Starting phenix.real_space_refine on Thu Feb 15 01:37:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7d_15220/02_2024/8a7d_15220.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7d_15220/02_2024/8a7d_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7d_15220/02_2024/8a7d_15220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7d_15220/02_2024/8a7d_15220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7d_15220/02_2024/8a7d_15220.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7d_15220/02_2024/8a7d_15220.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.61, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 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: 4.50 Conformation dependent library (CDL) restraints added in 2.0 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: 3.96 Time building geometry restraints manager: 4.83 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: 89.10 - 100.96: 16 100.96 - 112.81: 6132 112.81 - 124.66: 8595 124.66 - 136.51: 251 136.51 - 148.36: 1 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 2.440 nonbonded pdb=" OG SER C 148 " pdb=" OD1 ASP C 150 " model vdw 2.152 2.440 nonbonded pdb=" OG1 THR C 590 " pdb=" OE1 GLU C 591 " model vdw 2.187 2.440 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 ========== 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: 0.540 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: 2.920 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 33.760 Find NCS groups from input model: 0.310 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.570 ------------------------------------------------------------------------------- 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 11037 Z= 0.260 Angle : 0.761 33.705 14995 Z= 0.467 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 184 time to evaluate : 1.325 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: 0.2627 time to fit residues: 67.4097 Evaluate side-chains 142 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 138 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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: 10.0000 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 GLN ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 905 ASN P 49 ASN P 73 ASN ** 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 11037 Z= 0.548 Angle : 0.705 9.215 14995 Z= 0.363 Chirality : 0.051 0.223 1632 Planarity : 0.006 0.086 1972 Dihedral : 6.697 59.977 1631 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.43 % Favored : 93.13 % Rotamer: Outliers : 3.78 % Allowed : 12.67 % Favored : 83.56 % 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: -0.22 (0.24), residues: 1353 helix: 0.89 (0.35), residues: 217 sheet: -0.93 (0.32), residues: 261 loop : -0.08 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 259 HIS 0.008 0.002 HIS C 656 PHE 0.019 0.002 PHE Q1298 TYR 0.022 0.003 TYR C 252 ARG 0.004 0.001 ARG C 670 *********************** 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 189 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 144 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8115 (mtt-85) cc_final: 0.7826 (mtt180) REVERT: C 252 TYR cc_start: 0.8863 (m-80) cc_final: 0.8538 (m-80) REVERT: C 327 CYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7667 (m) REVERT: C 367 ASN cc_start: 0.8016 (t0) cc_final: 0.7646 (t0) REVERT: C 418 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8225 (mtpt) REVERT: C 423 ASN cc_start: 0.7418 (t0) cc_final: 0.7016 (p0) REVERT: C 430 HIS cc_start: 0.7212 (OUTLIER) cc_final: 0.6564 (m90) REVERT: C 508 ASP cc_start: 0.7824 (t0) cc_final: 0.7146 (p0) REVERT: C 553 MET cc_start: 0.7750 (mmp) cc_final: 0.7470 (mmm) REVERT: C 588 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6459 (ptt) REVERT: C 636 MET cc_start: 0.9115 (mmm) cc_final: 0.8723 (mmm) REVERT: C 962 ASP cc_start: 0.8661 (p0) cc_final: 0.8459 (p0) REVERT: C 976 ARG cc_start: 0.7968 (mtp85) cc_final: 0.7504 (ttm-80) REVERT: P 77 GLU cc_start: 0.7648 (tp30) cc_final: 0.7364 (pt0) REVERT: P 115 ARG cc_start: 0.7932 (ttp80) cc_final: 0.7520 (ttm110) REVERT: P 130 GLU cc_start: 0.7201 (tm-30) cc_final: 0.6959 (tm-30) outliers start: 45 outliers final: 23 residues processed: 180 average time/residue: 0.2434 time to fit residues: 61.8243 Evaluate side-chains 155 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 150 ASP 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 327 CYS 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 503 ASN Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 588 MET Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain C residue 757 VAL Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 801 THR Chi-restraints excluded: chain C residue 845 ASP 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 180 THR Chi-restraints excluded: chain Q residue 1289 ASP Chi-restraints excluded: chain Q residue 1527 HIS Chi-restraints excluded: chain Q residue 1558 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 452 GLN ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN P 98 GLN P 116 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11037 Z= 0.218 Angle : 0.561 7.960 14995 Z= 0.293 Chirality : 0.045 0.217 1632 Planarity : 0.005 0.079 1972 Dihedral : 6.106 56.699 1629 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.88 % Favored : 94.75 % Rotamer: Outliers : 3.61 % Allowed : 14.77 % Favored : 81.63 % 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: 0.01 (0.24), residues: 1353 helix: 1.15 (0.36), residues: 217 sheet: -0.82 (0.33), residues: 256 loop : 0.06 (0.22), residues: 880 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 0.015 0.001 PHE P 162 TYR 0.014 0.001 TYR C 463 ARG 0.005 0.000 ARG P 79 *********************** 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 203 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 160 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8106 (mtt-85) cc_final: 0.7806 (mtt180) REVERT: C 252 TYR cc_start: 0.8674 (m-80) cc_final: 0.8276 (m-80) REVERT: C 254 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7145 (tt0) REVERT: C 327 CYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7598 (m) REVERT: C 367 ASN cc_start: 0.7935 (t0) cc_final: 0.7584 (t0) REVERT: C 423 ASN cc_start: 0.7398 (t0) cc_final: 0.7030 (p0) REVERT: C 430 HIS cc_start: 0.6916 (OUTLIER) cc_final: 0.6365 (m-70) REVERT: C 459 MET cc_start: 0.6512 (tpt) cc_final: 0.6286 (tpt) REVERT: C 508 ASP cc_start: 0.7801 (t0) cc_final: 0.6960 (p0) REVERT: C 636 MET cc_start: 0.9065 (mmm) cc_final: 0.8665 (mmm) REVERT: C 976 ARG cc_start: 0.7860 (mtp85) cc_final: 0.7495 (mmm160) REVERT: P 79 ARG cc_start: 0.7402 (mtp85) cc_final: 0.7133 (mmt90) REVERT: P 115 ARG cc_start: 0.7934 (ttp80) cc_final: 0.7508 (ttm110) REVERT: P 130 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6959 (tm-30) REVERT: Q 1313 GLN cc_start: 0.7343 (pm20) cc_final: 0.7056 (pm20) REVERT: Q 1343 GLU cc_start: 0.6527 (tt0) cc_final: 0.6133 (tm-30) REVERT: Q 1401 GLN cc_start: 0.8145 (mt0) cc_final: 0.7648 (mm110) REVERT: Q 1573 ARG cc_start: 0.6292 (mtm180) cc_final: 0.5528 (ptp90) outliers start: 43 outliers final: 26 residues processed: 189 average time/residue: 0.2467 time to fit residues: 65.8090 Evaluate side-chains 164 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 135 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 192 LEU 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 327 CYS Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 498 VAL Chi-restraints excluded: chain C residue 588 MET Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain C residue 769 HIS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 929 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 91 ASN Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 1289 ASP Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1527 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.3980 chunk 92 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 130 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 HIS C 452 GLN ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 967 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN P 161 HIS P 196 GLN Q1291 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11037 Z= 0.343 Angle : 0.593 8.444 14995 Z= 0.308 Chirality : 0.046 0.218 1632 Planarity : 0.005 0.080 1972 Dihedral : 6.049 54.734 1629 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.06 % Favored : 93.57 % Rotamer: Outliers : 4.45 % Allowed : 15.18 % 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: -0.02 (0.24), residues: 1353 helix: 1.09 (0.36), residues: 217 sheet: -0.68 (0.32), residues: 274 loop : 0.02 (0.23), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 259 HIS 0.006 0.001 HIS C 562 PHE 0.017 0.001 PHE Q1298 TYR 0.016 0.002 TYR C 252 ARG 0.004 0.000 ARG C 741 *********************** 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 186 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 133 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7895 (mtt180) REVERT: C 252 TYR cc_start: 0.8741 (m-80) cc_final: 0.8363 (m-80) REVERT: C 254 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: C 327 CYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7663 (m) REVERT: C 367 ASN cc_start: 0.7987 (t0) cc_final: 0.7538 (t0) REVERT: C 418 LYS cc_start: 0.8701 (mtpp) cc_final: 0.8142 (mtpp) REVERT: C 430 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.6329 (m-70) REVERT: C 508 ASP cc_start: 0.7872 (t0) cc_final: 0.7035 (p0) REVERT: C 636 MET cc_start: 0.9080 (mmm) cc_final: 0.8710 (mmm) REVERT: C 976 ARG cc_start: 0.7865 (mtp85) cc_final: 0.7487 (ttm-80) REVERT: P 115 ARG cc_start: 0.7893 (ttp80) cc_final: 0.7447 (ttm110) REVERT: P 130 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6924 (tm-30) REVERT: Q 1345 MET cc_start: 0.7153 (ptm) cc_final: 0.6575 (ppp) REVERT: Q 1573 ARG cc_start: 0.6103 (mtm180) cc_final: 0.5636 (ptp90) outliers start: 53 outliers final: 38 residues processed: 174 average time/residue: 0.2334 time to fit residues: 57.8835 Evaluate side-chains 169 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 128 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 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 327 CYS Chi-restraints excluded: chain C residue 430 HIS Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 496 LEU Chi-restraints excluded: chain C residue 497 ASP 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 640 ASP Chi-restraints excluded: chain C residue 711 HIS Chi-restraints excluded: chain C residue 748 ASP Chi-restraints excluded: chain C residue 769 HIS Chi-restraints excluded: chain C residue 791 LEU Chi-restraints excluded: chain C residue 821 VAL Chi-restraints excluded: chain C residue 845 ASP Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 994 ASP 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 91 ASN Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 1289 ASP Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1339 GLU Chi-restraints excluded: chain Q residue 1527 HIS Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1568 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 4.9990 chunk 74 optimal weight: 0.4980 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 0.2980 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 967 ASN P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11037 Z= 0.211 Angle : 0.544 8.232 14995 Z= 0.283 Chirality : 0.044 0.210 1632 Planarity : 0.004 0.077 1972 Dihedral : 5.807 53.631 1629 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.25 % Favored : 94.38 % Rotamer: Outliers : 3.78 % Allowed : 16.02 % Favored : 80.20 % 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: 0.03 (0.24), residues: 1353 helix: 1.20 (0.36), residues: 217 sheet: -0.73 (0.32), residues: 272 loop : 0.06 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 807 HIS 0.012 0.001 HIS C 278 PHE 0.023 0.001 PHE P 162 TYR 0.013 0.001 TYR C 252 ARG 0.006 0.000 ARG P 79 *********************** 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 189 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 144 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8154 (mtt-85) cc_final: 0.7844 (mtt180) REVERT: C 252 TYR cc_start: 0.8659 (m-80) cc_final: 0.8252 (m-80) REVERT: C 254 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: C 327 CYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7582 (m) REVERT: C 367 ASN cc_start: 0.7927 (t0) cc_final: 0.7497 (t0) REVERT: C 418 LYS cc_start: 0.8699 (mtpp) cc_final: 0.8136 (mtpp) REVERT: C 430 HIS cc_start: 0.6761 (OUTLIER) cc_final: 0.6395 (m90) REVERT: C 508 ASP cc_start: 0.7844 (t0) cc_final: 0.6918 (p0) REVERT: C 636 MET cc_start: 0.9052 (mmm) cc_final: 0.8664 (mmm) REVERT: C 976 ARG cc_start: 0.7795 (mtp85) cc_final: 0.7426 (ttm-80) REVERT: P 79 ARG cc_start: 0.7405 (mtp85) cc_final: 0.6993 (mmt90) REVERT: P 115 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7462 (ttm110) REVERT: P 130 GLU cc_start: 0.7139 (tm-30) cc_final: 0.6918 (tm-30) REVERT: P 158 GLU cc_start: 0.7259 (tm-30) cc_final: 0.6829 (tm-30) REVERT: Q 1343 GLU cc_start: 0.6684 (tt0) cc_final: 0.6250 (tm-30) REVERT: Q 1401 GLN cc_start: 0.8124 (mt0) cc_final: 0.7293 (pp30) REVERT: Q 1573 ARG cc_start: 0.6274 (mtm180) cc_final: 0.5795 (ptp90) outliers start: 45 outliers final: 33 residues processed: 178 average time/residue: 0.2323 time to fit residues: 59.0245 Evaluate side-chains 168 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 132 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 150 ASP 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 327 CYS 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 640 ASP Chi-restraints excluded: chain C residue 711 HIS Chi-restraints excluded: chain C residue 748 ASP 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 821 VAL Chi-restraints excluded: chain C residue 845 ASP 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 91 ASN Chi-restraints excluded: chain P residue 103 ILE Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 1289 ASP Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1339 GLU Chi-restraints excluded: chain Q residue 1527 HIS Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1568 ASP Chi-restraints excluded: chain Q residue 1590 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 125 optimal weight: 40.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 452 GLN ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 HIS P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 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 : 0.005 0.039 11037 Z= 0.298 Angle : 0.579 13.702 14995 Z= 0.299 Chirality : 0.045 0.201 1632 Planarity : 0.004 0.079 1972 Dihedral : 5.754 51.733 1629 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.21 % Favored : 93.42 % Rotamer: Outliers : 4.70 % Allowed : 15.44 % Favored : 79.87 % 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: 0.02 (0.24), residues: 1353 helix: 1.32 (0.36), residues: 211 sheet: -0.74 (0.32), residues: 280 loop : 0.03 (0.23), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 259 HIS 0.006 0.001 HIS C 562 PHE 0.013 0.001 PHE Q1596 TYR 0.014 0.002 TYR C 252 ARG 0.004 0.000 ARG P 79 *********************** 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 192 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 136 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8206 (mtt-85) cc_final: 0.7886 (mtt180) REVERT: C 252 TYR cc_start: 0.8712 (m-80) cc_final: 0.8337 (m-80) REVERT: C 254 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7225 (tt0) REVERT: C 367 ASN cc_start: 0.7952 (t0) cc_final: 0.7505 (t0) REVERT: C 418 LYS cc_start: 0.8709 (mtpp) cc_final: 0.8123 (mtpp) REVERT: C 430 HIS cc_start: 0.6738 (OUTLIER) cc_final: 0.6379 (m90) REVERT: C 508 ASP cc_start: 0.7880 (t0) cc_final: 0.7019 (p0) REVERT: C 636 MET cc_start: 0.9065 (mmm) cc_final: 0.8687 (mmm) REVERT: C 670 ARG cc_start: 0.7396 (tpm170) cc_final: 0.6915 (tpm170) REVERT: C 976 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7475 (ttm-80) REVERT: P 130 GLU cc_start: 0.7275 (tm-30) cc_final: 0.7039 (tm-30) REVERT: Q 1343 GLU cc_start: 0.6705 (tt0) cc_final: 0.6261 (tm-30) REVERT: Q 1573 ARG cc_start: 0.6296 (mtm180) cc_final: 0.5807 (ptp90) outliers start: 56 outliers final: 46 residues processed: 181 average time/residue: 0.2435 time to fit residues: 62.0992 Evaluate side-chains 182 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 134 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 150 ASP 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 430 HIS Chi-restraints excluded: chain C residue 439 ASP Chi-restraints excluded: chain C residue 497 ASP 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 640 ASP Chi-restraints excluded: chain C residue 711 HIS Chi-restraints excluded: chain C residue 715 GLU Chi-restraints excluded: chain C residue 748 ASP 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 821 VAL Chi-restraints excluded: chain C residue 845 ASP Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 989 ARG Chi-restraints excluded: chain C residue 994 ASP 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 84 ILE Chi-restraints excluded: chain P residue 91 ASN Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 1289 ASP Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1339 GLU Chi-restraints excluded: chain Q residue 1399 CYS Chi-restraints excluded: chain Q residue 1527 HIS Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1568 ASP Chi-restraints excluded: chain Q residue 1590 THR Chi-restraints excluded: chain Q residue 1617 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 255 HIS C 278 HIS C 379 HIS ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11037 Z= 0.174 Angle : 0.537 13.153 14995 Z= 0.277 Chirality : 0.043 0.174 1632 Planarity : 0.004 0.075 1972 Dihedral : 5.432 50.945 1629 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.30 % Allowed : 4.88 % Favored : 94.83 % Rotamer: Outliers : 3.69 % Allowed : 16.11 % Favored : 80.20 % 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: 1.50 (0.36), residues: 211 sheet: -0.60 (0.33), residues: 265 loop : 0.10 (0.23), residues: 877 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 0.011 0.001 PHE Q1298 TYR 0.014 0.001 TYR C 463 ARG 0.007 0.000 ARG P 79 *********************** 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 190 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 146 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: C 150 ASP cc_start: 0.7732 (OUTLIER) cc_final: 0.7429 (p0) REVERT: C 151 ARG cc_start: 0.8156 (mtt-85) cc_final: 0.7826 (mtt180) REVERT: C 252 TYR cc_start: 0.8594 (m-80) cc_final: 0.8178 (m-80) REVERT: C 254 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7065 (tt0) REVERT: C 367 ASN cc_start: 0.7944 (t0) cc_final: 0.7524 (t0) REVERT: C 418 LYS cc_start: 0.8707 (mtpp) cc_final: 0.8127 (mtpp) REVERT: C 430 HIS cc_start: 0.6644 (OUTLIER) cc_final: 0.6328 (m90) REVERT: C 508 ASP cc_start: 0.7815 (t0) cc_final: 0.6853 (p0) REVERT: C 636 MET cc_start: 0.9014 (mmm) cc_final: 0.8567 (mmm) REVERT: C 976 ARG cc_start: 0.7777 (mtp85) cc_final: 0.7396 (ttm-80) REVERT: P 79 ARG cc_start: 0.7460 (mtp85) cc_final: 0.7082 (mmt90) REVERT: P 130 GLU cc_start: 0.7143 (tm-30) cc_final: 0.6917 (tm-30) REVERT: P 158 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6899 (tm-30) REVERT: Q 1302 GLU cc_start: 0.7428 (tp30) cc_final: 0.6843 (tm-30) REVERT: Q 1343 GLU cc_start: 0.6682 (tt0) cc_final: 0.6261 (tm-30) REVERT: Q 1573 ARG cc_start: 0.6288 (mtm180) cc_final: 0.5809 (ptp90) outliers start: 44 outliers final: 35 residues processed: 177 average time/residue: 0.2452 time to fit residues: 61.6654 Evaluate side-chains 174 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 136 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 150 ASP 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 439 ASP Chi-restraints excluded: chain C residue 497 ASP 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 715 GLU Chi-restraints excluded: chain C residue 748 ASP 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 91 ASN Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 1289 ASP Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1399 CYS Chi-restraints excluded: chain Q residue 1527 HIS Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1568 ASP Chi-restraints excluded: chain Q residue 1590 THR Chi-restraints excluded: chain Q residue 1617 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 118 optimal weight: 40.0000 chunk 124 optimal weight: 0.3980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 832 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN P 116 HIS P 161 HIS P 196 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11037 Z= 0.204 Angle : 0.538 12.998 14995 Z= 0.278 Chirality : 0.043 0.170 1632 Planarity : 0.004 0.075 1972 Dihedral : 5.340 50.880 1629 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.10 % Favored : 94.68 % Rotamer: Outliers : 3.78 % Allowed : 16.44 % Favored : 79.78 % 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: 1.35 (0.36), residues: 218 sheet: -0.63 (0.32), residues: 272 loop : 0.14 (0.23), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 807 HIS 0.008 0.001 HIS C 278 PHE 0.009 0.001 PHE P 162 TYR 0.014 0.001 TYR C 203 ARG 0.006 0.000 ARG P 79 *********************** 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 188 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 143 time to evaluate : 2.071 Fit side-chains revert: symmetry clash REVERT: C 150 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7417 (p0) REVERT: C 151 ARG cc_start: 0.8181 (mtt-85) cc_final: 0.7865 (mtt180) REVERT: C 254 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7063 (tt0) REVERT: C 367 ASN cc_start: 0.7946 (t0) cc_final: 0.7521 (t0) REVERT: C 418 LYS cc_start: 0.8714 (mtpp) cc_final: 0.8127 (mtpp) REVERT: C 508 ASP cc_start: 0.7839 (t0) cc_final: 0.6850 (p0) REVERT: C 636 MET cc_start: 0.9038 (mmm) cc_final: 0.8626 (mmm) REVERT: C 670 ARG cc_start: 0.7353 (tpm170) cc_final: 0.6883 (tpm170) REVERT: C 976 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7395 (ttm-80) REVERT: P 79 ARG cc_start: 0.7440 (mtp85) cc_final: 0.7106 (mmt90) REVERT: P 130 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6928 (tm-30) REVERT: P 158 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6884 (tm-30) REVERT: Q 1302 GLU cc_start: 0.7497 (tp30) cc_final: 0.6857 (tm-30) REVERT: Q 1343 GLU cc_start: 0.6645 (tt0) cc_final: 0.6239 (tm-30) REVERT: Q 1573 ARG cc_start: 0.6293 (mtm180) cc_final: 0.5816 (ptp90) outliers start: 45 outliers final: 37 residues processed: 176 average time/residue: 0.2424 time to fit residues: 59.7846 Evaluate side-chains 178 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 139 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 138 THR Chi-restraints excluded: chain C residue 150 ASP 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 439 ASP Chi-restraints excluded: chain C residue 497 ASP 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 715 GLU Chi-restraints excluded: chain C residue 748 ASP 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 845 ASP Chi-restraints excluded: chain C residue 857 THR Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 989 ARG Chi-restraints excluded: chain P residue 44 ARG Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 56 CYS Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 65 CYS Chi-restraints excluded: chain P residue 91 ASN Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 1289 ASP Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1399 CYS Chi-restraints excluded: chain Q residue 1527 HIS Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1568 ASP Chi-restraints excluded: chain Q residue 1590 THR Chi-restraints excluded: chain Q residue 1617 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 4.9990 chunk 121 optimal weight: 0.0010 chunk 124 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 0.0000 chunk 120 optimal weight: 20.0000 chunk 79 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 651 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11037 Z= 0.150 Angle : 0.521 13.040 14995 Z= 0.268 Chirality : 0.043 0.169 1632 Planarity : 0.004 0.072 1972 Dihedral : 4.915 51.640 1627 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.21 % Favored : 95.57 % Rotamer: Outliers : 3.36 % Allowed : 16.78 % Favored : 79.87 % 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: 0.27 (0.24), residues: 1353 helix: 1.43 (0.36), residues: 218 sheet: -0.54 (0.33), residues: 267 loop : 0.20 (0.23), residues: 868 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 0.009 0.001 PHE Q1298 TYR 0.015 0.001 TYR C 203 ARG 0.006 0.000 ARG P 79 *********************** 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 195 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 155 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: C 150 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7385 (p0) REVERT: C 151 ARG cc_start: 0.8170 (mtt-85) cc_final: 0.7881 (mtt180) REVERT: C 252 TYR cc_start: 0.8589 (m-80) cc_final: 0.8185 (m-80) REVERT: C 254 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7112 (tt0) REVERT: C 367 ASN cc_start: 0.7989 (t0) cc_final: 0.7555 (t0) REVERT: C 418 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8154 (mtpp) REVERT: C 430 HIS cc_start: 0.6764 (m-70) cc_final: 0.6487 (t-90) REVERT: C 489 ASP cc_start: 0.8266 (m-30) cc_final: 0.8066 (m-30) REVERT: C 508 ASP cc_start: 0.7831 (t0) cc_final: 0.6856 (p0) REVERT: C 609 HIS cc_start: 0.6877 (t70) cc_final: 0.6332 (t70) REVERT: C 670 ARG cc_start: 0.7193 (tpm170) cc_final: 0.6749 (tpm170) REVERT: C 976 ARG cc_start: 0.7773 (mtp85) cc_final: 0.7365 (ttm-80) REVERT: P 79 ARG cc_start: 0.7431 (mtp85) cc_final: 0.6925 (mmt90) REVERT: P 130 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6949 (tm-30) REVERT: P 158 GLU cc_start: 0.7077 (tm-30) cc_final: 0.6679 (tm-30) REVERT: Q 1302 GLU cc_start: 0.7500 (tp30) cc_final: 0.6852 (tm-30) REVERT: Q 1343 GLU cc_start: 0.6627 (tt0) cc_final: 0.6221 (tm-30) REVERT: Q 1573 ARG cc_start: 0.6319 (mtm180) cc_final: 0.5833 (ptp90) outliers start: 40 outliers final: 30 residues processed: 183 average time/residue: 0.2159 time to fit residues: 56.1998 Evaluate side-chains 179 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 150 ASP 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 439 ASP 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 715 GLU 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 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 91 ASN Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1399 CYS Chi-restraints excluded: chain Q residue 1527 HIS Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1568 ASP Chi-restraints excluded: chain Q residue 1590 THR Chi-restraints excluded: chain Q residue 1617 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 8.9990 chunk 78 optimal weight: 0.2980 chunk 60 optimal weight: 0.0980 chunk 89 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 chunk 123 optimal weight: 50.0000 chunk 107 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 HIS C 651 GLN P 98 GLN P 116 HIS P 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11037 Z= 0.153 Angle : 0.532 12.938 14995 Z= 0.272 Chirality : 0.043 0.167 1632 Planarity : 0.004 0.071 1972 Dihedral : 4.844 51.718 1627 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.51 % Favored : 95.27 % Rotamer: Outliers : 2.77 % Allowed : 18.04 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.41 % Cis-general : 0.00 % Twisted Proline : 1.23 % Twisted General : 0.00 % Rama-Z (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: 0.33 (0.24), residues: 1353 helix: 1.43 (0.36), residues: 218 sheet: -0.50 (0.33), residues: 268 loop : 0.25 (0.23), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 807 HIS 0.006 0.001 HIS C 562 PHE 0.009 0.001 PHE Q1298 TYR 0.012 0.001 TYR C 203 ARG 0.006 0.000 ARG P 79 ********************** 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 186 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 153 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: C 151 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7853 (mtt180) REVERT: C 254 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: C 283 GLN cc_start: 0.8318 (mm-40) cc_final: 0.8106 (mm-40) REVERT: C 418 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8155 (mtpp) REVERT: C 430 HIS cc_start: 0.6772 (m-70) cc_final: 0.6514 (t-90) REVERT: C 489 ASP cc_start: 0.8271 (m-30) cc_final: 0.8069 (m-30) REVERT: C 508 ASP cc_start: 0.7811 (t0) cc_final: 0.6873 (p0) REVERT: C 609 HIS cc_start: 0.6702 (t70) cc_final: 0.6210 (t70) REVERT: C 636 MET cc_start: 0.9097 (mpp) cc_final: 0.8830 (mmm) REVERT: C 670 ARG cc_start: 0.7182 (tpm170) cc_final: 0.6743 (tpm170) REVERT: C 959 GLN cc_start: 0.8571 (mt0) cc_final: 0.8303 (mp10) REVERT: C 976 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7345 (ttm-80) REVERT: P 79 ARG cc_start: 0.7412 (mtp85) cc_final: 0.6967 (mmt90) REVERT: P 114 LEU cc_start: 0.8133 (tp) cc_final: 0.7842 (tp) REVERT: P 130 GLU cc_start: 0.7150 (tm-30) cc_final: 0.6905 (tm-30) REVERT: P 158 GLU cc_start: 0.7052 (tm-30) cc_final: 0.6655 (tm-30) REVERT: Q 1302 GLU cc_start: 0.7465 (tp30) cc_final: 0.6808 (tm-30) REVERT: Q 1343 GLU cc_start: 0.6628 (tt0) cc_final: 0.6206 (tm-30) REVERT: Q 1401 GLN cc_start: 0.7962 (mt0) cc_final: 0.7654 (mm-40) REVERT: Q 1573 ARG cc_start: 0.6382 (mtm180) cc_final: 0.5917 (ptp90) outliers start: 33 outliers final: 30 residues processed: 179 average time/residue: 0.2453 time to fit residues: 61.2204 Evaluate side-chains 180 residues out of total 1192 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 1.202 ------------------------------------------------------------------------------- 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 150 ASP 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 439 ASP 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 715 GLU 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 C residue 989 ARG Chi-restraints excluded: chain P residue 52 GLU Chi-restraints excluded: chain P residue 56 CYS Chi-restraints excluded: chain P residue 63 VAL Chi-restraints excluded: chain P residue 65 CYS Chi-restraints excluded: chain P residue 91 ASN Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 135 LEU Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 1289 ASP Chi-restraints excluded: chain Q residue 1305 THR Chi-restraints excluded: chain Q residue 1399 CYS Chi-restraints excluded: chain Q residue 1527 HIS Chi-restraints excluded: chain Q residue 1534 VAL Chi-restraints excluded: chain Q residue 1568 ASP Chi-restraints excluded: chain Q residue 1590 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 0.0060 chunk 19 optimal weight: 0.2980 chunk 94 optimal weight: 0.0570 overall best weight: 0.3114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 982 ASN 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 = 0.4278 r_free = 0.4278 target = 0.200219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.133064 restraints weight = 12449.104| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 3.02 r_work: 0.3326 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11037 Z= 0.138 Angle : 0.528 13.010 14995 Z= 0.270 Chirality : 0.043 0.167 1632 Planarity : 0.004 0.069 1972 Dihedral : 4.792 51.826 1627 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.21 % Favored : 95.57 % Rotamer: Outliers : 2.68 % Allowed : 18.46 % Favored : 78.86 % 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: 0.38 (0.24), residues: 1353 helix: 1.51 (0.36), residues: 217 sheet: -0.41 (0.33), residues: 261 loop : 0.25 (0.23), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 807 HIS 0.008 0.001 HIS C 278 PHE 0.029 0.001 PHE P 162 TYR 0.012 0.001 TYR C 495 ARG 0.006 0.000 ARG P 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2621.35 seconds wall clock time: 50 minutes 50.20 seconds (3050.20 seconds total)