Starting phenix.real_space_refine (version: dev) on Wed Apr 6 03:17:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyp_0095/04_2022/6gyp_0095.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyp_0095/04_2022/6gyp_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_0095/04_2022/6gyp_0095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyp_0095/04_2022/6gyp_0095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyp_0095/04_2022/6gyp_0095.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gyp_0095/04_2022/6gyp_0095.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: 10.18, 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: 7.13 Conformation dependent library (CDL) restraints added in 2.7 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: 0.89 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: 5.46 Time building geometry restraints manager: 7.66 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 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. 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: 4.460 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: 14.520 Check model and map are aligned: 0.280 Convert atoms to be neutral: 0.150 Process input model: 48.600 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 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 : 4.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.08 % Favored : 92.83 % Rotamer Outliers : 0.50 % 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 *********************** 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 : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 536 average time/residue: 0.3294 time to fit residues: 256.4644 Evaluate side-chains 292 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 290 time to evaluate : 2.382 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1591 time to fit residues: 3.8059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 89 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 166 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 101 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 192 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 303 GLN ** 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 203 GLN A 310 ASN A 333 ASN A 335 GLN A 439 HIS ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 ASN C 189 HIS C 199 ASN C 394 ASN C 399 GLN ** C 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 34 ASN D 101 ASN D 188 ASN E 86 HIS 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: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.099 18247 Z= 0.278 Angle : 0.650 10.266 24715 Z= 0.341 Chirality : 0.043 0.198 2720 Planarity : 0.005 0.054 3128 Dihedral : 5.646 33.371 2344 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.77 % Rotamer Outliers : 2.66 % 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: -2.72 (0.16), residues: 2119 helix: -1.04 (0.14), residues: 1254 sheet: -3.31 (0.98), residues: 25 loop : -2.91 (0.18), residues: 840 *********************** 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 385 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 332 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 32 residues processed: 370 average time/residue: 0.2912 time to fit residues: 163.8803 Evaluate side-chains 311 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 279 time to evaluate : 2.446 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1750 time to fit residues: 13.2715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 160 optimal weight: 0.2980 chunk 131 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 192 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 191 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 154 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 399 GLN C 406 GLN C 543 ASN D 34 ASN E 252 HIS E 266 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6848 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 18247 Z= 0.244 Angle : 0.624 12.989 24715 Z= 0.322 Chirality : 0.043 0.188 2720 Planarity : 0.004 0.049 3128 Dihedral : 5.296 33.253 2344 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.32 % Favored : 93.63 % Rotamer Outliers : 1.61 % 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: -1.98 (0.17), residues: 2119 helix: -0.42 (0.14), residues: 1261 sheet: -2.09 (0.99), residues: 37 loop : -2.68 (0.19), residues: 821 *********************** 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 339 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 307 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 329 average time/residue: 0.2880 time to fit residues: 146.8453 Evaluate side-chains 284 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 269 time to evaluate : 2.347 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1857 time to fit residues: 8.4653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 8.9990 chunk 145 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 92 optimal weight: 0.0870 chunk 129 optimal weight: 0.9980 chunk 193 optimal weight: 9.9990 chunk 204 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 183 optimal weight: 10.0000 chunk 55 optimal weight: 0.0670 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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 203 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN C 360 ASN C 399 GLN E 252 HIS E 266 HIS E 492 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 18247 Z= 0.191 Angle : 0.605 15.624 24715 Z= 0.308 Chirality : 0.041 0.198 2720 Planarity : 0.004 0.045 3128 Dihedral : 5.044 35.122 2344 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.38 % Rotamer Outliers : 1.86 % 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: -1.46 (0.18), residues: 2119 helix: 0.01 (0.15), residues: 1267 sheet: -1.98 (0.96), residues: 37 loop : -2.51 (0.20), residues: 815 *********************** 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 338 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 301 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 14 residues processed: 324 average time/residue: 0.2853 time to fit residues: 143.3192 Evaluate side-chains 280 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 266 time to evaluate : 2.224 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1650 time to fit residues: 7.3643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 152 optimal weight: 0.0270 chunk 84 optimal weight: 0.4980 chunk 174 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 51 optimal weight: 0.5980 overall best weight: 0.6242 ------------------------------------------------------------------------------- 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 203 GLN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN E 266 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 18247 Z= 0.260 Angle : 0.636 18.193 24715 Z= 0.322 Chirality : 0.043 0.194 2720 Planarity : 0.004 0.042 3128 Dihedral : 4.949 33.683 2344 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.99 % Favored : 93.96 % Rotamer Outliers : 1.86 % 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: -1.26 (0.18), residues: 2119 helix: 0.18 (0.15), residues: 1269 sheet: -2.05 (0.94), residues: 37 loop : -2.44 (0.20), residues: 813 *********************** 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 322 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 285 time to evaluate : 2.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 16 residues processed: 305 average time/residue: 0.2857 time to fit residues: 135.0127 Evaluate side-chains 277 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 261 time to evaluate : 2.298 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1728 time to fit residues: 8.1299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.6980 chunk 184 optimal weight: 0.0000 chunk 40 optimal weight: 0.4980 chunk 120 optimal weight: 0.8980 chunk 50 optimal weight: 0.0270 chunk 205 optimal weight: 7.9990 chunk 170 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 overall best weight: 0.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN E 86 HIS E 252 HIS E 266 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.118 18247 Z= 0.225 Angle : 0.622 18.385 24715 Z= 0.317 Chirality : 0.042 0.194 2720 Planarity : 0.004 0.041 3128 Dihedral : 4.831 34.283 2344 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.85 % Favored : 94.10 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.18), residues: 2119 helix: 0.39 (0.15), residues: 1272 sheet: -1.99 (0.81), residues: 47 loop : -2.37 (0.20), residues: 800 *********************** 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 311 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 277 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 19 residues processed: 299 average time/residue: 0.2868 time to fit residues: 132.6911 Evaluate side-chains 277 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 258 time to evaluate : 2.157 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1772 time to fit residues: 9.0751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 116 optimal weight: 0.0980 chunk 149 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 204 optimal weight: 9.9990 chunk 127 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 94 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 552 ASN E 86 HIS ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6852 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.280 18247 Z= 0.330 Angle : 0.670 23.557 24715 Z= 0.344 Chirality : 0.043 0.227 2720 Planarity : 0.004 0.046 3128 Dihedral : 4.824 33.324 2344 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.85 % Favored : 94.10 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.18), residues: 2119 helix: 0.47 (0.15), residues: 1274 sheet: -1.96 (0.81), residues: 47 loop : -2.30 (0.20), residues: 798 *********************** 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 306 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 278 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 289 average time/residue: 0.3014 time to fit residues: 132.9895 Evaluate side-chains 270 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 258 time to evaluate : 2.111 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1860 time to fit residues: 7.1832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 0.0870 chunk 122 optimal weight: 0.5980 chunk 61 optimal weight: 0.3980 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.0670 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 160 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 543 ASN E 86 HIS ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 18247 Z= 0.191 Angle : 0.613 14.524 24715 Z= 0.307 Chirality : 0.041 0.186 2720 Planarity : 0.004 0.052 3128 Dihedral : 4.733 34.463 2344 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer Outliers : 1.10 % 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: -0.62 (0.19), residues: 2119 helix: 0.71 (0.15), residues: 1261 sheet: -1.86 (0.83), residues: 47 loop : -2.16 (0.20), residues: 811 *********************** 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 297 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 275 time to evaluate : 2.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 14 residues processed: 287 average time/residue: 0.2933 time to fit residues: 129.8139 Evaluate side-chains 277 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 263 time to evaluate : 2.331 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1966 time to fit residues: 7.8663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.1980 chunk 178 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 172 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 GLN D 188 ASN ** E 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 HIS E 492 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 18247 Z= 0.313 Angle : 0.686 12.124 24715 Z= 0.343 Chirality : 0.044 0.183 2720 Planarity : 0.004 0.049 3128 Dihedral : 4.844 32.727 2344 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.28 % Favored : 93.68 % Rotamer Outliers : 0.40 % 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: -0.73 (0.18), residues: 2119 helix: 0.60 (0.15), residues: 1269 sheet: -1.83 (0.81), residues: 47 loop : -2.20 (0.20), residues: 803 *********************** 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 269 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 261 time to evaluate : 2.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 264 average time/residue: 0.3015 time to fit residues: 123.1634 Evaluate side-chains 245 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 241 time to evaluate : 2.361 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1740 time to fit residues: 4.3962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.0000 chunk 122 optimal weight: 0.9990 chunk 95 optimal weight: 0.0170 chunk 139 optimal weight: 0.7980 chunk 211 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 17 optimal weight: 0.0980 chunk 129 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 overall best weight: 0.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN E 252 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6832 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 18247 Z= 0.192 Angle : 0.639 11.569 24715 Z= 0.320 Chirality : 0.042 0.182 2720 Planarity : 0.004 0.052 3128 Dihedral : 4.758 34.523 2344 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.81 (0.15), residues: 1255 sheet: -1.79 (0.83), residues: 47 loop : -2.07 (0.20), residues: 817 ********************** 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 276 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 267 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 270 average time/residue: 0.2883 time to fit residues: 120.9138 Evaluate side-chains 258 residues out of total 2014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 252 time to evaluate : 2.193 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1801 time to fit residues: 5.0657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 8.9990 chunk 51 optimal weight: 0.5980 chunk 155 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 70 optimal weight: 0.0970 chunk 172 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- 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** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.175780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.125711 restraints weight = 24976.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.122202 restraints weight = 19138.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124037 restraints weight = 21580.733| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 18247 Z= 0.266 Angle : 0.676 11.603 24715 Z= 0.337 Chirality : 0.043 0.190 2720 Planarity : 0.004 0.052 3128 Dihedral : 4.792 33.219 2344 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.13 % Favored : 93.82 % Rotamer Outliers : 0.30 % 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: -0.54 (0.19), residues: 2119 helix: 0.71 (0.15), residues: 1275 sheet: -1.85 (0.82), residues: 47 loop : -2.04 (0.21), residues: 797 =============================================================================== Job complete usr+sys time: 3585.75 seconds wall clock time: 66 minutes 24.83 seconds (3984.83 seconds total)