Starting phenix.real_space_refine on Tue May 13 19:40:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8a7d_15220/05_2025/8a7d_15220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8a7d_15220/05_2025/8a7d_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8a7d_15220/05_2025/8a7d_15220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8a7d_15220/05_2025/8a7d_15220.map" model { file = "/net/cci-nas-00/data/ceres_data/8a7d_15220/05_2025/8a7d_15220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8a7d_15220/05_2025/8a7d_15220.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.36, per 1000 atoms: 0.59 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: 2.63 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.37 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: 4.64 Time building geometry restraints manager: 3.15 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: 0.480 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: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.740 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.870 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (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 TRP 0.011 0.002 TRP C 259 HIS 0.007 0.001 HIS C 430 PHE 0.030 0.002 PHE Q1312 TYR 0.013 0.002 TYR C 252 ARG 0.005 0.001 ARG C 575 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 8) link_NAG-ASN : angle 4.07526 ( 24) hydrogen bonds : bond 0.15247 ( 306) hydrogen bonds : angle 8.01524 ( 852) metal coordination : bond 0.00349 ( 3) SS BOND : bond 0.00428 ( 37) SS BOND : angle 1.30494 ( 74) covalent geometry : bond 0.00404 (11037) covalent geometry : angle 0.76079 (14995) *********************** 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 : 1.084 Fit side-chains 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: 0.8709 (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: 0.7177 (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: 0.7389 (pp30) outliers start: 6 outliers final: 3 residues processed: 187 average time/residue: 0.2599 time to fit residues: 66.5526 Evaluate side-chains 142 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 113 optimal weight: 5.9990 chunk 102 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 105 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- 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 161 HIS P 176 ASN P 199 GLN Q1358 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 = 0.4219 r_free = 0.4219 target = 0.193766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.123873 restraints weight = 12443.074| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.94 r_work: 0.3235 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 11085 Z= 0.276 Angle : 0.677 9.210 15093 Z= 0.347 Chirality : 0.049 0.240 1632 Planarity : 0.005 0.079 1972 Dihedral : 6.425 58.108 1631 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.62 % Favored : 93.94 % Rotamer: Outliers : 2.60 % Allowed : 12.84 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.24), residues: 1353 helix: 0.95 (0.35), residues: 223 sheet: -0.89 (0.33), residues: 253 loop : 0.05 (0.23), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 259 HIS 0.007 0.001 HIS C 656 PHE 0.016 0.002 PHE C 486 TYR 0.020 0.002 TYR C 252 ARG 0.003 0.001 ARG C 670 Details of bonding type rmsd link_NAG-ASN : bond 0.00412 ( 8) link_NAG-ASN : angle 2.65802 ( 24) hydrogen bonds : bond 0.04416 ( 306) hydrogen bonds : angle 5.90725 ( 852) metal coordination : bond 0.00728 ( 3) SS BOND : bond 0.00429 ( 37) SS BOND : angle 1.24982 ( 74) covalent geometry : bond 0.00661 (11037) covalent geometry : angle 0.66524 (14995) *********************** 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 192 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7705 (mtt180) REVERT: C 252 TYR cc_start: 0.8863 (m-80) cc_final: 0.8522 (m-80) REVERT: C 367 ASN cc_start: 0.7872 (t0) cc_final: 0.7466 (t0) REVERT: C 418 LYS cc_start: 0.8252 (mtpp) cc_final: 0.7917 (mtpt) REVERT: C 423 ASN cc_start: 0.7109 (t0) cc_final: 0.6761 (p0) REVERT: C 430 HIS cc_start: 0.7085 (OUTLIER) cc_final: 0.6575 (m90) REVERT: C 508 ASP cc_start: 0.8178 (t0) cc_final: 0.7116 (p0) REVERT: C 588 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.6077 (ptt) REVERT: C 636 MET cc_start: 0.9141 (mmm) cc_final: 0.8670 (mmm) REVERT: C 849 GLU cc_start: 0.8209 (mp0) cc_final: 0.7514 (mt-10) REVERT: C 931 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8149 (pt0) REVERT: C 956 GLN cc_start: 0.7996 (mm-40) cc_final: 0.7724 (mp10) REVERT: C 976 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7258 (ttm110) REVERT: P 77 GLU cc_start: 0.7875 (tp30) cc_final: 0.7536 (pt0) REVERT: P 115 ARG cc_start: 0.7715 (ttp80) cc_final: 0.7079 (ttm110) REVERT: P 123 ARG cc_start: 0.8168 (mmm-85) cc_final: 0.7899 (ttt-90) REVERT: P 130 GLU cc_start: 0.7154 (tm-30) cc_final: 0.6883 (tm-30) REVERT: Q 1313 GLN cc_start: 0.7383 (pm20) cc_final: 0.7065 (pm20) REVERT: Q 1378 LYS cc_start: 0.7405 (mttt) cc_final: 0.7060 (ptmt) REVERT: Q 1398 GLN cc_start: 0.7272 (tt0) cc_final: 0.7062 (tm-30) REVERT: Q 1401 GLN cc_start: 0.8130 (mt0) cc_final: 0.7394 (tp-100) REVERT: Q 1518 MET cc_start: 0.4245 (pmm) cc_final: 0.3420 (mmp) REVERT: Q 1573 ARG cc_start: 0.6550 (ptp90) cc_final: 0.6330 (mtm180) outliers start: 31 outliers final: 14 residues processed: 183 average time/residue: 0.2470 time to fit residues: 63.3064 Evaluate side-chains 150 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 279 THR Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 588 MET 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 74 optimal weight: 0.7980 chunk 32 optimal weight: 0.0470 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 50 optimal weight: 0.7980 chunk 115 optimal weight: 30.0000 chunk 119 optimal weight: 30.0000 chunk 106 optimal weight: 4.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 HIS ** P 74 ASN ** 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 = 0.4248 r_free = 0.4248 target = 0.197225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.127224 restraints weight = 12667.423| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 3.07 r_work: 0.3269 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11085 Z= 0.140 Angle : 0.587 8.394 15093 Z= 0.302 Chirality : 0.045 0.217 1632 Planarity : 0.005 0.074 1972 Dihedral : 6.110 57.699 1630 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.66 % Favored : 94.90 % Rotamer: Outliers : 3.02 % Allowed : 13.93 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1353 helix: 1.24 (0.36), residues: 217 sheet: -0.94 (0.33), residues: 263 loop : 0.14 (0.23), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 PHE 0.016 0.001 PHE P 162 TYR 0.016 0.001 TYR C 463 ARG 0.006 0.000 ARG P 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00177 ( 8) link_NAG-ASN : angle 2.89059 ( 24) hydrogen bonds : bond 0.03695 ( 306) hydrogen bonds : angle 5.38498 ( 852) metal coordination : bond 0.00260 ( 3) SS BOND : bond 0.00337 ( 37) SS BOND : angle 1.22770 ( 74) covalent geometry : bond 0.00326 (11037) covalent geometry : angle 0.57082 (14995) *********************** 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 : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.7969 (mtt-85) cc_final: 0.7667 (mtt180) REVERT: C 252 TYR cc_start: 0.8647 (m-80) cc_final: 0.8239 (m-80) REVERT: C 254 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6859 (tt0) REVERT: C 284 LEU cc_start: 0.9000 (tp) cc_final: 0.8704 (tp) REVERT: C 367 ASN cc_start: 0.7924 (t0) cc_final: 0.7541 (t0) REVERT: C 418 LYS cc_start: 0.8287 (mtpp) cc_final: 0.7926 (mtpt) REVERT: C 423 ASN cc_start: 0.7214 (t0) cc_final: 0.6854 (p0) REVERT: C 430 HIS cc_start: 0.6740 (OUTLIER) cc_final: 0.6111 (m-70) REVERT: C 508 ASP cc_start: 0.8064 (t0) cc_final: 0.6898 (p0) REVERT: C 636 MET cc_start: 0.9054 (mmm) cc_final: 0.8520 (mmm) REVERT: C 956 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7509 (mt0) REVERT: C 976 ARG cc_start: 0.7658 (mtp85) cc_final: 0.7058 (ttm-80) REVERT: P 79 ARG cc_start: 0.7418 (mtp85) cc_final: 0.7043 (mmt90) REVERT: P 115 ARG cc_start: 0.7581 (ttp80) cc_final: 0.6905 (ttm110) REVERT: P 130 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6701 (tm-30) REVERT: Q 1313 GLN cc_start: 0.7342 (pm20) cc_final: 0.7035 (pm20) REVERT: Q 1378 LYS cc_start: 0.7398 (mttt) cc_final: 0.7045 (ptmt) REVERT: Q 1401 GLN cc_start: 0.8131 (mt0) cc_final: 0.7408 (tp-100) REVERT: Q 1518 MET cc_start: 0.4001 (pmm) cc_final: 0.3263 (mmp) REVERT: Q 1602 LEU cc_start: 0.6689 (tp) cc_final: 0.6343 (tp) outliers start: 36 outliers final: 19 residues processed: 184 average time/residue: 0.2391 time to fit residues: 61.4130 Evaluate side-chains 159 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 254 GLU 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 588 MET Chi-restraints excluded: chain C residue 711 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 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 103 ILE Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 190 THR Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1558 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 103 optimal weight: 9.9990 chunk 114 optimal weight: 0.0370 chunk 2 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 64 optimal weight: 0.0270 chunk 20 optimal weight: 0.3980 chunk 49 optimal weight: 6.9990 chunk 41 optimal weight: 0.0050 chunk 104 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.2530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 HIS C 711 HIS ** P 91 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 = 0.4267 r_free = 0.4267 target = 0.199987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129890 restraints weight = 12602.829| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.26 r_work: 0.3256 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11085 Z= 0.098 Angle : 0.547 8.130 15093 Z= 0.281 Chirality : 0.043 0.202 1632 Planarity : 0.004 0.069 1972 Dihedral : 5.689 56.673 1630 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.29 % Favored : 95.42 % Rotamer: Outliers : 2.35 % Allowed : 14.68 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.24), residues: 1353 helix: 1.35 (0.36), residues: 217 sheet: -0.73 (0.33), residues: 256 loop : 0.21 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 PHE 0.018 0.001 PHE Q1298 TYR 0.015 0.001 TYR C 463 ARG 0.004 0.000 ARG C 741 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 8) link_NAG-ASN : angle 1.99947 ( 24) hydrogen bonds : bond 0.03254 ( 306) hydrogen bonds : angle 5.01857 ( 852) metal coordination : bond 0.00060 ( 3) SS BOND : bond 0.00207 ( 37) SS BOND : angle 0.96438 ( 74) covalent geometry : bond 0.00215 (11037) covalent geometry : angle 0.53895 (14995) *********************** 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 202 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.7980 (mtt-85) cc_final: 0.7750 (mtt-85) REVERT: C 252 TYR cc_start: 0.8637 (m-80) cc_final: 0.8212 (m-80) REVERT: C 367 ASN cc_start: 0.7997 (t0) cc_final: 0.7628 (t0) REVERT: C 418 LYS cc_start: 0.8330 (mtpp) cc_final: 0.7893 (mtpp) REVERT: C 423 ASN cc_start: 0.7207 (t0) cc_final: 0.6852 (p0) REVERT: C 430 HIS cc_start: 0.6711 (OUTLIER) cc_final: 0.6220 (m90) REVERT: C 508 ASP cc_start: 0.7996 (t0) cc_final: 0.6825 (p0) REVERT: C 591 GLU cc_start: 0.6749 (pm20) cc_final: 0.6470 (pm20) REVERT: C 636 MET cc_start: 0.9024 (mmm) cc_final: 0.8497 (mmp) REVERT: C 849 GLU cc_start: 0.7917 (mp0) cc_final: 0.7599 (mt-10) REVERT: C 956 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7528 (mt0) REVERT: C 976 ARG cc_start: 0.7714 (mtp85) cc_final: 0.7089 (ttm-80) REVERT: P 79 ARG cc_start: 0.7510 (mtp85) cc_final: 0.7089 (mmt90) REVERT: P 115 ARG cc_start: 0.7542 (ttp80) cc_final: 0.6877 (ttm110) REVERT: P 130 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6669 (tm-30) REVERT: Q 1313 GLN cc_start: 0.7202 (pm20) cc_final: 0.6949 (pm20) REVERT: Q 1339 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7283 (mp0) REVERT: Q 1343 GLU cc_start: 0.6373 (tt0) cc_final: 0.5986 (tm-30) REVERT: Q 1401 GLN cc_start: 0.8091 (mt0) cc_final: 0.7209 (pp30) REVERT: Q 1518 MET cc_start: 0.4269 (pmm) cc_final: 0.3529 (mmp) REVERT: Q 1573 ARG cc_start: 0.6245 (mtm180) cc_final: 0.5786 (ptp90) outliers start: 28 outliers final: 17 residues processed: 191 average time/residue: 0.2349 time to fit residues: 63.0702 Evaluate side-chains 167 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 219 THR Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 588 MET Chi-restraints excluded: chain C residue 711 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 103 ILE Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1598 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 93 optimal weight: 10.0000 chunk 83 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 967 ASN ** P 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4254 r_free = 0.4254 target = 0.197668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.123765 restraints weight = 12499.157| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 3.03 r_work: 0.3272 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11085 Z= 0.166 Angle : 0.575 13.796 15093 Z= 0.295 Chirality : 0.045 0.210 1632 Planarity : 0.004 0.070 1972 Dihedral : 5.639 54.240 1630 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.80 % Favored : 94.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1353 helix: 1.18 (0.36), residues: 223 sheet: -0.72 (0.32), residues: 277 loop : 0.27 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 PHE 0.020 0.001 PHE P 162 TYR 0.013 0.001 TYR C 211 ARG 0.005 0.000 ARG C 741 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 8) link_NAG-ASN : angle 1.56175 ( 24) hydrogen bonds : bond 0.03295 ( 306) hydrogen bonds : angle 5.04051 ( 852) metal coordination : bond 0.00383 ( 3) SS BOND : bond 0.00289 ( 37) SS BOND : angle 1.03897 ( 74) covalent geometry : bond 0.00393 (11037) covalent geometry : angle 0.56926 (14995) *********************** 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 179 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8008 (mtt-85) cc_final: 0.7721 (mtt180) REVERT: C 252 TYR cc_start: 0.8712 (m-80) cc_final: 0.8302 (m-80) REVERT: C 254 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.6904 (tt0) REVERT: C 284 LEU cc_start: 0.9001 (tp) cc_final: 0.8790 (tp) REVERT: C 367 ASN cc_start: 0.7993 (t0) cc_final: 0.7587 (t0) REVERT: C 418 LYS cc_start: 0.8316 (mtpp) cc_final: 0.7852 (mtpp) REVERT: C 423 ASN cc_start: 0.7154 (t0) cc_final: 0.6801 (p0) REVERT: C 430 HIS cc_start: 0.6628 (OUTLIER) cc_final: 0.6138 (m90) REVERT: C 508 ASP cc_start: 0.7986 (t0) cc_final: 0.6788 (p0) REVERT: C 591 GLU cc_start: 0.6938 (pm20) cc_final: 0.6567 (pm20) REVERT: C 636 MET cc_start: 0.9041 (mmm) cc_final: 0.8498 (mmm) REVERT: C 956 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7561 (mt0) REVERT: C 976 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7093 (ttm-80) REVERT: P 79 ARG cc_start: 0.7527 (mtp85) cc_final: 0.7114 (mmt90) REVERT: P 130 GLU cc_start: 0.7051 (tm-30) cc_final: 0.6756 (tm-30) REVERT: Q 1289 ASP cc_start: 0.6677 (OUTLIER) cc_final: 0.6187 (p0) REVERT: Q 1339 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7263 (mp0) REVERT: Q 1343 GLU cc_start: 0.6453 (tt0) cc_final: 0.6066 (tm-30) REVERT: Q 1518 MET cc_start: 0.4275 (pmm) cc_final: 0.3547 (mmp) REVERT: Q 1573 ARG cc_start: 0.6212 (mtm180) cc_final: 0.5740 (ptp90) outliers start: 36 outliers final: 22 residues processed: 166 average time/residue: 0.2462 time to fit residues: 57.3727 Evaluate side-chains 166 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 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 588 MET Chi-restraints excluded: chain C residue 595 GLU Chi-restraints excluded: chain C residue 711 HIS 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 P residue 56 CYS Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 86 MET Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain Q residue 1289 ASP Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1527 HIS Chi-restraints excluded: chain Q residue 1534 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 99 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 126 optimal weight: 7.9990 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.4236 r_free = 0.4236 target = 0.195930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.127241 restraints weight = 12503.225| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.15 r_work: 0.3241 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11085 Z= 0.206 Angle : 0.601 14.313 15093 Z= 0.308 Chirality : 0.046 0.205 1632 Planarity : 0.005 0.074 1972 Dihedral : 5.669 54.098 1629 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.32 % Favored : 94.31 % Rotamer: Outliers : 3.02 % Allowed : 15.44 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1353 helix: 1.08 (0.35), residues: 223 sheet: -0.79 (0.32), residues: 277 loop : 0.21 (0.23), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 PHE 0.017 0.001 PHE Q1298 TYR 0.014 0.002 TYR C 211 ARG 0.004 0.000 ARG P 123 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 8) link_NAG-ASN : angle 1.55407 ( 24) hydrogen bonds : bond 0.03409 ( 306) hydrogen bonds : angle 5.16601 ( 852) metal coordination : bond 0.00486 ( 3) SS BOND : bond 0.00339 ( 37) SS BOND : angle 1.10617 ( 74) covalent geometry : bond 0.00493 (11037) covalent geometry : angle 0.59507 (14995) *********************** 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 178 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8031 (mtt-85) cc_final: 0.7734 (mtt180) REVERT: C 252 TYR cc_start: 0.8731 (m-80) cc_final: 0.8351 (m-80) REVERT: C 254 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6914 (tt0) REVERT: C 283 GLN cc_start: 0.8345 (mm-40) cc_final: 0.7709 (mt0) REVERT: C 367 ASN cc_start: 0.7902 (t0) cc_final: 0.7472 (t0) REVERT: C 418 LYS cc_start: 0.8256 (mtpp) cc_final: 0.7785 (mtpp) REVERT: C 423 ASN cc_start: 0.6978 (t0) cc_final: 0.6481 (p0) REVERT: C 430 HIS cc_start: 0.6616 (OUTLIER) cc_final: 0.6198 (m90) REVERT: C 508 ASP cc_start: 0.8041 (t0) cc_final: 0.6992 (p0) REVERT: C 591 GLU cc_start: 0.7023 (pm20) cc_final: 0.6567 (pm20) REVERT: C 636 MET cc_start: 0.9061 (mmm) cc_final: 0.8534 (mmm) REVERT: C 670 ARG cc_start: 0.7081 (tpm170) cc_final: 0.6638 (tpm170) REVERT: C 849 GLU cc_start: 0.7850 (mp0) cc_final: 0.7312 (mt-10) REVERT: C 956 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7679 (mt0) REVERT: C 976 ARG cc_start: 0.7707 (mtp85) cc_final: 0.7136 (ttm110) REVERT: P 130 GLU cc_start: 0.7067 (tm-30) cc_final: 0.6775 (tm-30) REVERT: P 158 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6653 (tm-30) REVERT: Q 1339 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7266 (mp0) REVERT: Q 1343 GLU cc_start: 0.6389 (tt0) cc_final: 0.5987 (tm-30) REVERT: Q 1518 MET cc_start: 0.4255 (pmm) cc_final: 0.3547 (mmp) REVERT: Q 1573 ARG cc_start: 0.6119 (mtm180) cc_final: 0.5657 (ptp90) outliers start: 36 outliers final: 27 residues processed: 168 average time/residue: 0.2434 time to fit residues: 57.2222 Evaluate side-chains 165 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 140 LEU 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 503 ASN 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 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 44 ARG Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 86 MET Chi-restraints excluded: chain P residue 103 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 52 optimal weight: 20.0000 chunk 16 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.198283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127887 restraints weight = 12678.015| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.14 r_work: 0.3287 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11085 Z= 0.135 Angle : 0.559 14.922 15093 Z= 0.286 Chirality : 0.044 0.184 1632 Planarity : 0.004 0.071 1972 Dihedral : 5.472 52.538 1629 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.80 % Favored : 94.90 % Rotamer: Outliers : 3.36 % Allowed : 15.94 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1353 helix: 1.14 (0.35), residues: 225 sheet: -0.75 (0.32), residues: 277 loop : 0.25 (0.23), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 PHE 0.016 0.001 PHE Q1298 TYR 0.013 0.001 TYR C 463 ARG 0.007 0.000 ARG P 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00212 ( 8) link_NAG-ASN : angle 1.38230 ( 24) hydrogen bonds : bond 0.03142 ( 306) hydrogen bonds : angle 4.96837 ( 852) metal coordination : bond 0.00277 ( 3) SS BOND : bond 0.00239 ( 37) SS BOND : angle 0.95524 ( 74) covalent geometry : bond 0.00316 (11037) covalent geometry : angle 0.55394 (14995) *********************** 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 182 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8049 (mtt-85) cc_final: 0.7758 (mtt180) REVERT: C 252 TYR cc_start: 0.8794 (m-80) cc_final: 0.8416 (m-80) REVERT: C 254 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7031 (tt0) REVERT: C 283 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7676 (mt0) REVERT: C 367 ASN cc_start: 0.7878 (t0) cc_final: 0.7444 (t0) REVERT: C 418 LYS cc_start: 0.8249 (mtpp) cc_final: 0.7765 (mtpp) REVERT: C 423 ASN cc_start: 0.7057 (t0) cc_final: 0.6662 (p0) REVERT: C 430 HIS cc_start: 0.6630 (OUTLIER) cc_final: 0.6225 (m90) REVERT: C 508 ASP cc_start: 0.8071 (t0) cc_final: 0.6851 (p0) REVERT: C 591 GLU cc_start: 0.6933 (pm20) cc_final: 0.6518 (pm20) REVERT: C 636 MET cc_start: 0.9110 (mmm) cc_final: 0.8581 (mmm) REVERT: C 670 ARG cc_start: 0.6925 (tpm170) cc_final: 0.6405 (tpm170) REVERT: C 849 GLU cc_start: 0.8040 (mp0) cc_final: 0.7439 (mt-10) REVERT: C 956 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7650 (mt0) REVERT: C 976 ARG cc_start: 0.7787 (mtp85) cc_final: 0.7178 (ttm-80) REVERT: P 79 ARG cc_start: 0.7455 (mtp85) cc_final: 0.6905 (mmt90) REVERT: P 130 GLU cc_start: 0.7196 (tm-30) cc_final: 0.6916 (tm-30) REVERT: P 158 GLU cc_start: 0.6978 (tm-30) cc_final: 0.6598 (tm-30) REVERT: Q 1339 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7415 (mp0) REVERT: Q 1343 GLU cc_start: 0.6359 (tt0) cc_final: 0.5974 (tm-30) REVERT: Q 1573 ARG cc_start: 0.6312 (mtm180) cc_final: 0.5824 (ptp90) outliers start: 40 outliers final: 32 residues processed: 171 average time/residue: 0.2357 time to fit residues: 57.3633 Evaluate side-chains 173 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 278 HIS 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 588 MET 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 769 HIS Chi-restraints excluded: chain C residue 791 LEU 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 86 MET Chi-restraints excluded: chain P residue 103 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 72 optimal weight: 0.0980 chunk 111 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.194078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.123809 restraints weight = 12543.970| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.01 r_work: 0.3231 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 11085 Z= 0.290 Angle : 0.654 14.739 15093 Z= 0.335 Chirality : 0.048 0.202 1632 Planarity : 0.005 0.077 1972 Dihedral : 5.795 56.323 1629 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.69 % Favored : 93.94 % Rotamer: Outliers : 3.27 % Allowed : 16.19 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1353 helix: 0.86 (0.35), residues: 226 sheet: -0.83 (0.32), residues: 275 loop : 0.11 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 124 HIS 0.007 0.001 HIS C 562 PHE 0.016 0.002 PHE Q1298 TYR 0.017 0.002 TYR C 211 ARG 0.005 0.001 ARG P 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00231 ( 8) link_NAG-ASN : angle 1.56554 ( 24) hydrogen bonds : bond 0.03613 ( 306) hydrogen bonds : angle 5.26865 ( 852) metal coordination : bond 0.00746 ( 3) SS BOND : bond 0.00446 ( 37) SS BOND : angle 1.26780 ( 74) covalent geometry : bond 0.00691 (11037) covalent geometry : angle 0.64664 (14995) *********************** 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 178 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 139 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8176 (mtt-85) cc_final: 0.7808 (mtt180) REVERT: C 252 TYR cc_start: 0.8873 (m-80) cc_final: 0.8529 (m-80) REVERT: C 254 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7094 (tt0) REVERT: C 283 GLN cc_start: 0.8497 (mm-40) cc_final: 0.7678 (mt0) REVERT: C 367 ASN cc_start: 0.7851 (t0) cc_final: 0.7400 (t0) REVERT: C 418 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7839 (mtpp) REVERT: C 430 HIS cc_start: 0.6555 (OUTLIER) cc_final: 0.6315 (m-70) REVERT: C 508 ASP cc_start: 0.8138 (t0) cc_final: 0.6991 (p0) REVERT: C 591 GLU cc_start: 0.7020 (pm20) cc_final: 0.6592 (pm20) REVERT: C 636 MET cc_start: 0.9140 (mmm) cc_final: 0.8628 (mmm) REVERT: C 670 ARG cc_start: 0.7037 (tpm170) cc_final: 0.6531 (tpm170) REVERT: C 884 LEU cc_start: 0.8980 (mt) cc_final: 0.8764 (mt) REVERT: C 956 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7688 (mt0) REVERT: C 976 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7333 (ttm110) REVERT: P 130 GLU cc_start: 0.7379 (tm-30) cc_final: 0.7087 (tm-30) REVERT: P 158 GLU cc_start: 0.7112 (tm-30) cc_final: 0.6693 (tm-30) REVERT: Q 1302 GLU cc_start: 0.7512 (tp30) cc_final: 0.6788 (tm-30) REVERT: Q 1339 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7373 (mp0) REVERT: Q 1343 GLU cc_start: 0.6380 (tt0) cc_final: 0.6030 (tm-30) REVERT: Q 1573 ARG cc_start: 0.6310 (mtm180) cc_final: 0.5762 (ptp90) REVERT: Q 1598 MET cc_start: 0.6931 (ttm) cc_final: 0.6013 (tpp) outliers start: 39 outliers final: 31 residues processed: 167 average time/residue: 0.2387 time to fit residues: 56.4556 Evaluate side-chains 169 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 278 HIS 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 588 MET Chi-restraints excluded: chain C residue 595 GLU 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 1345 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 19 optimal weight: 0.8980 chunk 121 optimal weight: 40.0000 chunk 59 optimal weight: 0.8980 chunk 32 optimal weight: 0.0000 chunk 57 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 64 optimal weight: 0.3980 chunk 75 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 379 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 = 0.4264 r_free = 0.4264 target = 0.198886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.128962 restraints weight = 12647.385| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.06 r_work: 0.3303 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11085 Z= 0.109 Angle : 0.558 15.336 15093 Z= 0.286 Chirality : 0.044 0.199 1632 Planarity : 0.004 0.072 1972 Dihedral : 5.402 52.363 1629 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.14 % Favored : 95.64 % Rotamer: Outliers : 2.52 % Allowed : 17.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.24), residues: 1353 helix: 1.09 (0.35), residues: 225 sheet: -0.79 (0.32), residues: 277 loop : 0.20 (0.23), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 PHE 0.029 0.001 PHE P 162 TYR 0.015 0.001 TYR C 463 ARG 0.007 0.000 ARG P 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00263 ( 8) link_NAG-ASN : angle 1.51218 ( 24) hydrogen bonds : bond 0.03100 ( 306) hydrogen bonds : angle 4.92357 ( 852) metal coordination : bond 0.00138 ( 3) SS BOND : bond 0.00198 ( 37) SS BOND : angle 0.90204 ( 74) covalent geometry : bond 0.00248 (11037) covalent geometry : angle 0.55247 (14995) *********************** 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 176 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8152 (mtt-85) cc_final: 0.7841 (mtt180) REVERT: C 252 TYR cc_start: 0.8723 (m-80) cc_final: 0.8312 (m-80) REVERT: C 254 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6687 (tt0) REVERT: C 367 ASN cc_start: 0.7835 (t0) cc_final: 0.7398 (t0) REVERT: C 430 HIS cc_start: 0.6494 (m90) cc_final: 0.6244 (t-90) REVERT: C 433 THR cc_start: 0.8807 (p) cc_final: 0.8326 (t) REVERT: C 508 ASP cc_start: 0.7962 (t0) cc_final: 0.6643 (p0) REVERT: C 591 GLU cc_start: 0.7054 (pm20) cc_final: 0.6631 (pm20) REVERT: C 609 HIS cc_start: 0.6869 (t70) cc_final: 0.6263 (t70) REVERT: C 670 ARG cc_start: 0.6822 (tpm170) cc_final: 0.6295 (tpm170) REVERT: C 849 GLU cc_start: 0.7908 (mp0) cc_final: 0.7323 (mt-10) REVERT: C 956 GLN cc_start: 0.8013 (mm-40) cc_final: 0.7630 (mt0) REVERT: C 976 ARG cc_start: 0.7727 (mtp85) cc_final: 0.7092 (ttm-80) REVERT: P 79 ARG cc_start: 0.7512 (mtp85) cc_final: 0.6892 (mmt90) REVERT: P 130 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6898 (tm-30) REVERT: P 158 GLU cc_start: 0.7013 (tm-30) cc_final: 0.6638 (tm-30) REVERT: Q 1302 GLU cc_start: 0.7412 (tp30) cc_final: 0.6760 (tm-30) REVERT: Q 1339 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7331 (mp0) REVERT: Q 1343 GLU cc_start: 0.6320 (tt0) cc_final: 0.5947 (tm-30) REVERT: Q 1518 MET cc_start: 0.4051 (pmm) cc_final: 0.3535 (mmp) REVERT: Q 1573 ARG cc_start: 0.6272 (mtm180) cc_final: 0.5784 (ptp90) outliers start: 30 outliers final: 27 residues processed: 170 average time/residue: 0.2419 time to fit residues: 58.2152 Evaluate side-chains 169 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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 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 769 HIS Chi-restraints excluded: chain C residue 791 LEU 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 65 CYS Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1345 MET 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 90 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.4242 r_free = 0.4242 target = 0.196602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.128319 restraints weight = 12496.432| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.24 r_work: 0.3264 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2454 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= 0.178 Angle : 0.586 15.044 15093 Z= 0.300 Chirality : 0.045 0.155 1632 Planarity : 0.005 0.074 1972 Dihedral : 5.284 52.830 1627 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.17 % Favored : 94.60 % Rotamer: Outliers : 2.77 % Allowed : 17.20 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1353 helix: 1.04 (0.35), residues: 225 sheet: -0.76 (0.32), residues: 277 loop : 0.18 (0.23), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 807 HIS 0.005 0.001 HIS C 562 PHE 0.015 0.001 PHE Q1298 TYR 0.013 0.002 TYR C 211 ARG 0.006 0.000 ARG P 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 8) link_NAG-ASN : angle 1.34305 ( 24) hydrogen bonds : bond 0.03234 ( 306) hydrogen bonds : angle 5.00790 ( 852) metal coordination : bond 0.00413 ( 3) SS BOND : bond 0.00290 ( 37) SS BOND : angle 1.02004 ( 74) covalent geometry : bond 0.00425 (11037) covalent geometry : angle 0.58091 (14995) ********************** 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 175 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8230 (mtt-85) cc_final: 0.7916 (mtt180) REVERT: C 252 TYR cc_start: 0.8861 (m-80) cc_final: 0.8517 (m-80) REVERT: C 254 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7120 (tt0) REVERT: C 283 GLN cc_start: 0.8450 (mm-40) cc_final: 0.7926 (mt0) REVERT: C 367 ASN cc_start: 0.7869 (t0) cc_final: 0.7433 (t0) REVERT: C 418 LYS cc_start: 0.8239 (mtpp) cc_final: 0.7795 (mtpp) REVERT: C 433 THR cc_start: 0.8790 (p) cc_final: 0.8301 (t) REVERT: C 459 MET cc_start: 0.6747 (tpt) cc_final: 0.5685 (ttp) REVERT: C 508 ASP cc_start: 0.8117 (t0) cc_final: 0.6858 (p0) REVERT: C 591 GLU cc_start: 0.7021 (pm20) cc_final: 0.6563 (pm20) REVERT: C 609 HIS cc_start: 0.6884 (t70) cc_final: 0.6382 (t70) REVERT: C 636 MET cc_start: 0.9068 (mpp) cc_final: 0.8793 (mmm) REVERT: C 670 ARG cc_start: 0.6868 (tpm170) cc_final: 0.6349 (tpm170) REVERT: C 849 GLU cc_start: 0.8059 (mp0) cc_final: 0.7441 (mt-10) REVERT: C 956 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7697 (mt0) REVERT: C 976 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7252 (ttm-80) REVERT: P 79 ARG cc_start: 0.7522 (mtp85) cc_final: 0.6919 (mmt90) REVERT: P 130 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6977 (tm-30) REVERT: P 158 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6771 (tm-30) REVERT: Q 1302 GLU cc_start: 0.7403 (tp30) cc_final: 0.6746 (tm-30) REVERT: Q 1339 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7344 (mp0) REVERT: Q 1343 GLU cc_start: 0.6353 (tt0) cc_final: 0.5973 (tm-30) REVERT: Q 1573 ARG cc_start: 0.6320 (mtm180) cc_final: 0.5821 (ptp90) outliers start: 33 outliers final: 30 residues processed: 166 average time/residue: 0.2353 time to fit residues: 55.2763 Evaluate side-chains 170 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 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 769 HIS Chi-restraints excluded: chain C residue 791 LEU 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 103 ILE Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1345 MET 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 32 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 93 optimal weight: 0.4980 chunk 112 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4269 r_free = 0.4269 target = 0.199354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.128271 restraints weight = 12469.759| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 3.06 r_work: 0.3295 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11085 Z= 0.110 Angle : 0.551 15.042 15093 Z= 0.282 Chirality : 0.043 0.162 1632 Planarity : 0.004 0.070 1972 Dihedral : 5.097 52.160 1627 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.43 % Favored : 95.34 % Rotamer: Outliers : 2.85 % Allowed : 17.03 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1353 helix: 1.17 (0.35), residues: 225 sheet: -0.69 (0.32), residues: 277 loop : 0.25 (0.23), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 PHE 0.014 0.001 PHE Q1298 TYR 0.012 0.001 TYR C 463 ARG 0.006 0.000 ARG P 79 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 8) link_NAG-ASN : angle 1.24979 ( 24) hydrogen bonds : bond 0.03017 ( 306) hydrogen bonds : angle 4.77511 ( 852) metal coordination : bond 0.00186 ( 3) SS BOND : bond 0.00194 ( 37) SS BOND : angle 0.87272 ( 74) covalent geometry : bond 0.00253 (11037) covalent geometry : angle 0.54716 (14995) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7084.73 seconds wall clock time: 122 minutes 36.16 seconds (7356.16 seconds total)