Starting phenix.real_space_refine on Wed Mar 4 04:39:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a7d_15220/03_2026/8a7d_15220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a7d_15220/03_2026/8a7d_15220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8a7d_15220/03_2026/8a7d_15220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a7d_15220/03_2026/8a7d_15220.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8a7d_15220/03_2026/8a7d_15220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a7d_15220/03_2026/8a7d_15220.map" } resolution = 3.06 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.027 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: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 Zn 1 6.06 5 S 100 5.16 5 C 6728 2.51 5 N 1861 2.21 5 O 2073 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10771 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 7256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 7256 Classifications: {'peptide': 921} Link IDs: {'PCIS': 3, 'PTRANS': 54, 'TRANS': 863} Chain: "P" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1309 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain: "Q" Number of atoms: 2085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2085 Classifications: {'peptide': 273} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 250} Chain breaks: 1 Chain: "C" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 106 Unusual residues: {' CA': 7, ' ZN': 1, 'NAG': 7} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Q" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.60, per 1000 atoms: 0.24 Number of scatterers: 10771 At special positions: 0 Unit cell: (125.736, 98.358, 137.904, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Ca 8 19.99 S 100 16.00 O 2073 8.00 N 1861 7.00 C 6728 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS C 144 " - pdb=" SG CYS C 235 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 332 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 414 " - pdb=" SG CYS C 428 " distance=2.03 Simple disulfide: pdb=" SG CYS C 424 " - pdb=" SG CYS C 440 " distance=2.03 Simple disulfide: pdb=" SG CYS C 457 " - pdb=" SG CYS C 473 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 583 " - pdb=" SG CYS C 622 " distance=2.04 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 643 " distance=2.03 Simple disulfide: pdb=" SG CYS C 710 " - pdb=" SG CYS C 881 " distance=2.02 Simple disulfide: pdb=" SG CYS C 713 " - pdb=" SG CYS C 878 " distance=2.03 Simple disulfide: pdb=" SG CYS C 732 " - pdb=" SG CYS P 120 " distance=2.03 Simple disulfide: pdb=" SG CYS C 753 " - pdb=" SG CYS C 835 " distance=2.03 Simple disulfide: pdb=" SG CYS C 775 " - pdb=" SG CYS C 781 " distance=2.03 Simple disulfide: pdb=" SG CYS C 947 " - pdb=" SG CYS C 975 " distance=2.03 Simple disulfide: pdb=" SG CYS C 960 " - pdb=" SG CYS C 971 " distance=2.03 Simple disulfide: pdb=" SG CYS C 983 " - pdb=" SG CYS C 990 " distance=2.03 Simple disulfide: pdb=" SG CYS C 999 " - pdb=" SG CYS C1011 " distance=2.03 Simple disulfide: pdb=" SG CYS P 56 " - pdb=" SG CYS P 70 " distance=2.03 Simple disulfide: pdb=" SG CYS P 65 " - pdb=" SG CYS P 85 " distance=2.02 Simple disulfide: pdb=" SG CYS P 76 " - pdb=" SG CYS P 125 " distance=2.03 Simple disulfide: pdb=" SG CYS P 109 " - pdb=" SG CYS P 139 " distance=2.04 Simple disulfide: pdb=" SG CYS P 146 " - pdb=" SG CYS P 181 " distance=2.03 Simple disulfide: pdb=" SG CYS P 197 " - pdb=" SG CYS P 205 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1285 " - pdb=" SG CYS Q1329 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1300 " - pdb=" SG CYS Q1310 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1314 " - pdb=" SG CYS Q1342 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1346 " - pdb=" SG CYS Q1399 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1362 " - pdb=" SG CYS Q1373 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1377 " - pdb=" SG CYS Q1410 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1478 " - pdb=" SG CYS Q1539 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1492 " - pdb=" SG CYS Q1502 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1506 " - pdb=" SG CYS Q1554 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1558 " - pdb=" SG CYS Q1576 " distance=2.02 Simple disulfide: pdb=" SG CYS Q1567 " - pdb=" SG CYS Q1583 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1584 " - pdb=" SG CYS Q1608 " distance=2.03 Simple disulfide: pdb=" SG CYS Q1600 " - pdb=" SG CYS Q1606 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG C1701 " - " ASN C 725 " " NAG C1702 " - " ASN C 480 " " NAG C1703 " - " ASN C 429 " " NAG C1704 " - " ASN C 402 " " NAG C1705 " - " ASN C 390 " " NAG C1706 " - " ASN C 601 " " NAG C1707 " - " ASN C 825 " " NAG Q1701 " - " ASN Q1323 " Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 599.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1708 " pdb="ZN ZN C1708 " - pdb=" NE2 HIS C 566 " pdb="ZN ZN C1708 " - pdb=" NE2 HIS C 572 " pdb="ZN ZN C1708 " - pdb=" NE2 HIS C 562 " 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 18 sheets defined 26.1% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 229 through 234 removed outlier: 4.665A pdb=" N LYS C 234 " --> pdb=" O LEU C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 275 removed outlier: 3.848A pdb=" N HIS C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 296 removed outlier: 4.007A pdb=" N ALA C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 292 through 296' Processing helix chain 'C' and resid 330 through 333 Processing helix chain 'C' and resid 334 through 344 removed outlier: 3.634A pdb=" N SER C 340 " --> pdb=" O GLU C 336 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR C 341 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 388 removed outlier: 4.595A pdb=" N GLN C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 430 through 432 No H-bonds generated for 'chain 'C' and resid 430 through 432' Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 444 through 449 removed outlier: 3.621A pdb=" N VAL C 449 " --> pdb=" O PRO C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 472 Processing helix chain 'C' and resid 480 through 484 Processing helix chain 'C' and resid 498 through 506 Processing helix chain 'C' and resid 534 through 538 removed outlier: 3.611A pdb=" N ALA C 537 " --> pdb=" O ASP C 534 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU C 538 " --> pdb=" O LYS C 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 534 through 538' Processing helix chain 'C' and resid 547 through 551 removed outlier: 3.511A pdb=" N TYR C 551 " --> pdb=" O PRO C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 557 through 568 removed outlier: 3.967A pdb=" N ILE C 561 " --> pdb=" O THR C 557 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS C 562 " --> pdb=" O HIS C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 662 Processing helix chain 'C' and resid 740 through 744 Processing helix chain 'C' and resid 762 through 766 Processing helix chain 'C' and resid 776 through 780 removed outlier: 4.061A pdb=" N GLN C 779 " --> pdb=" O PRO C 776 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY C 780 " --> pdb=" O GLU C 777 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 776 through 780' Processing helix chain 'C' and resid 875 through 879 Processing helix chain 'C' and resid 953 through 957 Processing helix chain 'C' and resid 1007 through 1012 Processing helix chain 'P' and resid 46 through 60 removed outlier: 3.618A pdb=" N VAL P 58 " --> pdb=" O GLN P 54 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN P 59 " --> pdb=" O HIS P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 72 removed outlier: 4.017A pdb=" N CYS P 70 " --> pdb=" O GLY P 66 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE P 71 " --> pdb=" O VAL P 67 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU P 72 " --> pdb=" O PHE P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 92 Processing helix chain 'P' and resid 93 through 95 No H-bonds generated for 'chain 'P' and resid 93 through 95' Processing helix chain 'P' and resid 96 through 118 removed outlier: 3.740A pdb=" N LEU P 107 " --> pdb=" O ILE P 103 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS P 108 " --> pdb=" O LYS P 104 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE P 118 " --> pdb=" O LEU P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 143 Processing helix chain 'P' and resid 144 through 152 removed outlier: 3.814A pdb=" N ALA P 148 " --> pdb=" O ASP P 144 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 160 Processing helix chain 'P' and resid 161 through 168 Processing helix chain 'P' and resid 168 through 180 removed outlier: 3.560A pdb=" N VAL P 172 " --> pdb=" O HIS P 168 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR P 180 " --> pdb=" O ASN P 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 182 through 202 Processing helix chain 'P' and resid 202 through 209 removed outlier: 3.946A pdb=" N SER P 206 " --> pdb=" O GLY P 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1359 through 1364 Processing helix chain 'Q' and resid 1521 through 1525 removed outlier: 4.215A pdb=" N ILE Q1525 " --> pdb=" O VAL Q1522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1548 through 1552 Processing helix chain 'Q' and resid 1573 through 1575 No H-bonds generated for 'chain 'Q' and resid 1573 through 1575' Processing helix chain 'Q' and resid 1576 through 1581 removed outlier: 4.061A pdb=" N GLY Q1580 " --> pdb=" O CYS Q1576 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1613 through 1617 Processing sheet with id=AA1, first strand: chain 'C' and resid 215 through 220 removed outlier: 5.635A pdb=" N GLN C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL C 212 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR C 120 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU C 258 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN C 122 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE C 256 " --> pdb=" O GLN C 122 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 215 through 220 removed outlier: 5.635A pdb=" N GLN C 216 " --> pdb=" O VAL C 212 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL C 212 " --> pdb=" O GLN C 216 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR C 120 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU C 258 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLN C 122 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE C 256 " --> pdb=" O GLN C 122 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N HIS C 255 " --> pdb=" O ARG C 95 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N ARG C 95 " --> pdb=" O HIS C 255 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 183 through 186 removed outlier: 3.774A pdb=" N ASP C 167 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE C 157 " --> pdb=" O VAL C 136 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N VAL C 136 " --> pdb=" O ILE C 157 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU C 238 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 391 through 401 removed outlier: 6.329A pdb=" N LYS C 351 " --> pdb=" O SER C 392 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU C 394 " --> pdb=" O LYS C 351 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 353 " --> pdb=" O GLU C 394 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ASP C 396 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR C 355 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU C 398 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL C 357 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL C 400 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN C 359 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N LEU C 513 " --> pdb=" O VAL C 352 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG C 354 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ILE C 515 " --> pdb=" O ARG C 354 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARG C 356 " --> pdb=" O ILE C 515 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N PHE C 517 " --> pdb=" O ARG C 356 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N VAL C 358 " --> pdb=" O PHE C 517 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASN C 514 " --> pdb=" O ILE C 544 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N LEU C 546 " --> pdb=" O ASN C 514 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE C 516 " --> pdb=" O LEU C 546 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 409 through 411 removed outlier: 5.992A pdb=" N LEU C 409 " --> pdb=" O LEU C 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 680 through 684 removed outlier: 5.056A pdb=" N VAL C 681 " --> pdb=" O GLU C 692 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N GLU C 692 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY C 683 " --> pdb=" O THR C 690 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 713 through 714 removed outlier: 3.658A pdb=" N ILE C 718 " --> pdb=" O LEU C 714 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU C 719 " --> pdb=" O SER C 871 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLU C 863 " --> pdb=" O THR C 801 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N TRP C 799 " --> pdb=" O ASP C 865 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA C 867 " --> pdb=" O THR C 797 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR C 797 " --> pdb=" O ALA C 867 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N LEU C 869 " --> pdb=" O SER C 795 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N SER C 795 " --> pdb=" O LEU C 869 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N SER C 871 " --> pdb=" O PRO C 793 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 781 through 791 removed outlier: 6.200A pdb=" N TYR C 851 " --> pdb=" O PHE C 787 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY C 852 " --> pdb=" O LEU C 819 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP C 815 " --> pdb=" O TYR C 856 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 885 through 891 removed outlier: 3.680A pdb=" N GLU C 930 " --> pdb=" O SER C 927 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 885 through 891 Processing sheet with id=AB2, first strand: chain 'C' and resid 981 through 984 Processing sheet with id=AB3, first strand: chain 'Q' and resid 1296 through 1299 Processing sheet with id=AB4, first strand: chain 'Q' and resid 1319 through 1321 Processing sheet with id=AB5, first strand: chain 'Q' and resid 1345 through 1346 Processing sheet with id=AB6, first strand: chain 'Q' and resid 1355 through 1357 Processing sheet with id=AB7, first strand: chain 'Q' and resid 1488 through 1491 Processing sheet with id=AB8, first strand: chain 'Q' and resid 1532 through 1533 removed outlier: 3.834A pdb=" N THR Q1532 " --> pdb=" O ILE Q1515 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE Q1515 " --> pdb=" O THR Q1532 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE Q1514 " --> pdb=" O HIS Q1553 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Q' and resid 1566 through 1568 removed outlier: 6.081A pdb=" N CYS Q1567 " --> pdb=" O PHE Q1596 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 334 hydrogen bonds defined for protein. 852 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: 2.28 Time building geometry restraints manager: 1.04 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: 3584 1.34 - 1.46: 2457 1.46 - 1.58: 4871 1.58 - 1.70: 1 1.70 - 1.83: 124 Bond restraints: 11037 Sorted by residual: bond pdb=" N ASP C 458 " pdb=" CA ASP C 458 " ideal model delta sigma weight residual 1.457 1.618 -0.161 1.29e-02 6.01e+03 1.55e+02 bond pdb=" C CYS C 457 " pdb=" N ASP C 458 " ideal model delta sigma weight residual 1.332 1.427 -0.094 1.40e-02 5.10e+03 4.54e+01 bond pdb=" N VAL Q1411 " pdb=" CA VAL Q1411 " ideal model delta sigma weight residual 1.465 1.495 -0.030 1.02e-02 9.61e+03 8.82e+00 bond pdb=" CA ASP C 458 " pdb=" C ASP C 458 " ideal model delta sigma weight residual 1.523 1.561 -0.038 1.34e-02 5.57e+03 7.87e+00 bond pdb=" C ASP C 458 " pdb=" N MET C 459 " ideal model delta sigma weight residual 1.332 1.363 -0.030 1.40e-02 5.10e+03 4.69e+00 ... (remaining 11032 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.74: 14986 6.74 - 13.48: 7 13.48 - 20.22: 0 20.22 - 26.96: 0 26.96 - 33.71: 2 Bond angle restraints: 14995 Sorted by residual: angle pdb=" O CYS C 457 " pdb=" C CYS C 457 " pdb=" N ASP C 458 " ideal model delta sigma weight residual 122.81 89.10 33.71 1.23e+00 6.61e-01 7.51e+02 angle pdb=" CA CYS C 457 " pdb=" C CYS C 457 " pdb=" N ASP C 458 " ideal model delta sigma weight residual 115.56 148.36 -32.80 1.30e+00 5.92e-01 6.37e+02 angle pdb=" C ASP C 458 " pdb=" N MET C 459 " pdb=" CA MET C 459 " ideal model delta sigma weight residual 121.54 133.08 -11.54 1.91e+00 2.74e-01 3.65e+01 angle pdb=" C CYS C 457 " pdb=" N ASP C 458 " pdb=" CA ASP C 458 " ideal model delta sigma weight residual 121.54 131.87 -10.33 1.91e+00 2.74e-01 2.93e+01 angle pdb=" N HIS C 430 " pdb=" CA HIS C 430 " pdb=" C HIS C 430 " ideal model delta sigma weight residual 110.80 119.79 -8.99 2.13e+00 2.20e-01 1.78e+01 ... (remaining 14990 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 6085 17.78 - 35.56: 547 35.56 - 53.34: 125 53.34 - 71.12: 30 71.12 - 88.90: 18 Dihedral angle restraints: 6805 sinusoidal: 2871 harmonic: 3934 Sorted by residual: dihedral pdb=" CA GLU C 777 " pdb=" C GLU C 777 " pdb=" N PRO C 778 " pdb=" CA PRO C 778 " ideal model delta harmonic sigma weight residual -180.00 -126.45 -53.55 0 5.00e+00 4.00e-02 1.15e+02 dihedral pdb=" CB CYS Q1558 " pdb=" SG CYS Q1558 " pdb=" SG CYS Q1576 " pdb=" CB CYS Q1576 " ideal model delta sinusoidal sigma weight residual -86.00 -152.08 66.08 1 1.00e+01 1.00e-02 5.71e+01 dihedral pdb=" CB CYS C 327 " pdb=" SG CYS C 327 " pdb=" SG CYS C 587 " pdb=" CB CYS C 587 " ideal model delta sinusoidal sigma weight residual 93.00 145.22 -52.22 1 1.00e+01 1.00e-02 3.72e+01 ... (remaining 6802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1475 0.078 - 0.156: 150 0.156 - 0.233: 2 0.233 - 0.311: 4 0.311 - 0.389: 1 Chirality restraints: 1632 Sorted by residual: chirality pdb=" C1 NAG C1704 " pdb=" ND2 ASN C 402 " pdb=" C2 NAG C1704 " pdb=" O5 NAG C1704 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CA ASP C 458 " pdb=" N ASP C 458 " pdb=" C ASP C 458 " pdb=" CB ASP C 458 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA HIS C 430 " pdb=" N HIS C 430 " pdb=" C HIS C 430 " pdb=" CB HIS C 430 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1629 not shown) Planarity restraints: 1980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1703 " 0.046 2.00e-02 2.50e+03 4.35e-02 2.36e+01 pdb=" C7 NAG C1703 " 0.026 2.00e-02 2.50e+03 pdb=" C8 NAG C1703 " -0.021 2.00e-02 2.50e+03 pdb=" N2 NAG C1703 " -0.075 2.00e-02 2.50e+03 pdb=" O7 NAG C1703 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 457 " 0.026 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C CYS C 457 " -0.067 2.00e-02 2.50e+03 pdb=" O CYS C 457 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP C 458 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU C 777 " 0.052 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO C 778 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 778 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 778 " 0.044 5.00e-02 4.00e+02 ... (remaining 1977 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 215 2.67 - 3.23: 10528 3.23 - 3.79: 16708 3.79 - 4.34: 23308 4.34 - 4.90: 37789 Nonbonded interactions: 88548 Sorted by model distance: nonbonded pdb=" OD2 ASP C 910 " pdb=" OH TYR C 921 " model vdw 2.115 3.040 nonbonded pdb=" OG SER C 148 " pdb=" OD1 ASP C 150 " model vdw 2.152 3.040 nonbonded pdb=" OG1 THR C 590 " pdb=" OE1 GLU C 591 " model vdw 2.187 3.040 nonbonded pdb=" OD2 ASP C 961 " pdb="CA CA C1713 " model vdw 2.202 2.510 nonbonded pdb=" OE1 GLU C 958 " pdb="CA CA C1713 " model vdw 2.213 2.510 ... (remaining 88543 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.130 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:1.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 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 : 0.004 0.161 11085 Z= 0.228 Angle : 0.781 33.705 15093 Z= 0.470 Chirality : 0.048 0.389 1632 Planarity : 0.005 0.079 1972 Dihedral : 14.794 88.905 4160 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.32 % Favored : 94.16 % Rotamer: Outliers : 0.50 % Allowed : 12.16 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.24), residues: 1353 helix: 0.16 (0.33), residues: 239 sheet: -0.72 (0.32), residues: 273 loop : 0.08 (0.23), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 575 TYR 0.013 0.002 TYR C 252 PHE 0.030 0.002 PHE Q1312 TRP 0.011 0.002 TRP C 259 HIS 0.007 0.001 HIS C 430 Details of bonding type rmsd covalent geometry : bond 0.00404 (11037) covalent geometry : angle 0.76079 (14995) SS BOND : bond 0.00428 ( 37) SS BOND : angle 1.30494 ( 74) hydrogen bonds : bond 0.15247 ( 306) hydrogen bonds : angle 8.01524 ( 852) metal coordination : bond 0.00349 ( 3) link_NAG-ASN : bond 0.00468 ( 8) link_NAG-ASN : angle 4.07526 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 184 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.7880 (mtt-85) cc_final: 0.7639 (mtt180) REVERT: C 252 TYR cc_start: 0.8708 (m-80) cc_final: 0.8259 (m-80) REVERT: C 284 LEU cc_start: 0.8759 (tp) cc_final: 0.8523 (tp) REVERT: C 367 ASN cc_start: 0.7985 (t0) cc_final: 0.7677 (t0) REVERT: C 423 ASN cc_start: 0.7413 (t0) cc_final: 0.7050 (p0) REVERT: C 429 ASN cc_start: 0.4934 (t0) cc_final: 0.4279 (p0) REVERT: C 430 HIS cc_start: 0.7185 (OUTLIER) cc_final: 0.6963 (m-70) REVERT: C 490 SER cc_start: 0.8197 (t) cc_final: 0.7580 (p) REVERT: C 508 ASP cc_start: 0.7943 (t0) cc_final: 0.7014 (p0) REVERT: C 553 MET cc_start: 0.7761 (mmp) cc_final: 0.7474 (mmm) REVERT: C 636 MET cc_start: 0.9122 (mmm) cc_final: 0.8706 (mmp) REVERT: C 922 TRP cc_start: 0.8714 (p90) cc_final: 0.8412 (p90) REVERT: C 931 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7880 (pt0) REVERT: C 976 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7379 (ttm-80) REVERT: P 77 GLU cc_start: 0.7660 (tp30) cc_final: 0.7288 (pt0) REVERT: P 79 ARG cc_start: 0.7113 (mtp85) cc_final: 0.6820 (mmt90) REVERT: P 100 LYS cc_start: 0.7539 (mtmt) cc_final: 0.7322 (mtpt) REVERT: P 115 ARG cc_start: 0.7854 (ttp80) cc_final: 0.7458 (ttm110) REVERT: P 158 GLU cc_start: 0.7495 (tp30) cc_final: 0.7278 (tm-30) REVERT: Q 1291 HIS cc_start: 0.7424 (m90) cc_final: 0.7176 (m-70) REVERT: Q 1341 LEU cc_start: 0.6994 (mt) cc_final: 0.6762 (pp) REVERT: Q 1343 GLU cc_start: 0.6749 (tt0) cc_final: 0.6390 (tm-30) REVERT: Q 1378 LYS cc_start: 0.7123 (mttt) cc_final: 0.6859 (ptmt) REVERT: Q 1401 GLN cc_start: 0.8018 (mt0) cc_final: 0.7388 (pp30) outliers start: 6 outliers final: 3 residues processed: 187 average time/residue: 0.1142 time to fit residues: 29.1482 Evaluate side-chains 140 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 136 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 795 SER Chi-restraints excluded: chain P residue 56 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 0.6980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN C 246 ASN C 292 ASN C 499 ASN C 619 ASN C 629 ASN C 650 ASN C 651 GLN C 680 GLN C 832 ASN C 905 ASN P 49 ASN ** P 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN P 112 HIS P 176 ASN P 199 GLN Q1358 GLN Q1398 GLN Q1487 ASN Q1565 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.196777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.125799 restraints weight = 12569.106| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 3.07 r_work: 0.3265 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11085 Z= 0.178 Angle : 0.616 8.820 15093 Z= 0.317 Chirality : 0.046 0.247 1632 Planarity : 0.005 0.075 1972 Dihedral : 6.181 58.724 1631 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.88 % Favored : 94.68 % Rotamer: Outliers : 2.10 % Allowed : 12.92 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.24), residues: 1353 helix: 1.25 (0.35), residues: 217 sheet: -0.82 (0.33), residues: 253 loop : 0.11 (0.23), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 79 TYR 0.017 0.002 TYR C 463 PHE 0.013 0.001 PHE C 486 TRP 0.012 0.001 TRP C 807 HIS 0.007 0.001 HIS C 430 Details of bonding type rmsd covalent geometry : bond 0.00415 (11037) covalent geometry : angle 0.60212 (14995) SS BOND : bond 0.00313 ( 37) SS BOND : angle 1.04165 ( 74) hydrogen bonds : bond 0.04461 ( 306) hydrogen bonds : angle 5.90957 ( 852) metal coordination : bond 0.00381 ( 3) link_NAG-ASN : bond 0.00552 ( 8) link_NAG-ASN : angle 3.02388 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.7616 (mtt180) REVERT: C 252 TYR cc_start: 0.8669 (m-80) cc_final: 0.8270 (m-80) REVERT: C 367 ASN cc_start: 0.7947 (t0) cc_final: 0.7555 (t0) REVERT: C 418 LYS cc_start: 0.8270 (mtpp) cc_final: 0.7938 (mtpt) REVERT: C 423 ASN cc_start: 0.7247 (t0) cc_final: 0.6899 (p0) REVERT: C 508 ASP cc_start: 0.8040 (t0) cc_final: 0.6833 (p0) REVERT: C 553 MET cc_start: 0.7376 (mmp) cc_final: 0.7023 (mmm) REVERT: C 609 HIS cc_start: 0.6887 (t70) cc_final: 0.6497 (t70) REVERT: C 636 MET cc_start: 0.9081 (mmm) cc_final: 0.8532 (mmp) REVERT: C 849 GLU cc_start: 0.7933 (mp0) cc_final: 0.7415 (mt-10) REVERT: C 931 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8068 (pt0) REVERT: C 956 GLN cc_start: 0.7905 (mm-40) cc_final: 0.7689 (mp10) REVERT: C 976 ARG cc_start: 0.7587 (mtp85) cc_final: 0.7019 (ttm-80) REVERT: P 77 GLU cc_start: 0.7856 (tp30) cc_final: 0.7601 (pt0) REVERT: P 115 ARG cc_start: 0.7530 (ttp80) cc_final: 0.6889 (ttm110) REVERT: P 130 GLU cc_start: 0.6928 (tm-30) cc_final: 0.6659 (tm-30) REVERT: Q 1313 GLN cc_start: 0.7196 (pm20) cc_final: 0.6905 (pm20) REVERT: Q 1378 LYS cc_start: 0.7544 (mttt) cc_final: 0.7178 (ptmt) REVERT: Q 1401 GLN cc_start: 0.8059 (mt0) cc_final: 0.7291 (pp30) REVERT: Q 1518 MET cc_start: 0.4204 (pmm) cc_final: 0.3377 (mmp) REVERT: Q 1573 ARG cc_start: 0.6576 (ptp90) cc_final: 0.6317 (mtm180) outliers start: 25 outliers final: 9 residues processed: 181 average time/residue: 0.0995 time to fit residues: 24.9996 Evaluate side-chains 161 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain P residue 44 ARG Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain Q residue 1305 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 11 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 115 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 967 ASN ** P 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN P 116 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.194229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.125121 restraints weight = 12580.686| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.90 r_work: 0.3246 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11085 Z= 0.257 Angle : 0.660 13.406 15093 Z= 0.338 Chirality : 0.048 0.221 1632 Planarity : 0.005 0.077 1972 Dihedral : 5.887 57.651 1627 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.91 % Favored : 93.72 % Rotamer: Outliers : 3.02 % Allowed : 13.76 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.24), residues: 1353 helix: 0.89 (0.35), residues: 229 sheet: -0.81 (0.32), residues: 269 loop : 0.11 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 79 TYR 0.016 0.002 TYR C 252 PHE 0.016 0.002 PHE Q1298 TRP 0.013 0.002 TRP C 807 HIS 0.007 0.001 HIS C 656 Details of bonding type rmsd covalent geometry : bond 0.00613 (11037) covalent geometry : angle 0.64659 (14995) SS BOND : bond 0.00441 ( 37) SS BOND : angle 1.39930 ( 74) hydrogen bonds : bond 0.04027 ( 306) hydrogen bonds : angle 5.55931 ( 852) metal coordination : bond 0.00667 ( 3) link_NAG-ASN : bond 0.00201 ( 8) link_NAG-ASN : angle 2.57826 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8107 (mtt-85) cc_final: 0.7757 (mtt180) REVERT: C 252 TYR cc_start: 0.8867 (m-80) cc_final: 0.8518 (m-80) REVERT: C 254 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7188 (tt0) REVERT: C 367 ASN cc_start: 0.7913 (t0) cc_final: 0.7501 (t0) REVERT: C 418 LYS cc_start: 0.8311 (mtpp) cc_final: 0.7937 (mtpt) REVERT: C 423 ASN cc_start: 0.7147 (t0) cc_final: 0.6780 (p0) REVERT: C 430 HIS cc_start: 0.6952 (OUTLIER) cc_final: 0.6460 (m-70) REVERT: C 508 ASP cc_start: 0.8127 (t0) cc_final: 0.7099 (p0) REVERT: C 553 MET cc_start: 0.7433 (mmp) cc_final: 0.7126 (mmm) REVERT: C 636 MET cc_start: 0.9132 (mmm) cc_final: 0.8685 (mmm) REVERT: C 956 GLN cc_start: 0.8032 (mm-40) cc_final: 0.7662 (mp10) REVERT: C 976 ARG cc_start: 0.7873 (mtp85) cc_final: 0.7317 (ttm110) REVERT: P 77 GLU cc_start: 0.7899 (tp30) cc_final: 0.7646 (pt0) REVERT: P 79 ARG cc_start: 0.7348 (mtp85) cc_final: 0.6974 (mmt90) REVERT: P 130 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6912 (tm-30) REVERT: Q 1313 GLN cc_start: 0.7327 (pm20) cc_final: 0.7016 (pm20) REVERT: Q 1343 GLU cc_start: 0.6309 (tt0) cc_final: 0.5943 (tm-30) REVERT: Q 1378 LYS cc_start: 0.7401 (mttt) cc_final: 0.7046 (ptpt) REVERT: Q 1398 GLN cc_start: 0.7950 (tt0) cc_final: 0.6725 (mp10) REVERT: Q 1401 GLN cc_start: 0.8134 (mt0) cc_final: 0.7414 (tp-100) REVERT: Q 1518 MET cc_start: 0.4160 (pmm) cc_final: 0.3365 (mmp) outliers start: 36 outliers final: 20 residues processed: 182 average time/residue: 0.1038 time to fit residues: 26.7328 Evaluate side-chains 154 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 239 MET Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 795 SER Chi-restraints excluded: chain C residue 801 THR Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain P residue 44 ARG Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 90 HIS Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1527 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 115 optimal weight: 30.0000 chunk 54 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 126 optimal weight: 20.0000 chunk 122 optimal weight: 20.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 680 GLN ** P 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.196808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.126815 restraints weight = 12649.265| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.05 r_work: 0.3274 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11085 Z= 0.150 Angle : 0.598 13.920 15093 Z= 0.303 Chirality : 0.045 0.203 1632 Planarity : 0.005 0.075 1972 Dihedral : 5.666 55.515 1627 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.03 % Favored : 94.60 % Rotamer: Outliers : 3.02 % Allowed : 14.93 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.24), residues: 1353 helix: 1.19 (0.36), residues: 216 sheet: -0.89 (0.33), residues: 256 loop : 0.15 (0.22), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 79 TYR 0.015 0.001 TYR C 463 PHE 0.012 0.001 PHE C 486 TRP 0.013 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 Details of bonding type rmsd covalent geometry : bond 0.00351 (11037) covalent geometry : angle 0.58292 (14995) SS BOND : bond 0.00339 ( 37) SS BOND : angle 1.06285 ( 74) hydrogen bonds : bond 0.03538 ( 306) hydrogen bonds : angle 5.32248 ( 852) metal coordination : bond 0.00309 ( 3) link_NAG-ASN : bond 0.00342 ( 8) link_NAG-ASN : angle 3.07334 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8037 (mtt-85) cc_final: 0.7729 (mtt180) REVERT: C 252 TYR cc_start: 0.8792 (m-80) cc_final: 0.8394 (m-80) REVERT: C 254 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: C 367 ASN cc_start: 0.7918 (t0) cc_final: 0.7500 (t0) REVERT: C 418 LYS cc_start: 0.8343 (mtpp) cc_final: 0.7907 (mtpp) REVERT: C 423 ASN cc_start: 0.7201 (t0) cc_final: 0.6844 (p0) REVERT: C 430 HIS cc_start: 0.6740 (OUTLIER) cc_final: 0.6252 (m-70) REVERT: C 508 ASP cc_start: 0.8064 (t0) cc_final: 0.6908 (p0) REVERT: C 553 MET cc_start: 0.7242 (mmp) cc_final: 0.7014 (mmm) REVERT: C 591 GLU cc_start: 0.6707 (pm20) cc_final: 0.6496 (pm20) REVERT: C 636 MET cc_start: 0.9121 (mmm) cc_final: 0.8645 (mmm) REVERT: C 849 GLU cc_start: 0.8064 (mp0) cc_final: 0.7462 (mt-10) REVERT: C 956 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7639 (mt0) REVERT: C 976 ARG cc_start: 0.7757 (mtp85) cc_final: 0.7208 (ttm110) REVERT: P 77 GLU cc_start: 0.7866 (tp30) cc_final: 0.7612 (pt0) REVERT: P 79 ARG cc_start: 0.7465 (mtp85) cc_final: 0.7068 (mmt90) REVERT: P 130 GLU cc_start: 0.7094 (tm-30) cc_final: 0.6820 (tm-30) REVERT: Q 1343 GLU cc_start: 0.6379 (tt0) cc_final: 0.5996 (tm-30) REVERT: Q 1518 MET cc_start: 0.4080 (pmm) cc_final: 0.3384 (mmp) outliers start: 36 outliers final: 22 residues processed: 168 average time/residue: 0.1001 time to fit residues: 24.0996 Evaluate side-chains 160 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 711 HIS Chi-restraints excluded: chain C residue 769 HIS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 795 SER Chi-restraints excluded: chain C residue 801 THR Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain P residue 44 ARG Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 56 CYS Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1339 GLU Chi-restraints excluded: chain Q residue 1534 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 94 optimal weight: 0.0470 chunk 54 optimal weight: 5.9990 chunk 114 optimal weight: 0.0010 chunk 123 optimal weight: 40.0000 chunk 39 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 overall best weight: 0.7288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 HIS C 379 HIS ** P 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.198722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129262 restraints weight = 12546.218| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.10 r_work: 0.3308 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11085 Z= 0.113 Angle : 0.575 14.199 15093 Z= 0.288 Chirality : 0.044 0.191 1632 Planarity : 0.004 0.071 1972 Dihedral : 5.600 53.036 1627 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.51 % Favored : 95.12 % Rotamer: Outliers : 3.02 % Allowed : 15.10 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.24), residues: 1353 helix: 1.19 (0.36), residues: 222 sheet: -0.73 (0.32), residues: 270 loop : 0.22 (0.23), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 79 TYR 0.013 0.001 TYR C 463 PHE 0.016 0.001 PHE P 162 TRP 0.014 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 Details of bonding type rmsd covalent geometry : bond 0.00259 (11037) covalent geometry : angle 0.55592 (14995) SS BOND : bond 0.00241 ( 37) SS BOND : angle 0.90186 ( 74) hydrogen bonds : bond 0.03209 ( 306) hydrogen bonds : angle 5.08683 ( 852) metal coordination : bond 0.00183 ( 3) link_NAG-ASN : bond 0.00352 ( 8) link_NAG-ASN : angle 3.54379 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8063 (mtt-85) cc_final: 0.7810 (mtt-85) REVERT: C 252 TYR cc_start: 0.8637 (m-80) cc_final: 0.8193 (m-80) REVERT: C 367 ASN cc_start: 0.7979 (t0) cc_final: 0.7586 (t0) REVERT: C 418 LYS cc_start: 0.8261 (mtpp) cc_final: 0.7800 (mtpp) REVERT: C 423 ASN cc_start: 0.7158 (t0) cc_final: 0.6800 (p0) REVERT: C 430 HIS cc_start: 0.6579 (OUTLIER) cc_final: 0.5956 (m-70) REVERT: C 508 ASP cc_start: 0.7903 (t0) cc_final: 0.6742 (p0) REVERT: C 591 GLU cc_start: 0.6966 (pm20) cc_final: 0.6616 (pm20) REVERT: C 636 MET cc_start: 0.8990 (mmm) cc_final: 0.8399 (mmm) REVERT: C 849 GLU cc_start: 0.7895 (mp0) cc_final: 0.7390 (mt-10) REVERT: C 884 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8513 (mt) REVERT: C 956 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7548 (mt0) REVERT: C 976 ARG cc_start: 0.7572 (mtp85) cc_final: 0.6943 (ttm-80) REVERT: P 79 ARG cc_start: 0.7413 (mtp85) cc_final: 0.7041 (mmt90) REVERT: P 130 GLU cc_start: 0.7048 (tm-30) cc_final: 0.6757 (tm-30) REVERT: Q 1343 GLU cc_start: 0.6462 (tt0) cc_final: 0.6058 (tm-30) REVERT: Q 1518 MET cc_start: 0.4255 (pmm) cc_final: 0.3526 (mmp) outliers start: 36 outliers final: 22 residues processed: 174 average time/residue: 0.1011 time to fit residues: 25.0638 Evaluate side-chains 165 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 711 HIS Chi-restraints excluded: chain C residue 715 GLU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 795 SER Chi-restraints excluded: chain C residue 801 THR Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 56 CYS Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1527 HIS Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1568 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 54 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 30 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 HIS ** P 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN P 116 HIS P 161 HIS Q1291 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.192924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.122671 restraints weight = 12630.555| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 3.01 r_work: 0.3208 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 11085 Z= 0.324 Angle : 0.696 13.722 15093 Z= 0.352 Chirality : 0.049 0.209 1632 Planarity : 0.005 0.078 1972 Dihedral : 5.924 57.527 1627 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.28 % Favored : 93.35 % Rotamer: Outliers : 3.36 % Allowed : 15.52 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.24), residues: 1353 helix: 0.79 (0.35), residues: 225 sheet: -0.75 (0.32), residues: 268 loop : 0.05 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 575 TYR 0.020 0.002 TYR C 211 PHE 0.016 0.002 PHE C 171 TRP 0.017 0.002 TRP C 259 HIS 0.007 0.001 HIS C 562 Details of bonding type rmsd covalent geometry : bond 0.00778 (11037) covalent geometry : angle 0.67278 (14995) SS BOND : bond 0.00498 ( 37) SS BOND : angle 1.33895 ( 74) hydrogen bonds : bond 0.03787 ( 306) hydrogen bonds : angle 5.41869 ( 852) metal coordination : bond 0.00898 ( 3) link_NAG-ASN : bond 0.00279 ( 8) link_NAG-ASN : angle 4.02384 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 141 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8077 (mtt-85) cc_final: 0.7717 (mtt180) REVERT: C 252 TYR cc_start: 0.8891 (m-80) cc_final: 0.8580 (m-80) REVERT: C 254 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7157 (tt0) REVERT: C 367 ASN cc_start: 0.7826 (t0) cc_final: 0.7381 (t0) REVERT: C 418 LYS cc_start: 0.8267 (mtpp) cc_final: 0.7833 (mtpp) REVERT: C 430 HIS cc_start: 0.6745 (OUTLIER) cc_final: 0.6243 (m-70) REVERT: C 508 ASP cc_start: 0.8140 (t0) cc_final: 0.6994 (p0) REVERT: C 591 GLU cc_start: 0.6778 (pm20) cc_final: 0.6420 (pm20) REVERT: C 636 MET cc_start: 0.9126 (mmm) cc_final: 0.8638 (mmm) REVERT: C 956 GLN cc_start: 0.8023 (mm-40) cc_final: 0.7663 (mt0) REVERT: C 976 ARG cc_start: 0.7812 (mtp85) cc_final: 0.7263 (ttm110) REVERT: P 79 ARG cc_start: 0.7391 (mtp85) cc_final: 0.6945 (mmt90) REVERT: P 130 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7050 (tm-30) REVERT: P 158 GLU cc_start: 0.7226 (tm-30) cc_final: 0.6828 (tm-30) REVERT: Q 1343 GLU cc_start: 0.6403 (tt0) cc_final: 0.6034 (tm-30) REVERT: Q 1518 MET cc_start: 0.4186 (pmm) cc_final: 0.3461 (mmp) outliers start: 40 outliers final: 30 residues processed: 169 average time/residue: 0.1002 time to fit residues: 24.5756 Evaluate side-chains 165 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 503 ASN Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 711 HIS Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 769 HIS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 795 SER Chi-restraints excluded: chain C residue 801 THR Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain P residue 44 ARG Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 56 CYS Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 65 CYS Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1339 GLU Chi-restraints excluded: chain Q residue 1527 HIS Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1568 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 57 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 HIS ** P 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 HIS P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.198129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.128527 restraints weight = 12552.335| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 3.06 r_work: 0.3286 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11085 Z= 0.118 Angle : 0.578 14.150 15093 Z= 0.292 Chirality : 0.044 0.179 1632 Planarity : 0.004 0.073 1972 Dihedral : 5.542 53.820 1627 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.21 % Favored : 95.42 % Rotamer: Outliers : 2.94 % Allowed : 16.69 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1353 helix: 1.04 (0.35), residues: 224 sheet: -0.67 (0.32), residues: 266 loop : 0.14 (0.23), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 123 TYR 0.016 0.001 TYR C 463 PHE 0.017 0.001 PHE Q1298 TRP 0.014 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 Details of bonding type rmsd covalent geometry : bond 0.00270 (11037) covalent geometry : angle 0.55727 (14995) SS BOND : bond 0.00257 ( 37) SS BOND : angle 0.94281 ( 74) hydrogen bonds : bond 0.03203 ( 306) hydrogen bonds : angle 5.04100 ( 852) metal coordination : bond 0.00182 ( 3) link_NAG-ASN : bond 0.00334 ( 8) link_NAG-ASN : angle 3.68165 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 144 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7762 (mtt-85) REVERT: C 252 TYR cc_start: 0.8618 (m-80) cc_final: 0.8198 (m-80) REVERT: C 254 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6776 (tt0) REVERT: C 367 ASN cc_start: 0.7883 (t0) cc_final: 0.7470 (t0) REVERT: C 418 LYS cc_start: 0.8226 (mtpp) cc_final: 0.7784 (mtpp) REVERT: C 433 THR cc_start: 0.8642 (p) cc_final: 0.8147 (t) REVERT: C 508 ASP cc_start: 0.7932 (t0) cc_final: 0.6654 (p0) REVERT: C 591 GLU cc_start: 0.6985 (pm20) cc_final: 0.6599 (pm20) REVERT: C 636 MET cc_start: 0.9023 (mmm) cc_final: 0.8436 (mmm) REVERT: C 849 GLU cc_start: 0.7746 (mp0) cc_final: 0.7280 (mt-10) REVERT: C 956 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7690 (mt0) REVERT: C 976 ARG cc_start: 0.7605 (mtp85) cc_final: 0.6973 (ttm-80) REVERT: P 79 ARG cc_start: 0.7553 (mtp85) cc_final: 0.7173 (mmt90) REVERT: P 130 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6728 (tm-30) REVERT: P 158 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6507 (tm-30) REVERT: Q 1343 GLU cc_start: 0.6439 (tt0) cc_final: 0.6021 (tm-30) REVERT: Q 1518 MET cc_start: 0.4091 (pmm) cc_final: 0.3542 (mmp) outliers start: 35 outliers final: 26 residues processed: 169 average time/residue: 0.1012 time to fit residues: 24.5255 Evaluate side-chains 164 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 588 MET Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 711 HIS Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 769 HIS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 795 SER Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 56 CYS Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 167 LEU Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1399 CYS Chi-restraints excluded: chain Q residue 1527 HIS Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1568 ASP Chi-restraints excluded: chain Q residue 1590 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 7 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 118 optimal weight: 40.0000 chunk 105 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 711 HIS P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.199326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130120 restraints weight = 12535.155| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.10 r_work: 0.3316 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11085 Z= 0.104 Angle : 0.562 13.681 15093 Z= 0.284 Chirality : 0.043 0.163 1632 Planarity : 0.004 0.070 1972 Dihedral : 5.328 52.333 1627 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.66 % Favored : 94.97 % Rotamer: Outliers : 2.52 % Allowed : 17.95 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.24), residues: 1353 helix: 1.21 (0.36), residues: 224 sheet: -0.67 (0.32), residues: 268 loop : 0.21 (0.23), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 123 TYR 0.013 0.001 TYR C 463 PHE 0.014 0.001 PHE Q1312 TRP 0.013 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 Details of bonding type rmsd covalent geometry : bond 0.00235 (11037) covalent geometry : angle 0.54627 (14995) SS BOND : bond 0.00189 ( 37) SS BOND : angle 0.87255 ( 74) hydrogen bonds : bond 0.03031 ( 306) hydrogen bonds : angle 4.84686 ( 852) metal coordination : bond 0.00133 ( 3) link_NAG-ASN : bond 0.00415 ( 8) link_NAG-ASN : angle 3.08728 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8102 (mtt-85) cc_final: 0.7856 (mtt180) REVERT: C 252 TYR cc_start: 0.8617 (m-80) cc_final: 0.8208 (m-80) REVERT: C 283 GLN cc_start: 0.8528 (mm-40) cc_final: 0.8061 (mm-40) REVERT: C 367 ASN cc_start: 0.7929 (t0) cc_final: 0.7526 (t0) REVERT: C 418 LYS cc_start: 0.8287 (mtpp) cc_final: 0.7834 (mtpp) REVERT: C 508 ASP cc_start: 0.7948 (t0) cc_final: 0.6681 (p0) REVERT: C 591 GLU cc_start: 0.6943 (pm20) cc_final: 0.6588 (pm20) REVERT: C 849 GLU cc_start: 0.7714 (mp0) cc_final: 0.7276 (mt-10) REVERT: C 956 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7654 (mt0) REVERT: C 976 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7160 (ttm-80) REVERT: P 79 ARG cc_start: 0.7460 (mtp85) cc_final: 0.7077 (mmt90) REVERT: P 123 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7358 (ttp80) REVERT: P 130 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6763 (tm-30) REVERT: P 158 GLU cc_start: 0.6881 (tm-30) cc_final: 0.6540 (tm-30) REVERT: Q 1302 GLU cc_start: 0.7353 (tp30) cc_final: 0.6784 (tm-30) REVERT: Q 1343 GLU cc_start: 0.6452 (tt0) cc_final: 0.6037 (tm-30) outliers start: 30 outliers final: 22 residues processed: 173 average time/residue: 0.1040 time to fit residues: 25.4135 Evaluate side-chains 163 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 711 HIS Chi-restraints excluded: chain C residue 719 LEU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 56 CYS Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1399 CYS Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1568 ASP Chi-restraints excluded: chain Q residue 1587 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 115 optimal weight: 30.0000 chunk 40 optimal weight: 0.9980 chunk 119 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 68 optimal weight: 0.0770 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.197452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.135608 restraints weight = 12497.140| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.62 r_work: 0.3265 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11085 Z= 0.165 Angle : 0.587 14.436 15093 Z= 0.296 Chirality : 0.045 0.157 1632 Planarity : 0.004 0.071 1972 Dihedral : 5.395 51.712 1627 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.95 % Favored : 94.83 % Rotamer: Outliers : 2.68 % Allowed : 17.95 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.24), residues: 1353 helix: 1.15 (0.35), residues: 223 sheet: -0.66 (0.32), residues: 268 loop : 0.18 (0.23), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 123 TYR 0.012 0.001 TYR C 211 PHE 0.015 0.001 PHE Q1298 TRP 0.012 0.001 TRP C 259 HIS 0.011 0.001 HIS C 711 Details of bonding type rmsd covalent geometry : bond 0.00392 (11037) covalent geometry : angle 0.57132 (14995) SS BOND : bond 0.00293 ( 37) SS BOND : angle 0.96112 ( 74) hydrogen bonds : bond 0.03185 ( 306) hydrogen bonds : angle 4.93715 ( 852) metal coordination : bond 0.00384 ( 3) link_NAG-ASN : bond 0.00317 ( 8) link_NAG-ASN : angle 3.16217 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8098 (mtt-85) cc_final: 0.7778 (mtt180) REVERT: C 254 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6839 (tt0) REVERT: C 283 GLN cc_start: 0.8615 (mm-40) cc_final: 0.8157 (mm-40) REVERT: C 367 ASN cc_start: 0.7933 (t0) cc_final: 0.7524 (t0) REVERT: C 418 LYS cc_start: 0.8273 (mtpp) cc_final: 0.7812 (mtpp) REVERT: C 508 ASP cc_start: 0.7990 (t0) cc_final: 0.6725 (p0) REVERT: C 591 GLU cc_start: 0.6829 (pm20) cc_final: 0.6456 (pm20) REVERT: C 636 MET cc_start: 0.8969 (mpp) cc_final: 0.8231 (mmp) REVERT: C 849 GLU cc_start: 0.7856 (mp0) cc_final: 0.7389 (mt-10) REVERT: C 956 GLN cc_start: 0.8062 (mm-40) cc_final: 0.7679 (mt0) REVERT: C 976 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7273 (ttm-80) REVERT: P 79 ARG cc_start: 0.7484 (mtp85) cc_final: 0.7114 (mmt90) REVERT: P 130 GLU cc_start: 0.7109 (tm-30) cc_final: 0.6817 (tm-30) REVERT: P 158 GLU cc_start: 0.6954 (tm-30) cc_final: 0.6584 (tm-30) REVERT: Q 1302 GLU cc_start: 0.7373 (tp30) cc_final: 0.6738 (tm-30) REVERT: Q 1343 GLU cc_start: 0.6410 (tt0) cc_final: 0.5976 (tm-30) outliers start: 32 outliers final: 25 residues processed: 169 average time/residue: 0.1010 time to fit residues: 24.1408 Evaluate side-chains 167 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 588 MET Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 769 HIS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 989 ARG Chi-restraints excluded: chain P residue 44 ARG Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 56 CYS Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1399 CYS Chi-restraints excluded: chain Q residue 1527 HIS Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1568 ASP Chi-restraints excluded: chain Q residue 1587 THR Chi-restraints excluded: chain Q residue 1590 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 59 optimal weight: 5.9990 chunk 101 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 133 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 46 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.198200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.127473 restraints weight = 12522.452| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.08 r_work: 0.3297 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11085 Z= 0.131 Angle : 0.571 14.772 15093 Z= 0.289 Chirality : 0.044 0.163 1632 Planarity : 0.004 0.070 1972 Dihedral : 5.336 51.692 1627 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.73 % Favored : 95.05 % Rotamer: Outliers : 2.10 % Allowed : 18.71 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.24), residues: 1353 helix: 1.18 (0.35), residues: 223 sheet: -0.66 (0.32), residues: 268 loop : 0.23 (0.23), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 123 TYR 0.011 0.001 TYR C 463 PHE 0.013 0.001 PHE Q1298 TRP 0.012 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 Details of bonding type rmsd covalent geometry : bond 0.00307 (11037) covalent geometry : angle 0.55690 (14995) SS BOND : bond 0.00227 ( 37) SS BOND : angle 0.90791 ( 74) hydrogen bonds : bond 0.03162 ( 306) hydrogen bonds : angle 4.90043 ( 852) metal coordination : bond 0.00292 ( 3) link_NAG-ASN : bond 0.00342 ( 8) link_NAG-ASN : angle 2.99863 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2706 Ramachandran restraints generated. 1353 Oldfield, 0 Emsley, 1353 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8069 (mtt-85) cc_final: 0.7736 (mtt180) REVERT: C 254 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6534 (tt0) REVERT: C 283 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8096 (mm-40) REVERT: C 367 ASN cc_start: 0.7928 (t0) cc_final: 0.7518 (t0) REVERT: C 418 LYS cc_start: 0.8274 (mtpp) cc_final: 0.7817 (mtpp) REVERT: C 459 MET cc_start: 0.6676 (tpt) cc_final: 0.5701 (ttp) REVERT: C 508 ASP cc_start: 0.7953 (t0) cc_final: 0.6643 (p0) REVERT: C 591 GLU cc_start: 0.6787 (pm20) cc_final: 0.6416 (pm20) REVERT: C 609 HIS cc_start: 0.6819 (t70) cc_final: 0.6261 (t70) REVERT: C 636 MET cc_start: 0.9046 (mpp) cc_final: 0.8773 (mmm) REVERT: C 849 GLU cc_start: 0.7763 (mp0) cc_final: 0.7298 (mt-10) REVERT: C 956 GLN cc_start: 0.8008 (mm-40) cc_final: 0.7635 (mt0) REVERT: C 976 ARG cc_start: 0.7717 (mtp85) cc_final: 0.7087 (ttm-80) REVERT: P 79 ARG cc_start: 0.7507 (mtp85) cc_final: 0.7131 (mmt90) REVERT: P 130 GLU cc_start: 0.6996 (tm-30) cc_final: 0.6713 (tm-30) REVERT: P 158 GLU cc_start: 0.6953 (tm-30) cc_final: 0.6588 (tm-30) REVERT: Q 1302 GLU cc_start: 0.7423 (tp30) cc_final: 0.6759 (tm-30) REVERT: Q 1343 GLU cc_start: 0.6463 (tt0) cc_final: 0.6026 (tm-30) outliers start: 25 outliers final: 23 residues processed: 165 average time/residue: 0.1073 time to fit residues: 25.0526 Evaluate side-chains 165 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 278 HIS Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 588 MET Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 725 ASN Chi-restraints excluded: chain C residue 769 HIS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 989 ARG Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 56 CYS Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1399 CYS Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1568 ASP Chi-restraints excluded: chain Q residue 1587 THR Chi-restraints excluded: chain Q residue 1590 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 105 optimal weight: 10.0000 chunk 18 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.197021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.129456 restraints weight = 12485.412| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 3.25 r_work: 0.3288 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11085 Z= 0.164 Angle : 0.584 14.709 15093 Z= 0.296 Chirality : 0.045 0.156 1632 Planarity : 0.004 0.070 1972 Dihedral : 5.402 51.113 1627 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.03 % Favored : 94.75 % Rotamer: Outliers : 2.60 % Allowed : 18.20 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.24), residues: 1353 helix: 1.12 (0.35), residues: 223 sheet: -0.62 (0.33), residues: 265 loop : 0.20 (0.23), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 123 TYR 0.012 0.001 TYR C 252 PHE 0.012 0.001 PHE Q1312 TRP 0.013 0.001 TRP C 259 HIS 0.006 0.001 HIS C 562 Details of bonding type rmsd covalent geometry : bond 0.00390 (11037) covalent geometry : angle 0.56900 (14995) SS BOND : bond 0.00274 ( 37) SS BOND : angle 0.97969 ( 74) hydrogen bonds : bond 0.03254 ( 306) hydrogen bonds : angle 4.98264 ( 852) metal coordination : bond 0.00432 ( 3) link_NAG-ASN : bond 0.00294 ( 8) link_NAG-ASN : angle 3.01107 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3359.38 seconds wall clock time: 57 minutes 56.85 seconds (3476.85 seconds total)