 chunk 573 optimal weight: 0.6980 chunk 319 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 228 optimal weight: 6.9990 chunk 362 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 HIS ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 GLN G 329 HIS ** F 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 329 HIS K 329 HIS ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 HIS H 285 HIS J 285 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 56742 Z= 0.398 Angle : 0.609 11.012 76602 Z= 0.323 Chirality : 0.046 0.234 8436 Planarity : 0.004 0.052 10044 Dihedral : 4.505 26.098 7920 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.48 % Allowed : 13.80 % Favored : 83.72 % 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: 1.05 (0.10), residues: 7146 helix: 2.05 (0.10), residues: 2610 sheet: 0.75 (0.13), residues: 1410 loop : -0.48 (0.11), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 276 HIS 0.012 0.001 HIS A 255 PHE 0.018 0.002 PHE I 261 TYR 0.024 0.002 TYR D 457 ARG 0.011 0.001 ARG I 707 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 364 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: A 361 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7944 (mtp180) REVERT: A 433 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8060 (ttp) REVERT: A 675 MET cc_start: -0.1893 (mtt) cc_final: -0.3233 (ttp) REVERT: A 682 MET cc_start: -0.0875 (ptm) cc_final: -0.2189 (ttt) REVERT: C 215 MET cc_start: 0.4284 (tmm) cc_final: 0.3610 (mmm) REVERT: C 251 ASP cc_start: 0.0384 (OUTLIER) cc_final: -0.1361 (p0) REVERT: C 334 MET cc_start: 0.6476 (tmt) cc_final: 0.5465 (ppp) REVERT: C 675 MET cc_start: -0.1545 (mtt) cc_final: -0.2542 (ttp) REVERT: G 302 LEU cc_start: 0.4937 (OUTLIER) cc_final: 0.4675 (tt) REVERT: G 336 MET cc_start: 0.5508 (OUTLIER) cc_final: 0.5169 (tpp) REVERT: G 464 HIS cc_start: 0.6839 (m-70) cc_final: 0.6634 (OUTLIER) REVERT: G 675 MET cc_start: -0.1550 (mtt) cc_final: -0.3036 (ttp) REVERT: F 170 MET cc_start: 0.4398 (mmp) cc_final: 0.3907 (mmt) REVERT: F 334 MET cc_start: 0.6093 (tmt) cc_final: 0.5841 (tmt) REVERT: F 675 MET cc_start: -0.1664 (mtt) cc_final: -0.2776 (tmt) REVERT: I 215 MET cc_start: 0.5363 (tpp) cc_final: 0.4871 (tpp) REVERT: I 325 MET cc_start: 0.7423 (tmm) cc_final: 0.7186 (tmm) REVERT: I 334 MET cc_start: 0.6183 (tmt) cc_final: 0.5764 (tmt) REVERT: I 464 HIS cc_start: 0.6847 (m-70) cc_final: 0.6636 (OUTLIER) REVERT: I 522 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8801 (tpp) REVERT: I 675 MET cc_start: -0.1534 (mtt) cc_final: -0.3045 (ttp) REVERT: K 349 MET cc_start: 0.8244 (mmt) cc_final: 0.7997 (ttt) REVERT: K 361 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7894 (mtp180) REVERT: K 675 MET cc_start: -0.1924 (mtt) cc_final: -0.3304 (ttp) REVERT: K 680 MET cc_start: 0.0787 (mtt) cc_final: 0.0418 (mpt) REVERT: B 130 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8836 (mp0) REVERT: H 408 MET cc_start: 0.7466 (mpm) cc_final: 0.6605 (ppp) REVERT: H 482 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9041 (mm) REVERT: J 408 MET cc_start: 0.7473 (mpm) cc_final: 0.6601 (ppp) REVERT: J 482 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9045 (mm) REVERT: L 130 GLU cc_start: 0.9268 (OUTLIER) cc_final: 0.8843 (mp0) outliers start: 146 outliers final: 62 residues processed: 459 average time/residue: 1.4670 time to fit residues: 843.3334 Evaluate side-chains 412 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 343 time to evaluate : 4.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 497 PHE Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 330 ASN Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 457 GLN Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 522 MET Chi-restraints excluded: chain C residue 638 SER Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 336 MET Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 529 GLN Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 638 SER Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 451 LEU Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 522 MET Chi-restraints excluded: chain I residue 529 GLN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 638 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 497 PHE Chi-restraints excluded: chain H residue 240 PHE Chi-restraints excluded: chain H residue 273 SER Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 497 PHE Chi-restraints excluded: chain H residue 510 ILE Chi-restraints excluded: chain J residue 240 PHE Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 497 PHE Chi-restraints excluded: chain J residue 510 ILE Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 315 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 666 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 393 optimal weight: 20.0000 chunk 504 optimal weight: 0.8980 chunk 390 optimal weight: 9.9990 chunk 581 optimal weight: 0.4980 chunk 385 optimal weight: 50.0000 chunk 688 optimal weight: 2.9990 chunk 430 optimal weight: 5.9990 chunk 419 optimal weight: 1.9990 chunk 317 optimal weight: 9.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 GLN ** A 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 457 GLN I 329 HIS I 337 ASN K 457 GLN D 208 GLN ** D 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.4189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 56742 Z= 0.227 Angle : 0.571 11.412 76602 Z= 0.298 Chirality : 0.045 0.230 8436 Planarity : 0.004 0.051 10044 Dihedral : 4.364 26.143 7920 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.78 % Allowed : 14.36 % 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: 1.19 (0.10), residues: 7146 helix: 2.14 (0.10), residues: 2616 sheet: 1.04 (0.13), residues: 1410 loop : -0.50 (0.11), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 276 HIS 0.010 0.001 HIS A 255 PHE 0.043 0.001 PHE L 497 TYR 0.023 0.001 TYR I 453 ARG 0.013 0.000 ARG B 490 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 374 time to evaluate : 4.798 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: A 361 ARG cc_start: 0.8280 (mtp85) cc_final: 0.7960 (mtp180) REVERT: A 433 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.7922 (ttp) REVERT: A 675 MET cc_start: -0.1744 (mtt) cc_final: -0.3169 (ttp) REVERT: C 136 MET cc_start: 0.7693 (mtt) cc_final: 0.5265 (mtt) REVERT: C 215 MET cc_start: 0.4411 (tmm) cc_final: 0.3556 (mmm) REVERT: C 251 ASP cc_start: 0.0213 (OUTLIER) cc_final: -0.1271 (p0) REVERT: C 334 MET cc_start: 0.6336 (tmt) cc_final: 0.5366 (ppp) REVERT: C 529 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8428 (pp30) REVERT: C 675 MET cc_start: -0.1353 (mtt) cc_final: -0.2669 (tmt) REVERT: G 302 LEU cc_start: 0.5055 (OUTLIER) cc_final: 0.4793 (tt) REVERT: G 675 MET cc_start: -0.1744 (mtt) cc_final: -0.2618 (pp-130) REVERT: F 215 MET cc_start: 0.5248 (tpp) cc_final: 0.3998 (ttt) REVERT: F 529 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8429 (pp30) REVERT: F 675 MET cc_start: -0.1674 (mtt) cc_final: -0.2830 (tmt) REVERT: I 136 MET cc_start: 0.7951 (mtt) cc_final: 0.7746 (mtt) REVERT: I 215 MET cc_start: 0.5316 (tpp) cc_final: 0.4329 (ttt) REVERT: I 334 MET cc_start: 0.6171 (tmt) cc_final: 0.5714 (tmt) REVERT: I 522 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8794 (tpp) REVERT: I 675 MET cc_start: -0.1726 (mtt) cc_final: -0.2630 (pp-130) REVERT: K 349 MET cc_start: 0.8230 (mmt) cc_final: 0.7969 (mtt) REVERT: K 361 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7965 (mtp180) REVERT: K 675 MET cc_start: -0.1845 (mtt) cc_final: -0.3276 (ttp) REVERT: K 680 MET cc_start: 0.0495 (mtt) cc_final: 0.0215 (mpt) REVERT: K 682 MET cc_start: -0.0705 (ptm) cc_final: -0.0946 (ptt) REVERT: B 130 GLU cc_start: 0.9253 (OUTLIER) cc_final: 0.8793 (mp0) REVERT: B 408 MET cc_start: 0.7132 (mpm) cc_final: 0.6471 (ppp) REVERT: H 408 MET cc_start: 0.7439 (mpm) cc_final: 0.6593 (ppp) REVERT: H 482 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9085 (mm) REVERT: J 408 MET cc_start: 0.7441 (mpm) cc_final: 0.6590 (ppp) REVERT: J 482 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9053 (mm) REVERT: L 130 GLU cc_start: 0.9251 (OUTLIER) cc_final: 0.8804 (mp0) REVERT: L 408 MET cc_start: 0.7548 (mpp) cc_final: 0.6915 (ppp) outliers start: 105 outliers final: 51 residues processed: 438 average time/residue: 1.5312 time to fit residues: 832.8799 Evaluate side-chains 416 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 355 time to evaluate : 4.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 273 SER Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 497 PHE Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 405 LEU Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 464 HIS Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 529 GLN Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 457 GLN Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain F residue 529 GLN Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 464 HIS Chi-restraints excluded: chain I residue 522 MET Chi-restraints excluded: chain I residue 529 GLN Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 638 SER Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 497 PHE Chi-restraints excluded: chain H residue 240 PHE Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 497 PHE Chi-restraints excluded: chain J residue 240 PHE Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 497 PHE Chi-restraints excluded: chain J residue 510 ILE Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 380 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 425 optimal weight: 5.9990 chunk 274 optimal weight: 7.9990 chunk 411 optimal weight: 10.0000 chunk 207 optimal weight: 30.0000 chunk 135 optimal weight: 40.0000 chunk 133 optimal weight: 20.0000 chunk 437 optimal weight: 7.9990 chunk 468 optimal weight: 0.9990 chunk 340 optimal weight: 1.9990 chunk 64 optimal weight: 30.0000 chunk 540 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN G 457 GLN I 329 HIS ** K 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 56742 Z= 0.360 Angle : 0.608 10.003 76602 Z= 0.319 Chirality : 0.046 0.233 8436 Planarity : 0.004 0.091 10044 Dihedral : 4.444 26.120 7920 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.76 % Allowed : 14.63 % Favored : 83.60 % 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: 1.06 (0.10), residues: 7146 helix: 2.03 (0.10), residues: 2616 sheet: 1.05 (0.13), residues: 1326 loop : -0.58 (0.10), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 276 HIS 0.009 0.001 HIS A 255 PHE 0.033 0.001 PHE F 323 TYR 0.025 0.002 TYR I 453 ARG 0.010 0.001 ARG F 361 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 365 time to evaluate : 4.825 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: A 349 MET cc_start: 0.8180 (mmt) cc_final: 0.7947 (mtt) REVERT: A 361 ARG cc_start: 0.8321 (mtp85) cc_final: 0.8002 (mtp180) REVERT: A 433 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.7987 (ttp) REVERT: A 675 MET cc_start: -0.1573 (mtt) cc_final: -0.3130 (ttp) REVERT: A 682 MET cc_start: -0.0952 (ptm) cc_final: -0.2234 (ttt) REVERT: C 136 MET cc_start: 0.7438 (mtt) cc_final: 0.7195 (mtt) REVERT: C 170 MET cc_start: 0.3612 (mmp) cc_final: 0.3289 (mmt) REVERT: C 215 MET cc_start: 0.4486 (tmm) cc_final: 0.3559 (mmm) REVERT: C 251 ASP cc_start: 0.0436 (OUTLIER) cc_final: -0.1193 (p0) REVERT: C 334 MET cc_start: 0.6377 (tmt) cc_final: 0.5639 (ppp) REVERT: C 529 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8420 (pp30) REVERT: C 675 MET cc_start: -0.1491 (mtt) cc_final: -0.2800 (tmt) REVERT: G 302 LEU cc_start: 0.5098 (OUTLIER) cc_final: 0.4843 (tt) REVERT: G 443 ASP cc_start: 0.6369 (t0) cc_final: 0.6167 (t70) REVERT: G 675 MET cc_start: -0.1659 (mtt) cc_final: -0.3030 (ttp) REVERT: F 136 MET cc_start: 0.7811 (mtt) cc_final: 0.5160 (mtt) REVERT: F 334 MET cc_start: 0.6093 (tmt) cc_final: 0.5491 (ppp) REVERT: F 529 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8422 (pp30) REVERT: F 675 MET cc_start: -0.1650 (mtt) cc_final: -0.2918 (tmt) REVERT: I 215 MET cc_start: 0.5203 (tpp) cc_final: 0.3934 (tpt) REVERT: I 334 MET cc_start: 0.6174 (tmt) cc_final: 0.5708 (tmt) REVERT: I 522 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8810 (tpp) REVERT: I 675 MET cc_start: -0.1639 (mtt) cc_final: -0.3013 (ttp) REVERT: K 361 ARG cc_start: 0.8307 (mtp85) cc_final: 0.7990 (mtp180) REVERT: K 675 MET cc_start: -0.1769 (mtt) cc_final: -0.3297 (ttp) REVERT: K 680 MET cc_start: 0.0563 (mtt) cc_final: 0.0213 (mpt) REVERT: B 130 GLU cc_start: 0.9265 (OUTLIER) cc_final: 0.8823 (mp0) REVERT: B 408 MET cc_start: 0.7196 (mpm) cc_final: 0.6430 (ppp) REVERT: H 408 MET cc_start: 0.7443 (mpm) cc_final: 0.6596 (ppp) REVERT: H 482 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9071 (mm) REVERT: J 408 MET cc_start: 0.7447 (mpm) cc_final: 0.6592 (ppp) REVERT: J 482 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9064 (mm) REVERT: L 130 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8831 (mp0) REVERT: L 408 MET cc_start: 0.7596 (mpp) cc_final: 0.6916 (ppp) outliers start: 104 outliers final: 54 residues processed: 430 average time/residue: 1.4769 time to fit residues: 796.5835 Evaluate side-chains 408 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 344 time to evaluate : 4.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 239 ILE Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 497 PHE Chi-restraints excluded: chain A residue 48 ASN Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 433 MET Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 465 THR Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 638 SER Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 178 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 302 LEU Chi-restraints excluded: chain G residue 465 THR Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain F residue 529 GLN Chi-restraints excluded: chain F residue 638 SER Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 178 VAL Chi-restraints excluded: chain I residue 465 THR Chi-restraints excluded: chain I residue 522 MET Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 178 VAL Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain K residue 638 SER Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 273 SER Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 497 PHE Chi-restraints excluded: chain H residue 240 PHE Chi-restraints excluded: chain H residue 273 SER Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 497 PHE Chi-restraints excluded: chain J residue 240 PHE Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 497 PHE Chi-restraints excluded: chain L residue 114 VAL Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain L residue 273 SER Chi-restraints excluded: chain L residue 315 ASP Chi-restraints excluded: chain L residue 380 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 626 optimal weight: 0.8980 chunk 659 optimal weight: 1.9990 chunk 601 optimal weight: 2.9990 chunk 641 optimal weight: 4.9990 chunk 385 optimal weight: 50.0000 chunk 279 optimal weight: 7.9990 chunk 503 optimal weight: 0.9990 chunk 196 optimal weight: 9.9990 chunk 579 optimal weight: 0.9980 chunk 606 optimal weight: 0.9980 chunk 639 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 266 HIS ** K 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 56742 Z= 0.166 Angle : 0.562 11.506 76602 Z= 0.290 Chirality : 0.044 0.228 8436 Planarity : 0.004 0.108 10044 Dihedral : 4.270 25.851 7920 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.95 % Allowed : 15.56 % Favored : 83.49 % 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: 1.23 (0.10), residues: 7146 helix: 2.21 (0.10), residues: 2616 sheet: 1.15 (0.13), residues: 1386 loop : -0.55 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP L 276 HIS 0.009 0.001 HIS A 255 PHE 0.025 0.001 PHE F 323 TYR 0.027 0.001 TYR I 453 ARG 0.007 0.000 ARG C 361 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 367 time to evaluate : 4.793 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: A 325 MET cc_start: 0.7359 (tmm) cc_final: 0.6882 (tmm) REVERT: A 361 ARG cc_start: 0.8346 (mtp85) cc_final: 0.8050 (mtp180) REVERT: A 522 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.8699 (tpt) REVERT: A 675 MET cc_start: -0.1407 (mtt) cc_final: -0.2670 (ttp) REVERT: C 170 MET cc_start: 0.4132 (mmp) cc_final: 0.3623 (mmt) REVERT: C 215 MET cc_start: 0.4318 (tmm) cc_final: 0.3539 (mmm) REVERT: C 334 MET cc_start: 0.6355 (tmt) cc_final: 0.6141 (tmt) REVERT: C 675 MET cc_start: -0.1482 (mtt) cc_final: -0.2764 (tmt) REVERT: G 65 MET cc_start: 0.8179 (ptp) cc_final: 0.7907 (ptp) REVERT: G 443 ASP cc_start: 0.6702 (t0) cc_final: 0.6500 (t70) REVERT: G 675 MET cc_start: -0.1481 (mtt) cc_final: -0.2706 (pp-130) REVERT: G 677 MET cc_start: 0.1892 (OUTLIER) cc_final: 0.1526 (tmm) REVERT: F 215 MET cc_start: 0.5667 (tpp) cc_final: 0.4482 (ttt) REVERT: F 334 MET cc_start: 0.6024 (tmt) cc_final: 0.5432 (ppp) REVERT: F 675 MET cc_start: -0.1497 (mtt) cc_final: -0.2830 (tmt) REVERT: I 65 MET cc_start: 0.8170 (ptp) cc_final: 0.7904 (ptp) REVERT: I 215 MET cc_start: 0.5319 (tpp) cc_final: 0.4539 (ttt) REVERT: I 334 MET cc_start: 0.6173 (tmt) cc_final: 0.5731 (tmt) REVERT: I 522 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8758 (tpp) REVERT: I 675 MET cc_start: -0.1356 (mtt) cc_final: -0.2621 (pp-130) REVERT: I 677 MET cc_start: 0.1910 (OUTLIER) cc_final: 0.1598 (tmm) REVERT: K 361 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7992 (mtp180) REVERT: K 522 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8697 (tpt) REVERT: K 675 MET cc_start: -0.1782 (mtt) cc_final: -0.3292 (ttp) REVERT: B 130 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8746 (mp0) REVERT: B 408 MET cc_start: 0.6988 (mpm) cc_final: 0.6353 (ppp) REVERT: H 408 MET cc_start: 0.7187 (mpm) cc_final: 0.6548 (ppp) REVERT: H 482 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9088 (mm) REVERT: J 408 MET cc_start: 0.7189 (mpm) cc_final: 0.6544 (ppp) REVERT: J 482 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9081 (mm) REVERT: L 130 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8754 (mp0) REVERT: L 408 MET cc_start: 0.7532 (mpp) cc_final: 0.6895 (ppp) outliers start: 56 outliers final: 28 residues processed: 393 average time/residue: 1.5479 time to fit residues: 759.1017 Evaluate side-chains 387 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 350 time to evaluate : 4.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 229 GLU Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 497 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 522 MET Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain G residue 349 MET Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 677 MET Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain I residue 48 ASN Chi-restraints excluded: chain I residue 522 MET Chi-restraints excluded: chain I residue 677 MET Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 93 ASP Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain K residue 522 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain D residue 240 PHE Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 497 PHE Chi-restraints excluded: chain H residue 240 PHE Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 497 PHE Chi-restraints excluded: chain J residue 240 PHE Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 497 PHE Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 240 PHE Chi-restraints excluded: chain L residue 380 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 421 optimal weight: 0.5980 chunk 678 optimal weight: 0.8980 chunk 413 optimal weight: 2.9990 chunk 321 optimal weight: 5.9990 chunk 471 optimal weight: 0.7980 chunk 711 optimal weight: 2.9990 chunk 654 optimal weight: 0.8980 chunk 566 optimal weight: 0.6980 chunk 58 optimal weight: 0.0470 chunk 437 optimal weight: 6.9990 chunk 347 optimal weight: 10.0000 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 329 HIS ** K 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 56742 Z= 0.145 Angle : 0.559 11.612 76602 Z= 0.287 Chirality : 0.044 0.227 8436 Planarity : 0.004 0.084 10044 Dihedral : 4.116 25.666 7920 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.92 % Allowed : 15.80 % Favored : 83.28 % 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: 1.33 (0.10), residues: 7146 helix: 2.26 (0.10), residues: 2616 sheet: 1.22 (0.13), residues: 1386 loop : -0.47 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 276 HIS 0.025 0.001 HIS D 266 PHE 0.027 0.001 PHE B 497 TYR 0.024 0.001 TYR I 453 ARG 0.010 0.000 ARG C 361 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14292 Ramachandran restraints generated. 7146 Oldfield, 0 Emsley, 7146 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 370 time to evaluate : 4.807 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: A 325 MET cc_start: 0.7308 (tmm) cc_final: 0.6835 (tmm) REVERT: A 361 ARG cc_start: 0.8354 (mtp85) cc_final: 0.8063 (mtp180) REVERT: A 522 MET cc_start: 0.8966 (tpp) cc_final: 0.8701 (tpt) REVERT: A 675 MET cc_start: -0.1434 (mtt) cc_final: -0.2499 (ptm) REVERT: A 680 MET cc_start: 0.1950 (OUTLIER) cc_final: 0.1596 (mpp) REVERT: C 170 MET cc_start: 0.4278 (mmp) cc_final: 0.3925 (mmt) REVERT: C 215 MET cc_start: 0.4287 (tmm) cc_final: 0.3709 (mmm) REVERT: C 675 MET cc_start: -0.1506 (mtt) cc_final: -0.2763 (tmt) REVERT: C 682 MET cc_start: -0.1695 (OUTLIER) cc_final: -0.2333 (ttt) REVERT: G 334 MET cc_start: 0.6027 (OUTLIER) cc_final: 0.5671 (ppp) REVERT: G 675 MET cc_start: -0.1415 (mtt) cc_final: -0.2564 (pp-130) REVERT: G 677 MET cc_start: 0.2012 (OUTLIER) cc_final: 0.1157 (tpt) REVERT: F 215 MET cc_start: 0.5981 (tpp) cc_final: 0.5369 (tmm) REVERT: F 334 MET cc_start: 0.6015 (tmt) cc_final: 0.5464 (ppp) REVERT: F 675 MET cc_start: -0.1500 (mtt) cc_final: -0.2815 (tmt) REVERT: F 682 MET cc_start: -0.1359 (OUTLIER) cc_final: -0.2131 (ttt) REVERT: I 215 MET cc_start: 0.5366 (tpp) cc_final: 0.4146 (tpt) REVERT: I 334 MET cc_start: 0.6318 (tmt) cc_final: 0.5960 (tmt) REVERT: I 396 MET cc_start: 0.6448 (ttp) cc_final: 0.5828 (tmm) REVERT: I 522 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8783 (tpp) REVERT: I 675 MET cc_start: -0.1733 (mtt) cc_final: -0.2220 (pp-130) REVERT: I 677 MET cc_start: 0.1984 (OUTLIER) cc_final: 0.1562 (tpp) REVERT: I 680 MET cc_start: 0.0335 (mpt) cc_final: 0.0119 (pmm) REVERT: K 361 ARG cc_start: 0.8302 (mtp85) cc_final: 0.8022 (mtp180) REVERT: K 522 MET cc_start: 0.8963 (tpp) cc_final: 0.8701 (tpt) REVERT: K 675 MET cc_start: -0.1618 (mtt) cc_final: -0.3204 (ttp) REVERT: B 130 GLU cc_start: 0.9215 (OUTLIER) cc_final: 0.8749 (mp0) REVERT: H 408 MET cc_start: 0.7197 (mpm) cc_final: 0.6540 (ppp) REVERT: H 482 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9078 (mm) REVERT: J 408 MET cc_start: 0.7203 (mpm) cc_final: 0.6538 (ppp) REVERT: J 482 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9068 (mm) REVERT: L 130 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.8760 (mp0) REVERT: L 408 MET cc_start: 0.7576 (mpp) cc_final: 0.6858 (ppp) outliers start: 54 outliers final: 23 residues processed: 395 average time/residue: 1.4688 time to fit residues: 730.7265 Evaluate side-chains 385 residues out of total 5898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 351 time to evaluate : 4.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 299 LYS Chi-restraints excluded: chain E residue 408 MET Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 497 PHE Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 261 PHE Chi-restraints excluded: chain C residue 682 MET Chi-restraints excluded: chain G residue 334 MET Chi-restraints excluded: chain G residue 493 HIS Chi-restraints excluded: chain G residue 677 MET Chi-restraints excluded: chain F residue 405 LEU Chi-restraints excluded: chain F residue 493 HIS Chi-restraints excluded: chain F residue 682 MET Chi-restraints excluded: chain I residue 522 MET Chi-restraints excluded: chain I residue 677 MET Chi-restraints excluded: chain K residue 48 ASN Chi-restraints excluded: chain K residue 405 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 497 PHE Chi-restraints excluded: chain H residue 240 PHE Chi-restraints excluded: chain H residue 482 LEU Chi-restraints excluded: chain H residue 497 PHE Chi-restraints excluded: chain J residue 240 PHE Chi-restraints excluded: chain J residue 273 SER Chi-restraints excluded: chain J residue 482 LEU Chi-restraints excluded: chain J residue 497 PHE Chi-restraints excluded: chain L residue 130 GLU Chi-restraints excluded: chain L residue 380 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 714 random chunks: chunk 449 optimal weight: 50.0000 chunk 603 optimal weight: 7.9990 chunk 173 optimal weight: 10.0000 chunk 522 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 157 optimal weight: 0.6980 chunk 567 optimal weight: 0.0670 chunk 237 optimal weight: 8.9990 chunk 582 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 overall best weight: 2.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 337 ASN ** G 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.153534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.090072 restraints weight = 124380.194| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.41 r_work: 0.2698 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.4565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 56742 Z= 0.251 Angle : 0.576 12.601 76602 Z= 0.297 Chirality : 0.045 0.228 8436 Planarity : 0.004 0.070 10044 Dihedral : 4.175 26.093 7920 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.88 % Allowed : 16.12 % Favored : 82.99 % 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: 1.27 (0.10), residues: 7146 helix: 2.17 (0.10), residues: 2628 sheet: 1.22 (0.13), residues: 1386 loop : -0.49 (0.11), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 276 HIS 0.013 0.001 HIS D 266 PHE 0.018 0.001 PHE F 323 TYR 0.025 0.001 TYR I 453 ARG 0.011 0.000 ARG F 361 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15854.93 seconds wall clock time: 276 minutes 14.77 seconds (16574.77 seconds total)