Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 18:15:36 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr3_23955/04_2023/7mr3_23955.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr3_23955/04_2023/7mr3_23955.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/7mr3_23955/04_2023/7mr3_23955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr3_23955/04_2023/7mr3_23955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr3_23955/04_2023/7mr3_23955.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mr3_23955/04_2023/7mr3_23955.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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 40 5.49 5 S 101 5.16 5 C 14801 2.51 5 N 4181 2.21 5 O 4492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 791": "OE1" <-> "OE2" Residue "C GLU 160": "OE1" <-> "OE2" Residue "C GLU 385": "OE1" <-> "OE2" Residue "C GLU 488": "OE1" <-> "OE2" Residue "C GLU 860": "OE1" <-> "OE2" Residue "C GLU 873": "OE1" <-> "OE2" Residue "C GLU 995": "OE1" <-> "OE2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 214": "OE1" <-> "OE2" Residue "D GLU 305": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 23615 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 9043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1128, 9043 Classifications: {'peptide': 1128} Link IDs: {'PTRANS': 50, 'TRANS': 1077} Chain breaks: 2 Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 4672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4672 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 25, 'TRANS': 579} Chain: "X" Number of atoms: 492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 492 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 12.01, per 1000 atoms: 0.51 Number of scatterers: 23615 At special positions: 0 Unit cell: (129.8, 119.9, 146.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 40 15.00 O 4492 8.00 N 4181 7.00 C 14801 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 9.00 Conformation dependent library (CDL) restraints added in 3.2 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5386 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 17 sheets defined 55.7% alpha, 8.4% beta 10 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.806A pdb=" N ALA B 48 " --> pdb=" O GLY B 45 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 49 " --> pdb=" O GLY B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 45 through 49' Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.763A pdb=" N LEU B 59 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 106 through 120 Processing helix chain 'B' and resid 121 through 124 Processing helix chain 'B' and resid 128 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 156 through 172 removed outlier: 3.543A pdb=" N CYS B 172 " --> pdb=" O TRP B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.678A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 5.744A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 240 removed outlier: 3.620A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.843A pdb=" N ARG B 259 " --> pdb=" O ARG B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 281 removed outlier: 3.683A pdb=" N SER B 279 " --> pdb=" O GLU B 276 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B 281 " --> pdb=" O ASN B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.866A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N PHE B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 removed outlier: 4.270A pdb=" N ASP B 314 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLU B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 4.363A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 366 through 378 Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.691A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.938A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.616A pdb=" N ASN B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 485 removed outlier: 3.525A pdb=" N GLN B 485 " --> pdb=" O GLY B 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 482 through 485' Processing helix chain 'B' and resid 510 through 534 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 560 through 574 removed outlier: 4.197A pdb=" N ALA B 570 " --> pdb=" O GLN B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 4.217A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 3.837A pdb=" N ALA B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 632 Processing helix chain 'B' and resid 634 through 656 Processing helix chain 'B' and resid 657 through 669 Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.858A pdb=" N LEU B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 701 removed outlier: 4.086A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 717 removed outlier: 3.629A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 745 Processing helix chain 'B' and resid 783 through 808 removed outlier: 3.565A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 836 removed outlier: 3.611A pdb=" N GLN B 835 " --> pdb=" O ASP B 832 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 843 Processing helix chain 'B' and resid 849 through 860 removed outlier: 4.048A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 945 Processing helix chain 'B' and resid 949 through 959 Processing helix chain 'B' and resid 969 through 980 Processing helix chain 'B' and resid 983 through 985 No H-bonds generated for 'chain 'B' and resid 983 through 985' Processing helix chain 'B' and resid 986 through 999 removed outlier: 3.625A pdb=" N GLN B 999 " --> pdb=" O THR B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 Processing helix chain 'B' and resid 1013 through 1017 removed outlier: 3.861A pdb=" N LYS B1017 " --> pdb=" O ALA B1014 " (cutoff:3.500A) Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 3.652A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1089 through 1093 removed outlier: 3.628A pdb=" N ALA B1092 " --> pdb=" O ASP B1089 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1105 removed outlier: 3.744A pdb=" N MET B1098 " --> pdb=" O THR B1094 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B1099 " --> pdb=" O GLN B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1107 through 1126 Processing helix chain 'B' and resid 1130 through 1135 Processing helix chain 'B' and resid 1163 through 1173 Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.634A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 88 through 103 removed outlier: 3.566A pdb=" N SER C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 4.065A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 185 through 199 removed outlier: 4.206A pdb=" N TYR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N SER C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.621A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 262 removed outlier: 3.759A pdb=" N THR C 262 " --> pdb=" O LYS C 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 259 through 262' Processing helix chain 'C' and resid 276 through 283 removed outlier: 3.713A pdb=" N GLU C 281 " --> pdb=" O PHE C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.646A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 removed outlier: 4.101A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.522A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 417 removed outlier: 3.670A pdb=" N SER C 417 " --> pdb=" O ASP C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 414 through 417' Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 430 through 434 removed outlier: 3.835A pdb=" N TYR C 434 " --> pdb=" O ALA C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 459 Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 Processing helix chain 'C' and resid 486 through 501 removed outlier: 3.873A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY C 501 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 513 removed outlier: 3.633A pdb=" N VAL C 511 " --> pdb=" O ASP C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 578 Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 589 through 599 Processing helix chain 'C' and resid 605 through 626 Processing helix chain 'C' and resid 633 through 645 removed outlier: 3.955A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 790 through 795 removed outlier: 4.102A pdb=" N TYR C 794 " --> pdb=" O ASP C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 805 No H-bonds generated for 'chain 'C' and resid 803 through 805' Processing helix chain 'C' and resid 806 through 812 Processing helix chain 'C' and resid 834 through 843 removed outlier: 4.185A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 852 Processing helix chain 'C' and resid 874 through 890 removed outlier: 4.037A pdb=" N ILE C 880 " --> pdb=" O SER C 876 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 890 " --> pdb=" O ASN C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 904 removed outlier: 4.611A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 933 removed outlier: 3.762A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 990 Processing helix chain 'C' and resid 1000 through 1004 removed outlier: 3.854A pdb=" N ASP C1003 " --> pdb=" O LEU C1000 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1031 Processing helix chain 'C' and resid 1038 through 1050 Processing helix chain 'C' and resid 1060 through 1076 Processing helix chain 'C' and resid 1087 through 1092 Processing helix chain 'C' and resid 1098 through 1120 removed outlier: 3.761A pdb=" N LEU C1114 " --> pdb=" O GLN C1110 " (cutoff:3.500A) Proline residue: C1115 - end of helix Processing helix chain 'D' and resid 3 through 13 Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 32 through 49 removed outlier: 3.694A pdb=" N THR D 36 " --> pdb=" O HIS D 32 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY D 49 " --> pdb=" O ASP D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 59 removed outlier: 3.713A pdb=" N LEU D 58 " --> pdb=" O PRO D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 72 Processing helix chain 'D' and resid 80 through 87 Processing helix chain 'D' and resid 110 through 125 Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 205 through 223 Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 240 through 245 Processing helix chain 'D' and resid 275 through 284 Processing helix chain 'D' and resid 309 through 315 Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.509A pdb=" N ARG D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 365 through 375 removed outlier: 4.006A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.911A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 392 removed outlier: 4.041A pdb=" N THR D 391 " --> pdb=" O GLN D 388 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP D 392 " --> pdb=" O ASP D 389 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 388 through 392' Processing helix chain 'D' and resid 400 through 424 removed outlier: 3.909A pdb=" N ALA D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ARG D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N TYR D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.519A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.514A pdb=" N LEU D 527 " --> pdb=" O PRO D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 542 removed outlier: 4.041A pdb=" N GLN D 542 " --> pdb=" O HIS D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 539 through 542' Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 582 through 592 Processing helix chain 'D' and resid 599 through 606 removed outlier: 3.529A pdb=" N SER D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER D 606 " --> pdb=" O ALA D 602 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.281A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N TYR B 441 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU B 20 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLY B 413 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE B 21 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU B 60 " --> pdb=" O MET B 382 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.302A pdb=" N GLN B 151 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.673A pdb=" N TYR B 768 " --> pdb=" O VAL B 777 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.307A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N SER B 814 " --> pdb=" O PRO B 750 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL B 752 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLY B 816 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU B 754 " --> pdb=" O GLY B 816 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LYS B 500 " --> pdb=" O LEU B 815 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL B 817 " --> pdb=" O LYS B 500 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TRP B 502 " --> pdb=" O VAL B 817 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1019 through 1024 removed outlier: 6.722A pdb=" N ASP B1067 " --> pdb=" O GLU B1020 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU B1022 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N PHE B1065 " --> pdb=" O GLU B1022 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N TYR B1024 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N LYS B1063 " --> pdb=" O TYR B1024 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B1068 " --> pdb=" O LEU B1079 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR B1156 " --> pdb=" O TYR B1140 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 61 removed outlier: 4.691A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG C 3 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N PHE C 240 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N TYR C 5 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU C 2 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU C 323 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N VAL C 4 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ALA C 325 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N HIS C 6 " --> pdb=" O ALA C 325 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP C 324 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN C 264 " --> pdb=" O ARG C 272 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG C 272 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.319A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 437 through 439 removed outlier: 7.184A pdb=" N LYS C 673 " --> pdb=" O GLN C 724 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N PHE C 376 " --> pdb=" O CYS C 782 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 442 through 443 removed outlier: 3.971A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 650 " --> pdb=" O ARG C 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 831 through 833 removed outlier: 5.067A pdb=" N GLN C 951 " --> pdb=" O CYS C 947 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS C 947 " --> pdb=" O GLN C 951 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N THR C 953 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU C 945 " --> pdb=" O THR C 953 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TRP C 955 " --> pdb=" O ILE C 943 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ILE C 943 " --> pdb=" O TRP C 955 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET C 941 " --> pdb=" O PRO C 957 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 831 through 833 removed outlier: 15.771A pdb=" N LEU C 956 " --> pdb=" O TRP C 967 " (cutoff:3.500A) removed outlier: 13.357A pdb=" N TRP C 967 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N GLN C 958 " --> pdb=" O LEU C 965 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N LEU C 965 " --> pdb=" O GLN C 958 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 91 through 92 Processing sheet with id=AB5, first strand: chain 'D' and resid 237 through 239 removed outlier: 3.586A pdb=" N SER D 238 " --> pdb=" O LEU D 201 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N CYS D 353 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N VAL D 168 " --> pdb=" O CYS D 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 535 through 537 removed outlier: 8.800A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N PHE D 546 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG D 576 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N HIS D 548 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 535 through 537 removed outlier: 8.800A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N TYR D 580 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU D 551 " --> pdb=" O TYR D 580 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 481 through 483 removed outlier: 6.548A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG D 509 " --> pdb=" O LEU D 502 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 3120 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 9.32 Time building geometry restraints manager: 9.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3971 1.32 - 1.44: 6595 1.44 - 1.57: 13402 1.57 - 1.70: 78 1.70 - 1.82: 169 Bond restraints: 24215 Sorted by residual: bond pdb=" CD GLN B1112 " pdb=" OE1 GLN B1112 " ideal model delta sigma weight residual 1.231 1.194 0.037 1.90e-02 2.77e+03 3.74e+00 bond pdb=" N GLU C 79 " pdb=" CA GLU C 79 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.29e+00 bond pdb=" C ILE B 473 " pdb=" N PRO B 474 " ideal model delta sigma weight residual 1.335 1.322 0.013 8.70e-03 1.32e+04 2.31e+00 bond pdb=" CG GLN B1112 " pdb=" CD GLN B1112 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.27e+00 bond pdb=" CA GLN D 387 " pdb=" CB GLN D 387 " ideal model delta sigma weight residual 1.524 1.544 -0.020 1.37e-02 5.33e+03 2.13e+00 ... (remaining 24210 not shown) Histogram of bond angle deviations from ideal: 96.75 - 104.26: 525 104.26 - 111.76: 11074 111.76 - 119.26: 9029 119.26 - 126.77: 11886 126.77 - 134.27: 514 Bond angle restraints: 33028 Sorted by residual: angle pdb=" N GLN B1112 " pdb=" CA GLN B1112 " pdb=" CB GLN B1112 " ideal model delta sigma weight residual 110.16 117.99 -7.83 1.48e+00 4.57e-01 2.80e+01 angle pdb=" CA GLN B1112 " pdb=" CB GLN B1112 " pdb=" CG GLN B1112 " ideal model delta sigma weight residual 114.10 123.96 -9.86 2.00e+00 2.50e-01 2.43e+01 angle pdb=" CB MET B 136 " pdb=" CG MET B 136 " pdb=" SD MET B 136 " ideal model delta sigma weight residual 112.70 126.43 -13.73 3.00e+00 1.11e-01 2.10e+01 angle pdb=" N ILE B 179 " pdb=" CA ILE B 179 " pdb=" C ILE B 179 " ideal model delta sigma weight residual 112.96 108.66 4.30 1.00e+00 1.00e+00 1.85e+01 angle pdb=" CA LEU C 655 " pdb=" CB LEU C 655 " pdb=" CG LEU C 655 " ideal model delta sigma weight residual 116.30 131.09 -14.79 3.50e+00 8.16e-02 1.78e+01 ... (remaining 33023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 12619 18.01 - 36.01: 1443 36.01 - 54.02: 315 54.02 - 72.03: 80 72.03 - 90.03: 29 Dihedral angle restraints: 14486 sinusoidal: 6176 harmonic: 8310 Sorted by residual: dihedral pdb=" CA GLU B1029 " pdb=" C GLU B1029 " pdb=" N PRO B1030 " pdb=" CA PRO B1030 " ideal model delta harmonic sigma weight residual 180.00 -148.18 -31.82 0 5.00e+00 4.00e-02 4.05e+01 dihedral pdb=" CA GLY B1137 " pdb=" C GLY B1137 " pdb=" N VAL B1138 " pdb=" CA VAL B1138 " ideal model delta harmonic sigma weight residual -180.00 -150.03 -29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA TRP B 878 " pdb=" C TRP B 878 " pdb=" N GLN B 879 " pdb=" CA GLN B 879 " ideal model delta harmonic sigma weight residual 180.00 151.37 28.63 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 14483 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2564 0.047 - 0.094: 792 0.094 - 0.141: 234 0.141 - 0.188: 30 0.188 - 0.235: 7 Chirality restraints: 3627 Sorted by residual: chirality pdb=" CA GLN B1112 " pdb=" N GLN B1112 " pdb=" C GLN B1112 " pdb=" CB GLN B1112 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR B 304 " pdb=" CA THR B 304 " pdb=" OG1 THR B 304 " pdb=" CG2 THR B 304 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA ASP C 484 " pdb=" N ASP C 484 " pdb=" C ASP C 484 " pdb=" CB ASP C 484 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 3624 not shown) Planarity restraints: 4202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 878 " 0.026 2.00e-02 2.50e+03 1.88e-02 8.84e+00 pdb=" CG TRP B 878 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B 878 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 878 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 878 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 878 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 878 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 878 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 878 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 878 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.045 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO C 658 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 960 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO C 961 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 961 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 961 " 0.036 5.00e-02 4.00e+02 ... (remaining 4199 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 4945 2.78 - 3.31: 21816 3.31 - 3.84: 38267 3.84 - 4.37: 42515 4.37 - 4.90: 74291 Nonbonded interactions: 181834 Sorted by model distance: nonbonded pdb=" OD1 ASN B 79 " pdb=" OH TYR B 97 " model vdw 2.250 2.440 nonbonded pdb=" OE2 GLU B 275 " pdb=" OG1 THR B 277 " model vdw 2.287 2.440 nonbonded pdb=" O ARG C 112 " pdb=" OG1 THR C 116 " model vdw 2.295 2.440 nonbonded pdb=" O SER C 459 " pdb=" OG SER C 459 " model vdw 2.296 2.440 nonbonded pdb=" OE1 GLN B 876 " pdb=" NE2 GLN B 879 " model vdw 2.304 2.520 ... (remaining 181829 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.030 Extract box with map and model: 5.490 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 62.700 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 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 : 0.005 0.055 24215 Z= 0.353 Angle : 0.833 14.787 33028 Z= 0.423 Chirality : 0.050 0.235 3627 Planarity : 0.006 0.069 4202 Dihedral : 16.388 90.034 9100 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -1.62 (0.15), residues: 2844 helix: -0.11 (0.13), residues: 1422 sheet: -1.14 (0.34), residues: 262 loop : -2.26 (0.16), residues: 1160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 2.826 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.3201 time to fit residues: 100.5609 Evaluate side-chains 138 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 2.753 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 7.9990 chunk 217 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 87 optimal weight: 0.0770 chunk 136 optimal weight: 2.9990 chunk 167 optimal weight: 5.9990 chunk 260 optimal weight: 20.0000 overall best weight: 1.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN B1103 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 24215 Z= 0.218 Angle : 0.571 9.612 33028 Z= 0.294 Chirality : 0.040 0.162 3627 Planarity : 0.004 0.061 4202 Dihedral : 12.330 70.499 3538 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2844 helix: 0.83 (0.14), residues: 1415 sheet: -1.06 (0.33), residues: 263 loop : -2.00 (0.17), residues: 1166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 2.757 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 166 average time/residue: 0.3413 time to fit residues: 94.5837 Evaluate side-chains 150 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 2.958 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2370 time to fit residues: 7.6805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 144 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 216 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 282 optimal weight: 10.0000 chunk 232 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 89 optimal weight: 20.0000 chunk 209 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 GLN ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 ASN B 594 GLN B 650 GLN C 6 HIS ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 HIS C 339 GLN C 522 HIS C 793 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.092 24215 Z= 0.690 Angle : 0.875 15.272 33028 Z= 0.443 Chirality : 0.050 0.217 3627 Planarity : 0.006 0.066 4202 Dihedral : 12.878 74.474 3538 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.15), residues: 2844 helix: 0.41 (0.13), residues: 1412 sheet: -1.49 (0.33), residues: 265 loop : -2.33 (0.17), residues: 1167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 2.914 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 20 residues processed: 163 average time/residue: 0.3343 time to fit residues: 91.5353 Evaluate side-chains 146 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 2.693 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2168 time to fit residues: 11.9081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 257 optimal weight: 5.9990 chunk 196 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 175 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 277 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 248 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 HIS D 387 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 24215 Z= 0.211 Angle : 0.564 9.729 33028 Z= 0.289 Chirality : 0.040 0.156 3627 Planarity : 0.004 0.060 4202 Dihedral : 12.656 78.651 3538 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2844 helix: 1.13 (0.14), residues: 1413 sheet: -1.33 (0.33), residues: 267 loop : -2.01 (0.18), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 2.954 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 11 residues processed: 163 average time/residue: 0.3299 time to fit residues: 90.3410 Evaluate side-chains 141 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 130 time to evaluate : 2.778 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2345 time to fit residues: 8.6840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 231 optimal weight: 20.0000 chunk 157 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 236 optimal weight: 6.9990 chunk 191 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 chunk 249 optimal weight: 10.0000 chunk 70 optimal weight: 0.0970 overall best weight: 3.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 24215 Z= 0.349 Angle : 0.632 11.635 33028 Z= 0.319 Chirality : 0.042 0.158 3627 Planarity : 0.004 0.062 4202 Dihedral : 12.654 78.848 3538 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2844 helix: 1.08 (0.14), residues: 1415 sheet: -1.30 (0.32), residues: 269 loop : -2.08 (0.18), residues: 1160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 2.745 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 154 average time/residue: 0.3302 time to fit residues: 85.8184 Evaluate side-chains 145 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 129 time to evaluate : 2.819 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2216 time to fit residues: 10.5301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 93 optimal weight: 8.9990 chunk 249 optimal weight: 8.9990 chunk 54 optimal weight: 0.2980 chunk 162 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 277 optimal weight: 9.9990 chunk 230 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 714 HIS C 137 GLN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 24215 Z= 0.273 Angle : 0.591 10.651 33028 Z= 0.299 Chirality : 0.041 0.239 3627 Planarity : 0.004 0.058 4202 Dihedral : 12.626 80.027 3538 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer Outliers : 0.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 2844 helix: 1.23 (0.14), residues: 1414 sheet: -1.36 (0.32), residues: 273 loop : -2.01 (0.18), residues: 1157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 2.639 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 149 average time/residue: 0.3379 time to fit residues: 84.4252 Evaluate side-chains 134 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 2.768 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2530 time to fit residues: 5.7799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 267 optimal weight: 9.9990 chunk 31 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 chunk 173 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 594 GLN C 162 GLN C 267 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 24215 Z= 0.196 Angle : 0.557 11.035 33028 Z= 0.280 Chirality : 0.039 0.170 3627 Planarity : 0.004 0.057 4202 Dihedral : 12.540 79.604 3538 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: -0.23 (0.16), residues: 2844 helix: 1.41 (0.14), residues: 1416 sheet: -1.21 (0.32), residues: 287 loop : -1.94 (0.18), residues: 1141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 159 average time/residue: 0.3468 time to fit residues: 91.8149 Evaluate side-chains 139 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 3.246 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2428 time to fit residues: 6.9012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 171 optimal weight: 0.4980 chunk 110 optimal weight: 0.0870 chunk 165 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 175 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 136 optimal weight: 0.0970 chunk 25 optimal weight: 10.0000 chunk 217 optimal weight: 0.3980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 GLN ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 24215 Z= 0.146 Angle : 0.537 11.695 33028 Z= 0.270 Chirality : 0.038 0.157 3627 Planarity : 0.004 0.053 4202 Dihedral : 12.430 78.256 3538 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.09 (0.16), residues: 2844 helix: 1.66 (0.14), residues: 1407 sheet: -1.01 (0.32), residues: 273 loop : -1.75 (0.18), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 162 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 169 average time/residue: 0.3396 time to fit residues: 95.7976 Evaluate side-chains 143 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 3.010 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2569 time to fit residues: 5.4370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 251 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 241 optimal weight: 20.0000 chunk 257 optimal weight: 0.4980 chunk 264 optimal weight: 10.0000 chunk 155 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 202 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 232 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 24215 Z= 0.179 Angle : 0.552 12.165 33028 Z= 0.275 Chirality : 0.039 0.150 3627 Planarity : 0.004 0.056 4202 Dihedral : 12.375 77.694 3538 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.16), residues: 2844 helix: 1.69 (0.14), residues: 1416 sheet: -0.91 (0.33), residues: 273 loop : -1.76 (0.18), residues: 1155 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 146 time to evaluate : 2.934 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 153 average time/residue: 0.3445 time to fit residues: 88.2978 Evaluate side-chains 144 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 140 time to evaluate : 2.841 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2286 time to fit residues: 5.5383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 256 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 272 optimal weight: 0.9980 chunk 166 optimal weight: 0.0020 chunk 129 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 285 optimal weight: 10.0000 chunk 263 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 24215 Z= 0.243 Angle : 0.584 12.513 33028 Z= 0.290 Chirality : 0.040 0.152 3627 Planarity : 0.004 0.056 4202 Dihedral : 12.425 77.778 3538 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.16), residues: 2844 helix: 1.63 (0.14), residues: 1416 sheet: -0.90 (0.32), residues: 283 loop : -1.77 (0.18), residues: 1145 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 144 average time/residue: 0.3656 time to fit residues: 88.0806 Evaluate side-chains 138 residues out of total 2423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 2.737 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2869 time to fit residues: 4.8679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 139 optimal weight: 0.1980 chunk 180 optimal weight: 0.8980 chunk 242 optimal weight: 10.0000 chunk 69 optimal weight: 0.4980 chunk 209 optimal weight: 0.0770 chunk 33 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 228 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 234 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 594 GLN ** D 463 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.102414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.078267 restraints weight = 55134.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.080583 restraints weight = 29845.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.082062 restraints weight = 20014.749| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 24215 Z= 0.148 Angle : 0.558 12.153 33028 Z= 0.276 Chirality : 0.038 0.156 3627 Planarity : 0.004 0.053 4202 Dihedral : 12.351 77.847 3538 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % 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: 0.26 (0.17), residues: 2844 helix: 1.74 (0.14), residues: 1414 sheet: -0.78 (0.33), residues: 281 loop : -1.64 (0.18), residues: 1149 =============================================================================== Job complete usr+sys time: 3250.66 seconds wall clock time: 60 minutes 56.30 seconds (3656.30 seconds total)