Starting phenix.real_space_refine on Sun Mar 17 13:05:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyp_0095/03_2024/6gyp_0095.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyp_0095/03_2024/6gyp_0095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyp_0095/03_2024/6gyp_0095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyp_0095/03_2024/6gyp_0095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyp_0095/03_2024/6gyp_0095.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyp_0095/03_2024/6gyp_0095.pdb" } resolution = 3.6 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= 0.007 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 68 5.16 5 C 11539 2.51 5 N 2932 2.21 5 O 3272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 295": "NH1" <-> "NH2" Residue "B ARG 375": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 591": "NH1" <-> "NH2" Residue "A ARG 17": "NH1" <-> "NH2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 308": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 330": "NH1" <-> "NH2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 409": "NH1" <-> "NH2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "A ARG 468": "NH1" <-> "NH2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 121": "NH1" <-> "NH2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 161": "NH1" <-> "NH2" Residue "D ARG 168": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "E TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 704": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17811 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4374 Classifications: {'peptide': 527} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 509} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3526 Classifications: {'peptide': 423} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 411} Chain breaks: 2 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "C" Number of atoms: 4362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4362 Classifications: {'peptide': 528} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 510} Unresolved chain links: 1 Chain breaks: 2 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 5 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1226 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 143} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 4265 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 35, 'TRANS': 476} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 10.14, per 1000 atoms: 0.57 Number of scatterers: 17811 At special positions: 0 Unit cell: (170.66, 143.1, 97.52, 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 68 16.00 O 3272 8.00 N 2932 7.00 C 11539 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 215 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.35 Conformation dependent library (CDL) restraints added in 3.0 seconds 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4180 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 10 sheets defined 60.8% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'B' and resid 58 through 72 removed outlier: 3.887A pdb=" N PHE B 64 " --> pdb=" O ASP B 60 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.921A pdb=" N TYR B 78 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 105 removed outlier: 4.154A pdb=" N MET B 100 " --> pdb=" O THR B 96 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 122 Processing helix chain 'B' and resid 125 through 130 removed outlier: 4.421A pdb=" N SER B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 135 removed outlier: 3.515A pdb=" N GLU B 135 " --> pdb=" O ASP B 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 136 through 146 Processing helix chain 'B' and resid 153 through 173 removed outlier: 4.132A pdb=" N TRP B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 181 removed outlier: 3.725A pdb=" N GLU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 Processing helix chain 'B' and resid 204 through 222 Processing helix chain 'B' and resid 230 through 241 removed outlier: 4.021A pdb=" N VAL B 234 " --> pdb=" O ASP B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 251 through 265 removed outlier: 3.567A pdb=" N SER B 255 " --> pdb=" O LEU B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 302 removed outlier: 4.124A pdb=" N ILE B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 357 removed outlier: 3.830A pdb=" N ILE B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 352 " --> pdb=" O ILE B 348 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LEU B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 385 Processing helix chain 'B' and resid 394 through 422 removed outlier: 3.712A pdb=" N PHE B 398 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ILE B 407 " --> pdb=" O ALA B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 444 removed outlier: 3.571A pdb=" N ASN B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.535A pdb=" N PHE B 453 " --> pdb=" O SER B 450 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 477 removed outlier: 3.949A pdb=" N MET B 460 " --> pdb=" O HIS B 456 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 494 removed outlier: 3.741A pdb=" N GLN B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 496 No H-bonds generated for 'chain 'B' and resid 495 through 496' Processing helix chain 'B' and resid 497 through 500 removed outlier: 3.681A pdb=" N PHE B 500 " --> pdb=" O PRO B 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 497 through 500' Processing helix chain 'B' and resid 501 through 524 removed outlier: 3.740A pdb=" N ASP B 505 " --> pdb=" O GLY B 501 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 523 " --> pdb=" O LEU B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 552 removed outlier: 3.910A pdb=" N ILE B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 560 Processing helix chain 'B' and resid 589 through 601 removed outlier: 4.110A pdb=" N ILE B 593 " --> pdb=" O ASP B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 607 removed outlier: 3.886A pdb=" N ASP B 605 " --> pdb=" O ASN B 602 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 607 " --> pdb=" O SER B 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 12 removed outlier: 3.923A pdb=" N LEU A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 56 through 66 removed outlier: 3.752A pdb=" N LYS A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.627A pdb=" N GLU A 78 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 94 removed outlier: 5.232A pdb=" N GLU A 89 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N TRP A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.738A pdb=" N VAL A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.584A pdb=" N VAL A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.635A pdb=" N MET A 270 " --> pdb=" O MET A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 288 removed outlier: 3.905A pdb=" N GLU A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU A 286 " --> pdb=" O LYS A 282 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 4.098A pdb=" N ILE A 350 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.932A pdb=" N ASN A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 379 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.857A pdb=" N VAL A 430 " --> pdb=" O CYS A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'C' and resid 56 through 74 removed outlier: 4.010A pdb=" N ASP C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N TYR C 70 " --> pdb=" O GLN C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 106 removed outlier: 4.452A pdb=" N GLU C 97 " --> pdb=" O ASP C 93 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU C 106 " --> pdb=" O TRP C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 122 removed outlier: 3.762A pdb=" N SER C 111 " --> pdb=" O GLN C 107 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 130 removed outlier: 4.065A pdb=" N SER C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 135 Processing helix chain 'C' and resid 136 through 144 Processing helix chain 'C' and resid 145 through 149 removed outlier: 3.973A pdb=" N ALA C 148 " --> pdb=" O ASP C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 173 Processing helix chain 'C' and resid 175 through 183 Processing helix chain 'C' and resid 185 through 193 removed outlier: 3.542A pdb=" N HIS C 189 " --> pdb=" O VAL C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 223 removed outlier: 3.616A pdb=" N CYS C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 241 removed outlier: 4.149A pdb=" N VAL C 234 " --> pdb=" O ASP C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 249 removed outlier: 3.570A pdb=" N ASP C 248 " --> pdb=" O THR C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 266 Processing helix chain 'C' and resid 279 through 302 removed outlier: 3.690A pdb=" N ILE C 284 " --> pdb=" O PRO C 280 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 316 Processing helix chain 'C' and resid 341 through 357 removed outlier: 3.534A pdb=" N TYR C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 385 Processing helix chain 'C' and resid 393 through 422 removed outlier: 3.573A pdb=" N ARG C 397 " --> pdb=" O SER C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 443 Processing helix chain 'C' and resid 444 through 448 removed outlier: 3.969A pdb=" N ALA C 448 " --> pdb=" O ASN C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 456 removed outlier: 3.732A pdb=" N HIS C 456 " --> pdb=" O PHE C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 477 removed outlier: 3.779A pdb=" N ILE C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 494 Processing helix chain 'C' and resid 495 through 496 No H-bonds generated for 'chain 'C' and resid 495 through 496' Processing helix chain 'C' and resid 497 through 500 removed outlier: 3.535A pdb=" N PHE C 500 " --> pdb=" O PRO C 497 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 497 through 500' Processing helix chain 'C' and resid 501 through 524 removed outlier: 3.583A pdb=" N ASP C 505 " --> pdb=" O GLY C 501 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 518 " --> pdb=" O LEU C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 552 removed outlier: 3.677A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE C 548 " --> pdb=" O ASP C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 562 Processing helix chain 'C' and resid 589 through 601 Processing helix chain 'C' and resid 602 through 606 removed outlier: 3.652A pdb=" N ASP C 605 " --> pdb=" O ASN C 602 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 606 " --> pdb=" O ILE C 603 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 602 through 606' Processing helix chain 'D' and resid 20 through 24 Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 83 through 97 Processing helix chain 'D' and resid 108 through 113 removed outlier: 3.811A pdb=" N LYS D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 122 Processing helix chain 'D' and resid 127 through 141 Processing helix chain 'D' and resid 143 through 150 Processing helix chain 'D' and resid 151 through 159 Processing helix chain 'D' and resid 163 through 169 Processing helix chain 'D' and resid 177 through 188 Processing helix chain 'E' and resid 30 through 35 Processing helix chain 'E' and resid 38 through 59 Processing helix chain 'E' and resid 81 through 94 Processing helix chain 'E' and resid 107 through 139 removed outlier: 3.969A pdb=" N VAL E 138 " --> pdb=" O LYS E 134 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS E 139 " --> pdb=" O LEU E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 170 removed outlier: 4.293A pdb=" N LEU E 151 " --> pdb=" O ASP E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 182 Processing helix chain 'E' and resid 183 through 192 Processing helix chain 'E' and resid 207 through 222 Processing helix chain 'E' and resid 227 through 233 Processing helix chain 'E' and resid 281 through 295 removed outlier: 3.690A pdb=" N THR E 285 " --> pdb=" O CYS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 349 removed outlier: 3.669A pdb=" N PHE E 338 " --> pdb=" O ARG E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 377 removed outlier: 3.641A pdb=" N PHE E 377 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 384 removed outlier: 3.524A pdb=" N ASN E 382 " --> pdb=" O ASN E 379 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY E 384 " --> pdb=" O GLU E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 408 Processing helix chain 'E' and resid 429 through 435 removed outlier: 3.996A pdb=" N VAL E 433 " --> pdb=" O LYS E 429 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN E 434 " --> pdb=" O ASP E 430 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE E 435 " --> pdb=" O LEU E 431 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 429 through 435' Processing helix chain 'E' and resid 436 through 444 removed outlier: 4.156A pdb=" N ASP E 440 " --> pdb=" O PHE E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 479 Proline residue: E 473 - end of helix Processing helix chain 'E' and resid 482 through 486 removed outlier: 3.508A pdb=" N PHE E 485 " --> pdb=" O HIS E 482 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN E 486 " --> pdb=" O ASP E 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 482 through 486' Processing helix chain 'E' and resid 487 through 491 removed outlier: 3.831A pdb=" N GLY E 491 " --> pdb=" O PRO E 488 " (cutoff:3.500A) Processing helix chain 'E' and resid 492 through 503 removed outlier: 3.638A pdb=" N GLN E 496 " --> pdb=" O ASN E 492 " (cutoff:3.500A) Processing helix chain 'E' and resid 504 through 506 No H-bonds generated for 'chain 'E' and resid 504 through 506' Processing helix chain 'E' and resid 526 through 532 removed outlier: 3.572A pdb=" N PHE E 530 " --> pdb=" O ASN E 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 89 through 90 removed outlier: 4.493A pdb=" N HIS C 152 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 527 through 528 Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 120 removed outlier: 3.968A pdb=" N VAL A 140 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 169 removed outlier: 6.434A pdb=" N ILE A 168 " --> pdb=" O GLY A 197 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 278 removed outlier: 6.736A pdb=" N ILE A 276 " --> pdb=" O ARG A 313 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LEU A 337 " --> pdb=" O THR A 360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 344 through 345 Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 412 removed outlier: 6.785A pdb=" N LYS A 411 " --> pdb=" O VAL A 477 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE A 452 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE A 478 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 454 " --> pdb=" O ILE A 478 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 51 removed outlier: 4.097A pdb=" N THR C 50 " --> pdb=" O ASP C 528 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 15 through 19 removed outlier: 3.502A pdb=" N PHE D 16 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE D 75 " --> pdb=" O ASN D 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 239 through 240 removed outlier: 3.742A pdb=" N GLN E 268 " --> pdb=" O LYS E 253 " (cutoff:3.500A) 807 hydrogen bonds defined for protein. 2367 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: 5.16 Time building geometry restraints manager: 7.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5520 1.34 - 1.46: 3975 1.46 - 1.58: 8647 1.58 - 1.70: 0 1.70 - 1.82: 105 Bond restraints: 18247 Sorted by residual: bond pdb=" CB ASP A 173 " pdb=" CG ASP A 173 " ideal model delta sigma weight residual 1.516 1.569 -0.053 2.50e-02 1.60e+03 4.47e+00 bond pdb=" CA GLU B 389 " pdb=" CB GLU B 389 " ideal model delta sigma weight residual 1.524 1.551 -0.028 1.31e-02 5.83e+03 4.46e+00 bond pdb=" N ASN A 371 " pdb=" CA ASN A 371 " ideal model delta sigma weight residual 1.457 1.484 -0.026 1.29e-02 6.01e+03 4.12e+00 bond pdb=" CB VAL A 151 " pdb=" CG1 VAL A 151 " ideal model delta sigma weight residual 1.521 1.461 0.060 3.30e-02 9.18e+02 3.32e+00 bond pdb=" CB CYS D 151 " pdb=" SG CYS D 151 " ideal model delta sigma weight residual 1.808 1.756 0.052 3.30e-02 9.18e+02 2.52e+00 ... (remaining 18242 not shown) Histogram of bond angle deviations from ideal: 96.38 - 104.22: 241 104.22 - 112.06: 8448 112.06 - 119.91: 7919 119.91 - 127.75: 7933 127.75 - 135.59: 174 Bond angle restraints: 24715 Sorted by residual: angle pdb=" C LYS A 368 " pdb=" N TRP A 369 " pdb=" CA TRP A 369 " ideal model delta sigma weight residual 121.54 132.94 -11.40 1.91e+00 2.74e-01 3.56e+01 angle pdb=" C ILE A 172 " pdb=" N ASP A 173 " pdb=" CA ASP A 173 " ideal model delta sigma weight residual 126.45 135.59 -9.14 1.77e+00 3.19e-01 2.67e+01 angle pdb=" C TYR B 57 " pdb=" N LEU B 58 " pdb=" CA LEU B 58 " ideal model delta sigma weight residual 120.09 126.34 -6.25 1.25e+00 6.40e-01 2.50e+01 angle pdb=" N LYS E 260 " pdb=" CA LYS E 260 " pdb=" C LYS E 260 " ideal model delta sigma weight residual 114.75 108.84 5.91 1.26e+00 6.30e-01 2.20e+01 angle pdb=" C TYR B 335 " pdb=" N ARG B 336 " pdb=" CA ARG B 336 " ideal model delta sigma weight residual 123.47 130.47 -7.00 1.53e+00 4.27e-01 2.10e+01 ... (remaining 24710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.32: 10252 15.32 - 30.64: 535 30.64 - 45.96: 136 45.96 - 61.28: 16 61.28 - 76.60: 15 Dihedral angle restraints: 10954 sinusoidal: 4535 harmonic: 6419 Sorted by residual: dihedral pdb=" CA ILE A 421 " pdb=" C ILE A 421 " pdb=" N THR A 422 " pdb=" CA THR A 422 " ideal model delta harmonic sigma weight residual -180.00 -142.18 -37.82 0 5.00e+00 4.00e-02 5.72e+01 dihedral pdb=" CB CYS B 99 " pdb=" SG CYS B 99 " pdb=" SG CYS B 215 " pdb=" CB CYS B 215 " ideal model delta sinusoidal sigma weight residual 93.00 157.53 -64.53 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CA LYS A 368 " pdb=" C LYS A 368 " pdb=" N TRP A 369 " pdb=" CA TRP A 369 " ideal model delta harmonic sigma weight residual 180.00 146.38 33.62 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 10951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2386 0.080 - 0.159: 309 0.159 - 0.239: 22 0.239 - 0.318: 2 0.318 - 0.398: 1 Chirality restraints: 2720 Sorted by residual: chirality pdb=" CB ILE A 301 " pdb=" CA ILE A 301 " pdb=" CG1 ILE A 301 " pdb=" CG2 ILE A 301 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.96e+00 chirality pdb=" CG LEU A 359 " pdb=" CB LEU A 359 " pdb=" CD1 LEU A 359 " pdb=" CD2 LEU A 359 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE A 421 " pdb=" CA ILE A 421 " pdb=" CG1 ILE A 421 " pdb=" CG2 ILE A 421 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2717 not shown) Planarity restraints: 3128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 150 " -0.026 2.00e-02 2.50e+03 1.91e-02 9.08e+00 pdb=" CG TRP A 150 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 150 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP A 150 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 150 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 150 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 150 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 150 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 150 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 150 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 443 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.86e+00 pdb=" C GLN A 443 " -0.048 2.00e-02 2.50e+03 pdb=" O GLN A 443 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A 444 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU E 90 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.66e+00 pdb=" C LEU E 90 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU E 90 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP E 91 " 0.016 2.00e-02 2.50e+03 ... (remaining 3125 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4367 2.79 - 3.32: 16220 3.32 - 3.84: 29461 3.84 - 4.37: 34632 4.37 - 4.90: 58967 Nonbonded interactions: 143647 Sorted by model distance: nonbonded pdb=" OG SER E 227 " pdb=" OE1 GLU E 230 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR B 78 " pdb=" OG1 THR B 464 " model vdw 2.272 2.440 nonbonded pdb=" OD1 ASP E 370 " pdb=" OG1 THR E 373 " model vdw 2.281 2.440 nonbonded pdb=" OD2 ASP B 60 " pdb=" OG1 THR B 705 " model vdw 2.301 2.440 nonbonded pdb=" O ASN E 308 " pdb=" OH TYR E 442 " model vdw 2.304 2.440 ... (remaining 143642 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 53 through 319 or resid 339 through 608)) selection = (chain 'C' and (resid 53 through 319 or resid 339 through 608)) } 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=0.00 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.190 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 47.310 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:2.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6602 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 : 0.006 0.068 18247 Z= 0.382 Angle : 0.946 12.340 24715 Z= 0.524 Chirality : 0.054 0.398 2720 Planarity : 0.007 0.065 3128 Dihedral : 10.749 76.602 6771 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.08 % Favored : 92.83 % Rotamer: Outliers : 0.50 % Allowed : 3.76 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -4.51 (0.13), residues: 2119 helix: -2.59 (0.11), residues: 1258 sheet: -4.60 (0.56), residues: 50 loop : -3.37 (0.17), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 150 HIS 0.013 0.002 HIS E 43 PHE 0.043 0.003 PHE A 434 TYR 0.035 0.002 TYR D 132 ARG 0.014 0.001 ARG A 95 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 530 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.7784 (mtt90) cc_final: 0.6871 (tmt170) REVERT: B 97 GLU cc_start: 0.8177 (pt0) cc_final: 0.7932 (tm-30) REVERT: B 134 SER cc_start: 0.9211 (m) cc_final: 0.8916 (p) REVERT: B 291 ARG cc_start: 0.7198 (mtt180) cc_final: 0.6504 (mtm110) REVERT: B 364 LYS cc_start: 0.8377 (mttp) cc_final: 0.8172 (mttt) REVERT: B 399 GLN cc_start: 0.7685 (tt0) cc_final: 0.6797 (tp40) REVERT: B 407 ILE cc_start: 0.7965 (tp) cc_final: 0.7643 (tp) REVERT: B 423 ASP cc_start: 0.8182 (t0) cc_final: 0.7326 (m-30) REVERT: B 444 ASN cc_start: 0.8435 (t0) cc_final: 0.8177 (t0) REVERT: B 450 SER cc_start: 0.8532 (p) cc_final: 0.8072 (p) REVERT: B 451 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7567 (mp0) REVERT: A 25 ASP cc_start: 0.8065 (t0) cc_final: 0.7739 (t0) REVERT: A 36 ILE cc_start: 0.8530 (mp) cc_final: 0.8224 (mm) REVERT: A 111 ASP cc_start: 0.8457 (m-30) cc_final: 0.8257 (m-30) REVERT: A 119 GLU cc_start: 0.7612 (tt0) cc_final: 0.7402 (tt0) REVERT: A 146 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8576 (mt-10) REVERT: A 164 ASN cc_start: 0.7831 (m110) cc_final: 0.7261 (p0) REVERT: A 282 LYS cc_start: 0.7741 (mmmt) cc_final: 0.7299 (tmtt) REVERT: A 307 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7420 (mmm-85) REVERT: A 319 GLN cc_start: 0.7854 (mt0) cc_final: 0.7596 (mt0) REVERT: A 332 ASP cc_start: 0.8799 (p0) cc_final: 0.8550 (p0) REVERT: A 373 GLU cc_start: 0.7917 (tp30) cc_final: 0.7666 (tp30) REVERT: A 381 LYS cc_start: 0.8345 (tppt) cc_final: 0.7969 (mtmt) REVERT: A 384 LYS cc_start: 0.7918 (tttt) cc_final: 0.7564 (ttmm) REVERT: A 388 LYS cc_start: 0.8655 (tttt) cc_final: 0.8416 (mtpp) REVERT: A 405 LEU cc_start: 0.7371 (mt) cc_final: 0.7169 (mt) REVERT: A 409 ARG cc_start: 0.7640 (ttm170) cc_final: 0.7200 (mtp85) REVERT: A 420 GLN cc_start: 0.8550 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 465 GLU cc_start: 0.8362 (pt0) cc_final: 0.7766 (pt0) REVERT: A 474 GLN cc_start: 0.8391 (tm130) cc_final: 0.7861 (tm-30) REVERT: C 87 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.6808 (ptt90) REVERT: C 101 PHE cc_start: 0.8365 (t80) cc_final: 0.8158 (t80) REVERT: C 120 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7830 (mm-30) REVERT: C 141 GLU cc_start: 0.7352 (mm-30) cc_final: 0.6959 (mt-10) REVERT: C 173 TYR cc_start: 0.8194 (m-80) cc_final: 0.7940 (m-80) REVERT: C 187 PRO cc_start: 0.6555 (Cg_exo) cc_final: 0.6304 (Cg_endo) REVERT: C 204 MET cc_start: 0.8825 (tpt) cc_final: 0.8602 (tpp) REVERT: C 230 ASP cc_start: 0.8738 (t0) cc_final: 0.8291 (t0) REVERT: C 280 PRO cc_start: 0.7342 (Cg_exo) cc_final: 0.7137 (Cg_endo) REVERT: C 347 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7665 (mttt) REVERT: C 367 LEU cc_start: 0.7919 (mt) cc_final: 0.7664 (tt) REVERT: C 371 ASP cc_start: 0.8574 (m-30) cc_final: 0.8203 (m-30) REVERT: C 382 TYR cc_start: 0.8594 (t80) cc_final: 0.8316 (t80) REVERT: C 387 LEU cc_start: 0.9049 (mt) cc_final: 0.8788 (mp) REVERT: C 411 SER cc_start: 0.8684 (m) cc_final: 0.8245 (p) REVERT: C 423 ASP cc_start: 0.8556 (t70) cc_final: 0.8137 (t0) REVERT: C 440 SER cc_start: 0.9221 (t) cc_final: 0.8973 (p) REVERT: C 451 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8094 (pt0) REVERT: C 460 MET cc_start: 0.8469 (tpt) cc_final: 0.7498 (tpp) REVERT: C 477 VAL cc_start: 0.7493 (t) cc_final: 0.7265 (m) REVERT: C 540 ILE cc_start: 0.6884 (mt) cc_final: 0.6643 (mt) REVERT: C 544 ASP cc_start: 0.8071 (m-30) cc_final: 0.7806 (m-30) REVERT: C 550 LEU cc_start: 0.7785 (tp) cc_final: 0.7547 (tp) REVERT: C 553 ASP cc_start: 0.7499 (t0) cc_final: 0.7022 (t0) REVERT: C 556 PHE cc_start: 0.7325 (m-80) cc_final: 0.6820 (m-80) REVERT: C 593 ILE cc_start: 0.8684 (mt) cc_final: 0.8189 (tp) REVERT: C 600 GLU cc_start: 0.8412 (tt0) cc_final: 0.8175 (tp30) REVERT: D 12 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8083 (mt-10) REVERT: D 15 ARG cc_start: 0.8509 (mtt-85) cc_final: 0.8102 (mtp85) REVERT: D 17 THR cc_start: 0.9278 (m) cc_final: 0.9012 (p) REVERT: D 18 VAL cc_start: 0.8504 (t) cc_final: 0.8111 (m) REVERT: D 21 LYS cc_start: 0.8766 (tttt) cc_final: 0.8546 (ttpp) REVERT: D 98 ARG cc_start: 0.8535 (ttp-110) cc_final: 0.7994 (ptm-80) REVERT: D 104 ASP cc_start: 0.7948 (t0) cc_final: 0.7390 (t0) REVERT: D 117 ASP cc_start: 0.7074 (t0) cc_final: 0.6873 (m-30) REVERT: D 118 SER cc_start: 0.8647 (m) cc_final: 0.8219 (p) REVERT: D 127 ASP cc_start: 0.6983 (t0) cc_final: 0.6670 (t0) REVERT: D 165 GLU cc_start: 0.7543 (pp20) cc_final: 0.7016 (pp20) REVERT: D 180 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7231 (mt-10) REVERT: D 189 GLU cc_start: 0.8173 (tp30) cc_final: 0.7933 (tp30) REVERT: E 60 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6691 (tp-100) REVERT: E 78 LEU cc_start: 0.9073 (tp) cc_final: 0.8859 (mt) REVERT: E 146 ILE cc_start: 0.8340 (tt) cc_final: 0.8044 (tp) REVERT: E 152 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7417 (tp30) REVERT: E 160 HIS cc_start: 0.6825 (t70) cc_final: 0.6623 (t70) REVERT: E 161 TRP cc_start: 0.7456 (t-100) cc_final: 0.7207 (t-100) REVERT: E 244 ARG cc_start: 0.6047 (tpp-160) cc_final: 0.5825 (tpp80) REVERT: E 251 TYR cc_start: 0.6014 (t80) cc_final: 0.3752 (t80) REVERT: E 371 GLU cc_start: 0.5961 (tp30) cc_final: 0.4732 (pt0) REVERT: E 401 PHE cc_start: 0.6309 (t80) cc_final: 0.6013 (t80) REVERT: E 409 PHE cc_start: 0.5956 (m-10) cc_final: 0.5465 (t80) REVERT: E 461 MET cc_start: 0.8437 (mmm) cc_final: 0.8179 (mmm) outliers start: 10 outliers final: 2 residues processed: 536 average time/residue: 0.3323 time to fit residues: 257.5677 Evaluate side-chains 324 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 322 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 338 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 8.9990 chunk 160 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 192 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 67 ASN B 235 GLN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 543 ASN A 23 HIS A 108 HIS ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 310 ASN A 333 ASN A 335 GLN C 67 ASN C 189 HIS C 199 ASN C 394 ASN C 399 GLN D 34 ASN D 101 ASN D 188 ASN E 143 ASN E 177 ASN E 191 ASN E 266 HIS E 379 ASN E 383 HIS E 492 ASN E 505 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18247 Z= 0.286 Angle : 0.634 10.717 24715 Z= 0.333 Chirality : 0.043 0.194 2720 Planarity : 0.005 0.053 3128 Dihedral : 5.776 45.197 2347 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.37 % Favored : 93.58 % Rotamer: Outliers : 2.51 % Allowed : 9.68 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.16), residues: 2119 helix: -1.02 (0.14), residues: 1256 sheet: -3.45 (0.84), residues: 31 loop : -2.96 (0.18), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 150 HIS 0.007 0.001 HIS A 291 PHE 0.022 0.002 PHE B 476 TYR 0.028 0.002 TYR E 49 ARG 0.010 0.001 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 348 time to evaluate : 2.056 Fit side-chains REVERT: B 87 ARG cc_start: 0.7686 (mtt90) cc_final: 0.6959 (tmt170) REVERT: B 135 GLU cc_start: 0.7549 (mp0) cc_final: 0.7149 (mp0) REVERT: B 202 ASP cc_start: 0.8825 (t0) cc_final: 0.8567 (t0) REVERT: B 226 MET cc_start: 0.8383 (mtm) cc_final: 0.7993 (mtt) REVERT: B 301 TYR cc_start: 0.8421 (t80) cc_final: 0.8129 (t80) REVERT: B 364 LYS cc_start: 0.8459 (mttp) cc_final: 0.8105 (mttt) REVERT: B 399 GLN cc_start: 0.7503 (tt0) cc_final: 0.7038 (tp40) REVERT: B 407 ILE cc_start: 0.8088 (tp) cc_final: 0.7811 (tp) REVERT: B 423 ASP cc_start: 0.8154 (t0) cc_final: 0.7205 (m-30) REVERT: B 451 GLU cc_start: 0.7925 (tm-30) cc_final: 0.7524 (mp0) REVERT: A 36 ILE cc_start: 0.8587 (mp) cc_final: 0.8277 (mm) REVERT: A 66 MET cc_start: 0.8014 (OUTLIER) cc_final: 0.7796 (ttt) REVERT: A 82 GLN cc_start: 0.8481 (pt0) cc_final: 0.8115 (pm20) REVERT: A 119 GLU cc_start: 0.7599 (tt0) cc_final: 0.7320 (tt0) REVERT: A 126 GLU cc_start: 0.7783 (tp30) cc_final: 0.7521 (mm-30) REVERT: A 138 LEU cc_start: 0.8255 (pp) cc_final: 0.8024 (tt) REVERT: A 146 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8451 (mt-10) REVERT: A 164 ASN cc_start: 0.7830 (m110) cc_final: 0.7166 (p0) REVERT: A 282 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7748 (tttm) REVERT: A 330 ARG cc_start: 0.6986 (mmt180) cc_final: 0.6741 (mmp80) REVERT: A 373 GLU cc_start: 0.7698 (tp30) cc_final: 0.7444 (tp30) REVERT: A 381 LYS cc_start: 0.8198 (tppt) cc_final: 0.7782 (ptpt) REVERT: A 384 LYS cc_start: 0.8123 (tttt) cc_final: 0.7770 (ttmm) REVERT: A 400 THR cc_start: 0.8685 (m) cc_final: 0.8386 (p) REVERT: A 409 ARG cc_start: 0.7751 (ttm170) cc_final: 0.7461 (mmm-85) REVERT: A 417 GLU cc_start: 0.7101 (tp30) cc_final: 0.6803 (tp30) REVERT: C 83 ARG cc_start: 0.7753 (ptt-90) cc_final: 0.7414 (mmp-170) REVERT: C 87 ARG cc_start: 0.8197 (mmm-85) cc_final: 0.6866 (ptt90) REVERT: C 101 PHE cc_start: 0.8424 (t80) cc_final: 0.8196 (t80) REVERT: C 120 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7764 (mm-30) REVERT: C 208 MET cc_start: 0.8452 (ttm) cc_final: 0.8239 (ttm) REVERT: C 230 ASP cc_start: 0.8850 (t0) cc_final: 0.8422 (t0) REVERT: C 347 LYS cc_start: 0.7844 (mmtt) cc_final: 0.7547 (mttt) REVERT: C 382 TYR cc_start: 0.8638 (t80) cc_final: 0.8404 (t80) REVERT: C 411 SER cc_start: 0.8653 (m) cc_final: 0.8287 (p) REVERT: C 423 ASP cc_start: 0.8417 (t70) cc_final: 0.8115 (t0) REVERT: C 440 SER cc_start: 0.9197 (t) cc_final: 0.8995 (p) REVERT: C 460 MET cc_start: 0.8594 (tpt) cc_final: 0.7697 (tpp) REVERT: C 540 ILE cc_start: 0.6984 (mt) cc_final: 0.6746 (mt) REVERT: C 544 ASP cc_start: 0.7891 (m-30) cc_final: 0.7663 (m-30) REVERT: C 550 LEU cc_start: 0.7812 (tp) cc_final: 0.7594 (tp) REVERT: C 553 ASP cc_start: 0.7201 (t0) cc_final: 0.6882 (t0) REVERT: C 556 PHE cc_start: 0.7458 (m-80) cc_final: 0.7077 (m-80) REVERT: C 600 GLU cc_start: 0.8509 (tt0) cc_final: 0.8216 (tp30) REVERT: D 98 ARG cc_start: 0.8572 (ttp-110) cc_final: 0.7798 (ptm-80) REVERT: D 104 ASP cc_start: 0.8135 (t0) cc_final: 0.7749 (t0) REVERT: D 127 ASP cc_start: 0.6970 (t0) cc_final: 0.6667 (t0) REVERT: E 35 ASP cc_start: 0.7600 (m-30) cc_final: 0.7196 (t0) REVERT: E 60 GLN cc_start: 0.7117 (mm-40) cc_final: 0.6678 (tp-100) REVERT: E 152 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7599 (tp30) REVERT: E 156 LYS cc_start: 0.8320 (mttt) cc_final: 0.7463 (tptm) REVERT: E 161 TRP cc_start: 0.7340 (t-100) cc_final: 0.7110 (t-100) REVERT: E 409 PHE cc_start: 0.5981 (m-10) cc_final: 0.5660 (t80) outliers start: 50 outliers final: 28 residues processed: 386 average time/residue: 0.2898 time to fit residues: 169.9708 Evaluate side-chains 323 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 294 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 133 SER Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 0.0980 chunk 59 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 chunk 131 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 192 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 171 optimal weight: 0.9990 chunk 191 optimal weight: 9.9990 chunk 65 optimal weight: 0.0570 chunk 154 optimal weight: 0.8980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN C 406 GLN C 543 ASN D 34 ASN E 86 HIS E 252 HIS E 266 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18247 Z= 0.200 Angle : 0.590 11.291 24715 Z= 0.304 Chirality : 0.042 0.192 2720 Planarity : 0.004 0.049 3128 Dihedral : 5.416 53.971 2347 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.04 % Favored : 93.91 % Rotamer: Outliers : 2.76 % Allowed : 10.99 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.95 (0.17), residues: 2119 helix: -0.37 (0.14), residues: 1261 sheet: -2.83 (1.08), residues: 25 loop : -2.70 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 150 HIS 0.011 0.001 HIS A 291 PHE 0.020 0.001 PHE B 476 TYR 0.019 0.001 TYR E 49 ARG 0.011 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 335 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.7617 (mtt90) cc_final: 0.6884 (tmt170) REVERT: B 135 GLU cc_start: 0.7507 (mp0) cc_final: 0.7297 (mp0) REVERT: B 202 ASP cc_start: 0.8818 (t0) cc_final: 0.8520 (t0) REVERT: B 214 ARG cc_start: 0.7533 (ttm110) cc_final: 0.6999 (mtp85) REVERT: B 226 MET cc_start: 0.8344 (mtm) cc_final: 0.7966 (mtt) REVERT: B 291 ARG cc_start: 0.7602 (ttm-80) cc_final: 0.6575 (mtm110) REVERT: B 301 TYR cc_start: 0.8441 (t80) cc_final: 0.8048 (t80) REVERT: B 364 LYS cc_start: 0.8447 (mttp) cc_final: 0.8081 (mttt) REVERT: B 399 GLN cc_start: 0.7511 (tt0) cc_final: 0.6970 (tp40) REVERT: B 423 ASP cc_start: 0.8119 (t0) cc_final: 0.7190 (m-30) REVERT: B 444 ASN cc_start: 0.8281 (t0) cc_final: 0.8069 (t0) REVERT: B 451 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7571 (mp0) REVERT: B 595 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7742 (mm-30) REVERT: A 36 ILE cc_start: 0.8653 (mp) cc_final: 0.8263 (mm) REVERT: A 82 GLN cc_start: 0.8496 (pt0) cc_final: 0.8154 (pm20) REVERT: A 119 GLU cc_start: 0.7695 (tt0) cc_final: 0.7493 (tt0) REVERT: A 126 GLU cc_start: 0.7709 (tp30) cc_final: 0.7447 (mm-30) REVERT: A 146 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8529 (mt-10) REVERT: A 162 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5699 (tt) REVERT: A 164 ASN cc_start: 0.7799 (m110) cc_final: 0.7077 (p0) REVERT: A 282 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7816 (tttm) REVERT: A 373 GLU cc_start: 0.7824 (tp30) cc_final: 0.7506 (tp30) REVERT: A 381 LYS cc_start: 0.8222 (tppt) cc_final: 0.7856 (mtmt) REVERT: A 400 THR cc_start: 0.8742 (m) cc_final: 0.8520 (p) REVERT: A 409 ARG cc_start: 0.7755 (ttm170) cc_final: 0.7487 (mmm-85) REVERT: A 420 GLN cc_start: 0.8635 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 83 ARG cc_start: 0.7753 (ptt-90) cc_final: 0.7400 (mmp-170) REVERT: C 87 ARG cc_start: 0.8217 (mmm-85) cc_final: 0.6901 (ptt90) REVERT: C 120 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7817 (mm-30) REVERT: C 133 ILE cc_start: 0.8633 (tt) cc_final: 0.8413 (tp) REVERT: C 195 ASN cc_start: 0.7574 (OUTLIER) cc_final: 0.7305 (p0) REVERT: C 208 MET cc_start: 0.8490 (ttm) cc_final: 0.8269 (ttm) REVERT: C 230 ASP cc_start: 0.8892 (t0) cc_final: 0.8478 (t0) REVERT: C 347 LYS cc_start: 0.7823 (mmtt) cc_final: 0.7538 (mttt) REVERT: C 411 SER cc_start: 0.8679 (m) cc_final: 0.8334 (p) REVERT: C 423 ASP cc_start: 0.8358 (t70) cc_final: 0.8049 (t0) REVERT: C 440 SER cc_start: 0.9147 (t) cc_final: 0.8939 (p) REVERT: C 460 MET cc_start: 0.8577 (tpt) cc_final: 0.7768 (tpp) REVERT: C 540 ILE cc_start: 0.6913 (mt) cc_final: 0.6689 (mt) REVERT: C 544 ASP cc_start: 0.7882 (m-30) cc_final: 0.7562 (m-30) REVERT: C 550 LEU cc_start: 0.7822 (tp) cc_final: 0.7591 (tp) REVERT: C 553 ASP cc_start: 0.7263 (t0) cc_final: 0.6858 (t0) REVERT: C 556 PHE cc_start: 0.7156 (m-80) cc_final: 0.6770 (m-80) REVERT: C 600 GLU cc_start: 0.8419 (tt0) cc_final: 0.8106 (tp30) REVERT: D 98 ARG cc_start: 0.8495 (ttp-110) cc_final: 0.7890 (ptm-80) REVERT: D 104 ASP cc_start: 0.8121 (t0) cc_final: 0.7682 (t0) REVERT: D 117 ASP cc_start: 0.7703 (m-30) cc_final: 0.7395 (m-30) REVERT: D 127 ASP cc_start: 0.6911 (t0) cc_final: 0.6615 (t0) REVERT: E 35 ASP cc_start: 0.7548 (m-30) cc_final: 0.7181 (t0) REVERT: E 60 GLN cc_start: 0.7081 (mm-40) cc_final: 0.6627 (tp-100) REVERT: E 76 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7852 (mmtt) REVERT: E 152 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7598 (tp30) REVERT: E 156 LYS cc_start: 0.8315 (mttt) cc_final: 0.7461 (tptp) REVERT: E 243 LYS cc_start: 0.8213 (mtmm) cc_final: 0.7973 (mptt) REVERT: E 409 PHE cc_start: 0.6091 (m-10) cc_final: 0.5729 (t80) outliers start: 55 outliers final: 35 residues processed: 371 average time/residue: 0.2865 time to fit residues: 160.5241 Evaluate side-chains 334 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 296 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 418 TYR Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 34 ASN Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 10.0000 chunk 145 optimal weight: 0.4980 chunk 100 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 193 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 219 GLN ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS C 205 GLN C 399 GLN C 552 ASN E 86 HIS E 266 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18247 Z= 0.300 Angle : 0.623 12.973 24715 Z= 0.319 Chirality : 0.043 0.185 2720 Planarity : 0.004 0.045 3128 Dihedral : 5.293 54.719 2347 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.84 % Favored : 93.11 % Rotamer: Outliers : 3.76 % Allowed : 12.39 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.56 (0.18), residues: 2119 helix: -0.08 (0.15), residues: 1268 sheet: -2.14 (0.99), residues: 37 loop : -2.53 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 150 HIS 0.015 0.001 HIS A 291 PHE 0.020 0.002 PHE A 356 TYR 0.019 0.001 TYR E 49 ARG 0.006 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 299 time to evaluate : 2.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.7704 (mtt90) cc_final: 0.6919 (tmt170) REVERT: B 103 MET cc_start: 0.6893 (mtt) cc_final: 0.5953 (mpp) REVERT: B 135 GLU cc_start: 0.7552 (mp0) cc_final: 0.7334 (mp0) REVERT: B 202 ASP cc_start: 0.8858 (t0) cc_final: 0.8579 (t0) REVERT: B 214 ARG cc_start: 0.7509 (ttm110) cc_final: 0.7038 (mtp85) REVERT: B 226 MET cc_start: 0.8452 (mtm) cc_final: 0.8083 (mtt) REVERT: B 301 TYR cc_start: 0.8412 (t80) cc_final: 0.8016 (t80) REVERT: B 371 ASP cc_start: 0.7775 (m-30) cc_final: 0.7478 (t0) REVERT: B 382 TYR cc_start: 0.7499 (m-80) cc_final: 0.6891 (m-80) REVERT: B 399 GLN cc_start: 0.7538 (tt0) cc_final: 0.7017 (tp40) REVERT: B 423 ASP cc_start: 0.8164 (t0) cc_final: 0.7395 (m-30) REVERT: B 444 ASN cc_start: 0.8184 (t0) cc_final: 0.7976 (t0) REVERT: B 451 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7650 (mp0) REVERT: B 595 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7652 (mm-30) REVERT: A 36 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8279 (mm) REVERT: A 82 GLN cc_start: 0.8503 (pt0) cc_final: 0.8176 (pm20) REVERT: A 109 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7526 (tt) REVERT: A 126 GLU cc_start: 0.7633 (tp30) cc_final: 0.7377 (mm-30) REVERT: A 146 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8323 (mt-10) REVERT: A 162 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5697 (tt) REVERT: A 282 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7891 (tttm) REVERT: A 373 GLU cc_start: 0.7849 (tp30) cc_final: 0.7477 (tp30) REVERT: A 381 LYS cc_start: 0.8179 (tppt) cc_final: 0.7819 (mtmt) REVERT: A 400 THR cc_start: 0.8733 (m) cc_final: 0.8505 (p) REVERT: A 409 ARG cc_start: 0.7720 (ttm170) cc_final: 0.7454 (mmm-85) REVERT: A 420 GLN cc_start: 0.8588 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 83 ARG cc_start: 0.7652 (ptt-90) cc_final: 0.7362 (mmp-170) REVERT: C 87 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.6991 (ptt90) REVERT: C 120 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7779 (mm-30) REVERT: C 195 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7309 (p0) REVERT: C 230 ASP cc_start: 0.8896 (t0) cc_final: 0.8463 (t0) REVERT: C 347 LYS cc_start: 0.7841 (mmtt) cc_final: 0.7542 (mtpt) REVERT: C 411 SER cc_start: 0.8706 (m) cc_final: 0.8378 (p) REVERT: C 423 ASP cc_start: 0.8335 (t70) cc_final: 0.8006 (t0) REVERT: C 440 SER cc_start: 0.9134 (t) cc_final: 0.8928 (p) REVERT: C 540 ILE cc_start: 0.7109 (mt) cc_final: 0.6828 (mt) REVERT: C 544 ASP cc_start: 0.7821 (m-30) cc_final: 0.7552 (m-30) REVERT: C 550 LEU cc_start: 0.7906 (tp) cc_final: 0.7665 (tp) REVERT: C 553 ASP cc_start: 0.7211 (t0) cc_final: 0.6838 (t0) REVERT: C 556 PHE cc_start: 0.7360 (m-80) cc_final: 0.6897 (m-80) REVERT: C 595 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7500 (tm-30) REVERT: C 600 GLU cc_start: 0.8452 (tt0) cc_final: 0.8138 (tp30) REVERT: D 21 LYS cc_start: 0.8413 (tttp) cc_final: 0.7759 (tptt) REVERT: D 98 ARG cc_start: 0.8507 (ttp-110) cc_final: 0.7705 (ptm-80) REVERT: D 104 ASP cc_start: 0.8279 (t0) cc_final: 0.7891 (t0) REVERT: D 127 ASP cc_start: 0.7007 (t0) cc_final: 0.6727 (t0) REVERT: D 165 GLU cc_start: 0.7545 (pp20) cc_final: 0.7341 (pp20) REVERT: E 35 ASP cc_start: 0.7617 (m-30) cc_final: 0.7292 (t0) REVERT: E 60 GLN cc_start: 0.7135 (mm-40) cc_final: 0.6671 (tp-100) REVERT: E 76 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7894 (mmtt) REVERT: E 152 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7614 (tp30) outliers start: 75 outliers final: 44 residues processed: 349 average time/residue: 0.2831 time to fit residues: 150.1521 Evaluate side-chains 325 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 276 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 58 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.6980 chunk 116 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 chunk 152 optimal weight: 0.0770 chunk 84 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 HIS ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN E 86 HIS E 266 HIS E 492 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18247 Z= 0.240 Angle : 0.602 11.724 24715 Z= 0.306 Chirality : 0.042 0.184 2720 Planarity : 0.004 0.045 3128 Dihedral : 5.141 49.395 2347 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.23 % Favored : 93.72 % Rotamer: Outliers : 3.51 % Allowed : 13.10 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.18), residues: 2119 helix: 0.12 (0.15), residues: 1274 sheet: -2.21 (0.94), residues: 37 loop : -2.46 (0.20), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 161 HIS 0.009 0.001 HIS A 291 PHE 0.019 0.001 PHE C 597 TYR 0.019 0.001 TYR E 49 ARG 0.006 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 292 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.7693 (mtt90) cc_final: 0.6911 (tmt170) REVERT: B 103 MET cc_start: 0.7208 (mtt) cc_final: 0.6944 (mtt) REVERT: B 119 MET cc_start: 0.7854 (ttp) cc_final: 0.7512 (ttp) REVERT: B 135 GLU cc_start: 0.7560 (mp0) cc_final: 0.7348 (mp0) REVERT: B 202 ASP cc_start: 0.8839 (t0) cc_final: 0.8590 (t0) REVERT: B 214 ARG cc_start: 0.7469 (ttm110) cc_final: 0.6989 (mtp85) REVERT: B 226 MET cc_start: 0.8358 (mtm) cc_final: 0.7998 (mtt) REVERT: B 301 TYR cc_start: 0.8380 (t80) cc_final: 0.7982 (t80) REVERT: B 371 ASP cc_start: 0.7807 (m-30) cc_final: 0.7428 (t0) REVERT: B 382 TYR cc_start: 0.7565 (m-80) cc_final: 0.7032 (m-80) REVERT: B 399 GLN cc_start: 0.7539 (tt0) cc_final: 0.7000 (tp40) REVERT: B 423 ASP cc_start: 0.8216 (t0) cc_final: 0.7424 (m-30) REVERT: B 444 ASN cc_start: 0.8187 (t0) cc_final: 0.7957 (t0) REVERT: B 451 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7653 (mp0) REVERT: B 595 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7841 (mm-30) REVERT: A 36 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8285 (mm) REVERT: A 82 GLN cc_start: 0.8514 (pt0) cc_final: 0.8190 (pm20) REVERT: A 109 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7469 (tt) REVERT: A 126 GLU cc_start: 0.7690 (tp30) cc_final: 0.7437 (mm-30) REVERT: A 146 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 162 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5717 (tt) REVERT: A 164 ASN cc_start: 0.7805 (m110) cc_final: 0.7141 (p0) REVERT: A 282 LYS cc_start: 0.8297 (mmmt) cc_final: 0.7881 (tttm) REVERT: A 284 TYR cc_start: 0.8330 (t80) cc_final: 0.7936 (t80) REVERT: A 373 GLU cc_start: 0.7938 (tp30) cc_final: 0.7525 (tp30) REVERT: A 381 LYS cc_start: 0.8246 (tppt) cc_final: 0.7926 (mtmt) REVERT: A 400 THR cc_start: 0.8758 (m) cc_final: 0.8524 (p) REVERT: A 409 ARG cc_start: 0.7738 (ttm170) cc_final: 0.7299 (mtp85) REVERT: A 420 GLN cc_start: 0.8624 (tm-30) cc_final: 0.7841 (tm-30) REVERT: C 83 ARG cc_start: 0.7661 (ptt-90) cc_final: 0.7425 (mmp-170) REVERT: C 87 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7108 (ptt90) REVERT: C 120 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7792 (mm-30) REVERT: C 135 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7997 (tm-30) REVERT: C 347 LYS cc_start: 0.7839 (mmtt) cc_final: 0.7506 (mtpt) REVERT: C 411 SER cc_start: 0.8698 (m) cc_final: 0.8361 (p) REVERT: C 423 ASP cc_start: 0.8340 (t70) cc_final: 0.8004 (t0) REVERT: C 540 ILE cc_start: 0.7111 (mt) cc_final: 0.6802 (mt) REVERT: C 544 ASP cc_start: 0.7772 (m-30) cc_final: 0.7500 (m-30) REVERT: C 550 LEU cc_start: 0.7928 (tp) cc_final: 0.7638 (tt) REVERT: C 553 ASP cc_start: 0.7207 (t0) cc_final: 0.6850 (t0) REVERT: C 556 PHE cc_start: 0.7349 (m-80) cc_final: 0.6906 (m-80) REVERT: C 595 GLU cc_start: 0.7759 (tm-30) cc_final: 0.7469 (tm-30) REVERT: C 600 GLU cc_start: 0.8522 (tt0) cc_final: 0.8173 (tp30) REVERT: D 21 LYS cc_start: 0.8356 (tttp) cc_final: 0.7725 (tptt) REVERT: D 98 ARG cc_start: 0.8478 (ttp-110) cc_final: 0.7969 (ptm-80) REVERT: D 104 ASP cc_start: 0.8293 (t0) cc_final: 0.7885 (t0) REVERT: D 127 ASP cc_start: 0.6953 (t0) cc_final: 0.6685 (t0) REVERT: E 35 ASP cc_start: 0.7610 (m-30) cc_final: 0.7289 (t0) REVERT: E 76 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7896 (mmtt) REVERT: E 152 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7671 (tp30) REVERT: E 467 ARG cc_start: 0.6129 (mmt-90) cc_final: 0.5842 (tpp-160) outliers start: 70 outliers final: 50 residues processed: 338 average time/residue: 0.2743 time to fit residues: 141.6962 Evaluate side-chains 323 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 269 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 432 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 449 LYS Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.0040 chunk 184 optimal weight: 4.9990 chunk 40 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 0.0060 chunk 205 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18247 Z= 0.198 Angle : 0.574 11.142 24715 Z= 0.292 Chirality : 0.041 0.185 2720 Planarity : 0.003 0.044 3128 Dihedral : 4.949 44.178 2347 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.01 % Rotamer: Outliers : 3.51 % Allowed : 13.00 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.18), residues: 2119 helix: 0.40 (0.15), residues: 1259 sheet: -2.30 (0.93), residues: 35 loop : -2.36 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 161 HIS 0.010 0.001 HIS A 291 PHE 0.021 0.001 PHE B 476 TYR 0.020 0.001 TYR E 49 ARG 0.005 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 294 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.7736 (mtt90) cc_final: 0.6933 (tmt170) REVERT: B 103 MET cc_start: 0.7264 (mtt) cc_final: 0.7005 (mtt) REVERT: B 119 MET cc_start: 0.7870 (ttp) cc_final: 0.7589 (ttp) REVERT: B 202 ASP cc_start: 0.8743 (t0) cc_final: 0.8516 (t0) REVERT: B 214 ARG cc_start: 0.7443 (ttm110) cc_final: 0.6945 (mtp85) REVERT: B 226 MET cc_start: 0.8336 (mtm) cc_final: 0.7988 (mtt) REVERT: B 301 TYR cc_start: 0.8387 (t80) cc_final: 0.8065 (t80) REVERT: B 371 ASP cc_start: 0.7766 (m-30) cc_final: 0.7279 (t0) REVERT: B 382 TYR cc_start: 0.7498 (m-80) cc_final: 0.6980 (m-80) REVERT: B 399 GLN cc_start: 0.7587 (tt0) cc_final: 0.7028 (tp40) REVERT: B 423 ASP cc_start: 0.8155 (t0) cc_final: 0.7402 (m-30) REVERT: B 444 ASN cc_start: 0.8126 (t0) cc_final: 0.7889 (t0) REVERT: B 451 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7662 (mp0) REVERT: B 595 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7855 (mm-30) REVERT: A 36 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8291 (mm) REVERT: A 82 GLN cc_start: 0.8497 (pt0) cc_final: 0.8185 (pm20) REVERT: A 109 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7544 (tt) REVERT: A 146 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8376 (mt-10) REVERT: A 162 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5801 (tt) REVERT: A 164 ASN cc_start: 0.7738 (m110) cc_final: 0.7099 (p0) REVERT: A 282 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7882 (tttm) REVERT: A 284 TYR cc_start: 0.8247 (t80) cc_final: 0.7951 (t80) REVERT: A 373 GLU cc_start: 0.8040 (tp30) cc_final: 0.7639 (tp30) REVERT: A 381 LYS cc_start: 0.8262 (tppt) cc_final: 0.7905 (mtmt) REVERT: A 400 THR cc_start: 0.8764 (m) cc_final: 0.8550 (p) REVERT: A 409 ARG cc_start: 0.7772 (ttm170) cc_final: 0.7332 (mtp85) REVERT: A 420 GLN cc_start: 0.8639 (tm-30) cc_final: 0.7844 (tm-30) REVERT: C 83 ARG cc_start: 0.7628 (ptt-90) cc_final: 0.7420 (mmp-170) REVERT: C 87 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.7061 (ptt90) REVERT: C 120 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7754 (mm-30) REVERT: C 135 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7964 (tm-30) REVERT: C 195 ASN cc_start: 0.7520 (OUTLIER) cc_final: 0.7246 (p0) REVERT: C 230 ASP cc_start: 0.8869 (t0) cc_final: 0.8473 (t0) REVERT: C 347 LYS cc_start: 0.7815 (mmtt) cc_final: 0.7497 (mtpt) REVERT: C 411 SER cc_start: 0.8738 (m) cc_final: 0.8413 (p) REVERT: C 417 MET cc_start: 0.8303 (mmm) cc_final: 0.7774 (mmt) REVERT: C 423 ASP cc_start: 0.8314 (t70) cc_final: 0.7981 (t0) REVERT: C 540 ILE cc_start: 0.7118 (mt) cc_final: 0.6783 (mt) REVERT: C 544 ASP cc_start: 0.7846 (m-30) cc_final: 0.7508 (m-30) REVERT: C 550 LEU cc_start: 0.7841 (tp) cc_final: 0.7555 (tt) REVERT: C 553 ASP cc_start: 0.7191 (t0) cc_final: 0.6830 (t0) REVERT: C 556 PHE cc_start: 0.7257 (m-80) cc_final: 0.6807 (m-80) REVERT: C 595 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7415 (tm-30) REVERT: C 600 GLU cc_start: 0.8747 (tt0) cc_final: 0.8021 (tp30) REVERT: C 601 TYR cc_start: 0.7075 (m-80) cc_final: 0.6714 (m-80) REVERT: D 21 LYS cc_start: 0.8249 (ttpp) cc_final: 0.7630 (tptt) REVERT: D 98 ARG cc_start: 0.8484 (ttp-110) cc_final: 0.7899 (ptm-80) REVERT: D 104 ASP cc_start: 0.8271 (t0) cc_final: 0.7835 (t0) REVERT: E 35 ASP cc_start: 0.7601 (m-30) cc_final: 0.7304 (t0) REVERT: E 152 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7637 (tp30) REVERT: E 252 HIS cc_start: 0.6371 (t-90) cc_final: 0.6105 (t70) REVERT: E 409 PHE cc_start: 0.6292 (t80) cc_final: 0.5867 (t80) REVERT: E 467 ARG cc_start: 0.6184 (mmt-90) cc_final: 0.5781 (ttm-80) outliers start: 70 outliers final: 55 residues processed: 338 average time/residue: 0.2893 time to fit residues: 148.5360 Evaluate side-chains 335 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 276 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 449 LYS Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 172 optimal weight: 0.0370 chunk 114 optimal weight: 0.2980 chunk 204 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 124 optimal weight: 0.0020 chunk 94 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 overall best weight: 0.3866 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN C 474 GLN E 266 HIS E 408 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18247 Z= 0.184 Angle : 0.567 10.863 24715 Z= 0.289 Chirality : 0.041 0.182 2720 Planarity : 0.003 0.043 3128 Dihedral : 4.811 39.860 2347 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.80 % Favored : 94.15 % Rotamer: Outliers : 3.51 % Allowed : 13.85 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.18), residues: 2119 helix: 0.61 (0.15), residues: 1261 sheet: -2.29 (0.82), residues: 41 loop : -2.27 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 161 HIS 0.012 0.001 HIS A 291 PHE 0.017 0.001 PHE B 476 TYR 0.020 0.001 TYR E 49 ARG 0.004 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 296 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.7742 (mtt90) cc_final: 0.6932 (tmt170) REVERT: B 103 MET cc_start: 0.7149 (mtt) cc_final: 0.6918 (mtt) REVERT: B 119 MET cc_start: 0.7850 (ttp) cc_final: 0.7514 (ttp) REVERT: B 202 ASP cc_start: 0.8738 (t0) cc_final: 0.8519 (t0) REVERT: B 214 ARG cc_start: 0.7451 (ttm110) cc_final: 0.6821 (mtp85) REVERT: B 226 MET cc_start: 0.8336 (mtm) cc_final: 0.7989 (mtt) REVERT: B 301 TYR cc_start: 0.8372 (t80) cc_final: 0.8045 (t80) REVERT: B 371 ASP cc_start: 0.7785 (m-30) cc_final: 0.7274 (t0) REVERT: B 382 TYR cc_start: 0.7389 (m-80) cc_final: 0.6966 (m-80) REVERT: B 399 GLN cc_start: 0.7602 (tt0) cc_final: 0.7037 (tp40) REVERT: B 423 ASP cc_start: 0.8128 (t0) cc_final: 0.7374 (m-30) REVERT: B 444 ASN cc_start: 0.8074 (t0) cc_final: 0.7851 (t0) REVERT: B 451 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7731 (mp0) REVERT: B 595 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7914 (mm-30) REVERT: A 36 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8310 (mm) REVERT: A 82 GLN cc_start: 0.8521 (pt0) cc_final: 0.8182 (pm20) REVERT: A 109 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7566 (tt) REVERT: A 146 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8421 (mt-10) REVERT: A 164 ASN cc_start: 0.7641 (m110) cc_final: 0.7008 (p0) REVERT: A 282 LYS cc_start: 0.8242 (mmmt) cc_final: 0.7870 (tttm) REVERT: A 284 TYR cc_start: 0.8163 (t80) cc_final: 0.7895 (t80) REVERT: A 373 GLU cc_start: 0.8053 (tp30) cc_final: 0.7629 (tp30) REVERT: A 381 LYS cc_start: 0.8178 (tppt) cc_final: 0.7830 (mtmt) REVERT: A 409 ARG cc_start: 0.7814 (ttm170) cc_final: 0.7355 (mtp85) REVERT: A 420 GLN cc_start: 0.8636 (tm-30) cc_final: 0.7859 (tm-30) REVERT: C 87 ARG cc_start: 0.8210 (mmm-85) cc_final: 0.7046 (ptt90) REVERT: C 120 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7749 (mm-30) REVERT: C 195 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7248 (p0) REVERT: C 230 ASP cc_start: 0.8860 (t0) cc_final: 0.8481 (t0) REVERT: C 347 LYS cc_start: 0.7806 (mmtt) cc_final: 0.7500 (mtpt) REVERT: C 411 SER cc_start: 0.8717 (m) cc_final: 0.8403 (p) REVERT: C 417 MET cc_start: 0.8301 (mmm) cc_final: 0.7721 (mmt) REVERT: C 423 ASP cc_start: 0.8277 (t70) cc_final: 0.7916 (t0) REVERT: C 544 ASP cc_start: 0.7825 (m-30) cc_final: 0.7483 (m-30) REVERT: C 550 LEU cc_start: 0.7842 (tp) cc_final: 0.7562 (tt) REVERT: C 553 ASP cc_start: 0.7168 (t0) cc_final: 0.6728 (t0) REVERT: C 556 PHE cc_start: 0.7242 (m-80) cc_final: 0.6788 (m-80) REVERT: C 595 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7376 (tm-30) REVERT: C 600 GLU cc_start: 0.8855 (tt0) cc_final: 0.7956 (tp30) REVERT: C 601 TYR cc_start: 0.6955 (m-80) cc_final: 0.6479 (m-80) REVERT: D 21 LYS cc_start: 0.8147 (ttpp) cc_final: 0.7532 (tptt) REVERT: D 98 ARG cc_start: 0.8422 (ttp-110) cc_final: 0.7901 (ptm-80) REVERT: D 104 ASP cc_start: 0.8260 (t0) cc_final: 0.7840 (t0) REVERT: E 35 ASP cc_start: 0.7558 (m-30) cc_final: 0.7270 (t0) REVERT: E 76 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7883 (mmtt) REVERT: E 152 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7611 (tp30) REVERT: E 252 HIS cc_start: 0.6334 (t-90) cc_final: 0.6115 (t70) REVERT: E 409 PHE cc_start: 0.6300 (t80) cc_final: 0.5665 (t80) REVERT: E 467 ARG cc_start: 0.6091 (mmt-90) cc_final: 0.5853 (ttm-80) outliers start: 70 outliers final: 54 residues processed: 342 average time/residue: 0.2970 time to fit residues: 155.1177 Evaluate side-chains 336 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 278 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 449 LYS Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 590 PHE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 39 optimal weight: 0.0570 chunk 129 optimal weight: 0.5980 chunk 139 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 160 optimal weight: 0.6980 chunk 185 optimal weight: 6.9990 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN D 188 ASN E 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18247 Z= 0.211 Angle : 0.590 11.160 24715 Z= 0.299 Chirality : 0.041 0.178 2720 Planarity : 0.003 0.051 3128 Dihedral : 4.760 34.906 2347 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.01 % Rotamer: Outliers : 3.51 % Allowed : 14.20 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.18), residues: 2119 helix: 0.69 (0.15), residues: 1267 sheet: -2.21 (0.82), residues: 41 loop : -2.19 (0.20), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 161 HIS 0.013 0.001 HIS A 291 PHE 0.015 0.001 PHE B 476 TYR 0.020 0.001 TYR E 49 ARG 0.004 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 287 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.7731 (mtt90) cc_final: 0.6921 (tmt170) REVERT: B 103 MET cc_start: 0.7178 (mtt) cc_final: 0.6972 (mtt) REVERT: B 119 MET cc_start: 0.7874 (ttp) cc_final: 0.7559 (ttp) REVERT: B 135 GLU cc_start: 0.7500 (mp0) cc_final: 0.7263 (mp0) REVERT: B 214 ARG cc_start: 0.7429 (ttm110) cc_final: 0.6820 (mtp85) REVERT: B 226 MET cc_start: 0.8300 (mtm) cc_final: 0.7969 (mtt) REVERT: B 301 TYR cc_start: 0.8353 (t80) cc_final: 0.8026 (t80) REVERT: B 371 ASP cc_start: 0.7784 (m-30) cc_final: 0.7282 (t0) REVERT: B 382 TYR cc_start: 0.7392 (m-80) cc_final: 0.6937 (m-80) REVERT: B 399 GLN cc_start: 0.7595 (tt0) cc_final: 0.7059 (tp40) REVERT: B 423 ASP cc_start: 0.8127 (t0) cc_final: 0.7377 (m-30) REVERT: B 444 ASN cc_start: 0.8090 (t0) cc_final: 0.7856 (t0) REVERT: B 451 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7709 (mp0) REVERT: A 36 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8278 (mm) REVERT: A 82 GLN cc_start: 0.8547 (pt0) cc_final: 0.8196 (pm20) REVERT: A 109 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7496 (tt) REVERT: A 146 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8412 (mt-10) REVERT: A 163 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6863 (mp) REVERT: A 282 LYS cc_start: 0.8334 (mmmt) cc_final: 0.7678 (mmtm) REVERT: A 373 GLU cc_start: 0.8072 (tp30) cc_final: 0.7640 (tp30) REVERT: A 381 LYS cc_start: 0.8170 (tppt) cc_final: 0.7831 (ptpt) REVERT: A 409 ARG cc_start: 0.7861 (ttm170) cc_final: 0.7550 (mmm-85) REVERT: A 420 GLN cc_start: 0.8638 (tm-30) cc_final: 0.7745 (tm-30) REVERT: C 87 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7042 (ptt90) REVERT: C 120 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7748 (mm-30) REVERT: C 195 ASN cc_start: 0.7502 (OUTLIER) cc_final: 0.7222 (p0) REVERT: C 230 ASP cc_start: 0.8881 (t0) cc_final: 0.8407 (t0) REVERT: C 347 LYS cc_start: 0.7783 (mmtt) cc_final: 0.7477 (mtpt) REVERT: C 411 SER cc_start: 0.8710 (m) cc_final: 0.8390 (p) REVERT: C 417 MET cc_start: 0.8306 (mmm) cc_final: 0.7726 (mmt) REVERT: C 423 ASP cc_start: 0.8273 (t70) cc_final: 0.7912 (t0) REVERT: C 544 ASP cc_start: 0.7752 (m-30) cc_final: 0.7517 (m-30) REVERT: C 550 LEU cc_start: 0.7841 (tp) cc_final: 0.7545 (tt) REVERT: C 553 ASP cc_start: 0.7238 (t0) cc_final: 0.6813 (t0) REVERT: C 556 PHE cc_start: 0.7255 (m-80) cc_final: 0.6797 (m-80) REVERT: C 600 GLU cc_start: 0.8854 (tt0) cc_final: 0.7959 (tp30) REVERT: C 601 TYR cc_start: 0.7116 (m-80) cc_final: 0.6652 (m-80) REVERT: D 21 LYS cc_start: 0.8173 (tttp) cc_final: 0.7638 (tptt) REVERT: D 98 ARG cc_start: 0.8465 (ttp-110) cc_final: 0.7893 (ptm-80) REVERT: D 104 ASP cc_start: 0.8293 (t0) cc_final: 0.7902 (t0) REVERT: E 35 ASP cc_start: 0.7604 (m-30) cc_final: 0.7329 (t0) REVERT: E 76 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7878 (mmtt) REVERT: E 80 ILE cc_start: 0.8285 (mp) cc_final: 0.8035 (tp) REVERT: E 152 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7571 (tp30) REVERT: E 409 PHE cc_start: 0.6379 (t80) cc_final: 0.5803 (t80) REVERT: E 467 ARG cc_start: 0.6332 (mmt-90) cc_final: 0.5998 (ttm-80) outliers start: 70 outliers final: 56 residues processed: 332 average time/residue: 0.2861 time to fit residues: 144.4762 Evaluate side-chains 335 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 274 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.9980 chunk 178 optimal weight: 20.0000 chunk 190 optimal weight: 9.9990 chunk 114 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 172 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 189 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN D 188 ASN E 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18247 Z= 0.293 Angle : 0.635 11.972 24715 Z= 0.321 Chirality : 0.043 0.219 2720 Planarity : 0.004 0.053 3128 Dihedral : 4.871 32.898 2347 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.77 % Rotamer: Outliers : 3.41 % Allowed : 14.30 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.18), residues: 2119 helix: 0.63 (0.15), residues: 1265 sheet: -2.20 (0.88), residues: 37 loop : -2.18 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 161 HIS 0.011 0.001 HIS A 291 PHE 0.028 0.002 PHE C 597 TYR 0.028 0.001 TYR E 49 ARG 0.004 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 283 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.7699 (mtt90) cc_final: 0.7034 (tmt170) REVERT: B 103 MET cc_start: 0.7272 (mtt) cc_final: 0.7028 (mtt) REVERT: B 119 MET cc_start: 0.7872 (ttp) cc_final: 0.7602 (ttp) REVERT: B 214 ARG cc_start: 0.7429 (ttm110) cc_final: 0.6856 (mtp85) REVERT: B 226 MET cc_start: 0.8381 (mtm) cc_final: 0.8072 (mtt) REVERT: B 301 TYR cc_start: 0.8339 (t80) cc_final: 0.8011 (t80) REVERT: B 371 ASP cc_start: 0.7755 (m-30) cc_final: 0.7325 (t0) REVERT: B 382 TYR cc_start: 0.7401 (m-80) cc_final: 0.6937 (m-80) REVERT: B 399 GLN cc_start: 0.7598 (tt0) cc_final: 0.7029 (tp40) REVERT: B 423 ASP cc_start: 0.8208 (t0) cc_final: 0.7445 (m-30) REVERT: B 444 ASN cc_start: 0.8087 (t0) cc_final: 0.7866 (t0) REVERT: B 451 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7739 (pm20) REVERT: B 555 MET cc_start: 0.7050 (mmt) cc_final: 0.6800 (mmm) REVERT: A 36 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8327 (mm) REVERT: A 82 GLN cc_start: 0.8546 (pt0) cc_final: 0.8206 (pm20) REVERT: A 126 GLU cc_start: 0.7658 (tp30) cc_final: 0.7426 (mm-30) REVERT: A 146 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8277 (mt-10) REVERT: A 163 LEU cc_start: 0.7036 (mp) cc_final: 0.6754 (mp) REVERT: A 164 ASN cc_start: 0.7675 (m110) cc_final: 0.6982 (p0) REVERT: A 282 LYS cc_start: 0.8371 (mmmt) cc_final: 0.7675 (mmtm) REVERT: A 373 GLU cc_start: 0.8099 (tp30) cc_final: 0.7651 (tp30) REVERT: A 381 LYS cc_start: 0.8152 (tppt) cc_final: 0.7822 (ptpt) REVERT: A 409 ARG cc_start: 0.8043 (ttm170) cc_final: 0.7816 (mmm-85) REVERT: A 420 GLN cc_start: 0.8649 (tm-30) cc_final: 0.7754 (tm-30) REVERT: C 87 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.7113 (ptt90) REVERT: C 195 ASN cc_start: 0.7430 (OUTLIER) cc_final: 0.7156 (p0) REVERT: C 347 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7493 (mtpt) REVERT: C 399 GLN cc_start: 0.7692 (tt0) cc_final: 0.7184 (pt0) REVERT: C 411 SER cc_start: 0.8646 (m) cc_final: 0.8310 (p) REVERT: C 417 MET cc_start: 0.8369 (mmm) cc_final: 0.7767 (mmt) REVERT: C 423 ASP cc_start: 0.8311 (t70) cc_final: 0.7974 (t0) REVERT: C 550 LEU cc_start: 0.7821 (tp) cc_final: 0.7522 (tt) REVERT: C 553 ASP cc_start: 0.7268 (t0) cc_final: 0.6846 (t0) REVERT: C 556 PHE cc_start: 0.7372 (m-80) cc_final: 0.6892 (m-80) REVERT: C 600 GLU cc_start: 0.8969 (tt0) cc_final: 0.7974 (tp30) REVERT: C 601 TYR cc_start: 0.7139 (m-80) cc_final: 0.6591 (m-80) REVERT: D 21 LYS cc_start: 0.8245 (tttp) cc_final: 0.7700 (tptt) REVERT: D 98 ARG cc_start: 0.8477 (ttp-110) cc_final: 0.7880 (ptm-80) REVERT: D 104 ASP cc_start: 0.8338 (t0) cc_final: 0.7970 (t0) REVERT: E 35 ASP cc_start: 0.7610 (m-30) cc_final: 0.7371 (t0) REVERT: E 152 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7629 (tp30) REVERT: E 409 PHE cc_start: 0.6349 (t80) cc_final: 0.5830 (t80) REVERT: E 467 ARG cc_start: 0.6320 (mmt-90) cc_final: 0.6017 (ttm-80) outliers start: 68 outliers final: 59 residues processed: 327 average time/residue: 0.3106 time to fit residues: 156.6560 Evaluate side-chains 332 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 271 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 449 LYS Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 76 VAL Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 110 SER Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 414 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.5980 chunk 122 optimal weight: 0.5980 chunk 95 optimal weight: 0.0980 chunk 139 optimal weight: 0.0970 chunk 211 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 168 optimal weight: 5.9990 chunk 17 optimal weight: 0.0970 chunk 129 optimal weight: 0.5980 chunk 103 optimal weight: 0.4980 chunk 133 optimal weight: 0.4980 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN D 188 ASN E 86 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18247 Z= 0.169 Angle : 0.607 10.387 24715 Z= 0.304 Chirality : 0.041 0.229 2720 Planarity : 0.003 0.055 3128 Dihedral : 4.715 34.592 2347 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 2.81 % Allowed : 15.20 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.19), residues: 2119 helix: 0.85 (0.15), residues: 1247 sheet: -2.07 (0.80), residues: 43 loop : -2.09 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP E 161 HIS 0.015 0.001 HIS A 291 PHE 0.039 0.001 PHE C 476 TYR 0.034 0.001 TYR E 49 ARG 0.004 0.000 ARG E 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4238 Ramachandran restraints generated. 2119 Oldfield, 0 Emsley, 2119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 289 time to evaluate : 2.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 ARG cc_start: 0.7689 (mtt90) cc_final: 0.6971 (tmt170) REVERT: B 103 MET cc_start: 0.7058 (mtt) cc_final: 0.6688 (mtt) REVERT: B 119 MET cc_start: 0.7840 (ttp) cc_final: 0.7502 (ttp) REVERT: B 135 GLU cc_start: 0.7426 (mp0) cc_final: 0.7209 (mp0) REVERT: B 214 ARG cc_start: 0.7456 (ttm110) cc_final: 0.6839 (mtp85) REVERT: B 226 MET cc_start: 0.8293 (mtm) cc_final: 0.7980 (mtt) REVERT: B 301 TYR cc_start: 0.8330 (t80) cc_final: 0.8006 (t80) REVERT: B 371 ASP cc_start: 0.7775 (m-30) cc_final: 0.7228 (t0) REVERT: B 382 TYR cc_start: 0.7289 (m-80) cc_final: 0.6888 (m-80) REVERT: B 399 GLN cc_start: 0.7591 (tt0) cc_final: 0.7026 (tp40) REVERT: B 423 ASP cc_start: 0.8120 (t0) cc_final: 0.7396 (m-30) REVERT: B 444 ASN cc_start: 0.8061 (t0) cc_final: 0.7833 (t0) REVERT: B 555 MET cc_start: 0.7005 (mmt) cc_final: 0.6795 (mmm) REVERT: A 36 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8264 (mm) REVERT: A 82 GLN cc_start: 0.8533 (pt0) cc_final: 0.8101 (pm20) REVERT: A 146 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8396 (mt-10) REVERT: A 163 LEU cc_start: 0.7060 (mp) cc_final: 0.6795 (mp) REVERT: A 164 ASN cc_start: 0.7630 (m110) cc_final: 0.6932 (p0) REVERT: A 282 LYS cc_start: 0.8255 (mmmt) cc_final: 0.7639 (mmtm) REVERT: A 373 GLU cc_start: 0.8135 (tp30) cc_final: 0.7704 (tp30) REVERT: A 381 LYS cc_start: 0.8170 (tppt) cc_final: 0.7837 (ptpt) REVERT: A 409 ARG cc_start: 0.8052 (ttm170) cc_final: 0.7799 (mmm-85) REVERT: A 420 GLN cc_start: 0.8516 (tm-30) cc_final: 0.7681 (tm-30) REVERT: C 87 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7024 (ptt90) REVERT: C 195 ASN cc_start: 0.7436 (OUTLIER) cc_final: 0.7166 (p0) REVERT: C 347 LYS cc_start: 0.7772 (mmtt) cc_final: 0.7484 (mtpt) REVERT: C 357 GLN cc_start: 0.7828 (pt0) cc_final: 0.7062 (tm-30) REVERT: C 399 GLN cc_start: 0.7582 (tt0) cc_final: 0.7082 (pt0) REVERT: C 411 SER cc_start: 0.8706 (m) cc_final: 0.8366 (p) REVERT: C 417 MET cc_start: 0.8363 (mmm) cc_final: 0.7815 (mmt) REVERT: C 423 ASP cc_start: 0.8248 (t70) cc_final: 0.7869 (t0) REVERT: C 473 TYR cc_start: 0.6927 (t80) cc_final: 0.6677 (t80) REVERT: C 544 ASP cc_start: 0.7464 (m-30) cc_final: 0.7178 (m-30) REVERT: C 550 LEU cc_start: 0.7861 (tp) cc_final: 0.7568 (tt) REVERT: C 553 ASP cc_start: 0.7140 (t0) cc_final: 0.6749 (t0) REVERT: C 556 PHE cc_start: 0.7267 (m-80) cc_final: 0.6837 (m-80) REVERT: C 600 GLU cc_start: 0.8970 (tt0) cc_final: 0.8042 (tp30) REVERT: D 21 LYS cc_start: 0.8099 (tttp) cc_final: 0.7587 (tptt) REVERT: D 98 ARG cc_start: 0.8428 (ttp-110) cc_final: 0.7803 (ptm-80) REVERT: D 104 ASP cc_start: 0.8306 (t0) cc_final: 0.7882 (t0) REVERT: E 35 ASP cc_start: 0.7499 (m-30) cc_final: 0.7264 (t0) REVERT: E 80 ILE cc_start: 0.8312 (mp) cc_final: 0.8008 (tp) REVERT: E 152 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7609 (tp30) REVERT: E 409 PHE cc_start: 0.6331 (t80) cc_final: 0.5814 (t80) REVERT: E 467 ARG cc_start: 0.6358 (mmt-90) cc_final: 0.6096 (ttm-80) outliers start: 56 outliers final: 49 residues processed: 327 average time/residue: 0.2861 time to fit residues: 143.0124 Evaluate side-chains 321 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 270 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 304 SER Chi-restraints excluded: chain B residue 343 VAL Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 450 SER Chi-restraints excluded: chain B residue 545 ILE Chi-restraints excluded: chain B residue 596 GLU Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 303 TYR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 311 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 356 PHE Chi-restraints excluded: chain A residue 360 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 367 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 475 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain C residue 103 MET Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 279 ASP Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 418 TYR Chi-restraints excluded: chain C residue 428 LEU Chi-restraints excluded: chain C residue 463 ILE Chi-restraints excluded: chain C residue 545 ILE Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 162 SER Chi-restraints excluded: chain D residue 166 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 359 PHE Chi-restraints excluded: chain E residue 414 THR Chi-restraints excluded: chain E residue 466 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 155 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 172 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 147 optimal weight: 0.0980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 86 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.176000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.125962 restraints weight = 24984.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121975 restraints weight = 18634.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.123930 restraints weight = 21005.418| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18247 Z= 0.236 Angle : 0.631 11.266 24715 Z= 0.317 Chirality : 0.043 0.218 2720 Planarity : 0.004 0.056 3128 Dihedral : 4.707 33.251 2347 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.01 % Rotamer: Outliers : 3.06 % Allowed : 14.95 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.19), residues: 2119 helix: 0.81 (0.15), residues: 1258 sheet: -2.12 (0.77), residues: 43 loop : -2.06 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 161 HIS 0.015 0.001 HIS A 291 PHE 0.035 0.002 PHE C 476 TYR 0.032 0.001 TYR E 49 ARG 0.004 0.000 ARG E 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3793.26 seconds wall clock time: 69 minutes 37.32 seconds (4177.32 seconds total)