Starting phenix.real_space_refine on Sat Jul 4 00:10:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xsr_33432/07_2026/7xsr_33432.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xsr_33432/07_2026/7xsr_33432.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xsr_33432/07_2026/7xsr_33432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xsr_33432/07_2026/7xsr_33432.map" model { file = "/net/cci-nas-00/data/ceres_data/7xsr_33432/07_2026/7xsr_33432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xsr_33432/07_2026/7xsr_33432.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xsr_33432/07_2026/7xsr_33432.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xsr_33432/07_2026/7xsr_33432.cif" } resolution = 2.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.044 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 Zn 4 6.06 5 P 49 5.49 5 S 57 5.16 5 C 10558 2.51 5 N 2934 2.21 5 O 3305 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 131 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16907 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 10378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1287, 10378 Classifications: {'peptide': 1287} Link IDs: {'PTRANS': 60, 'TRANS': 1226} Chain breaks: 3 Chain: "C" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5482 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 20, 'TRANS': 655} Chain breaks: 1 Chain: "A" Number of atoms: 331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 331 Classifications: {'RNA': 15} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 11, 'rna3p_pyr': 2} Link IDs: {'rna2p': 1, 'rna3p': 13} Chain: "D" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 712 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 8, 'rna3p_pur': 2, 'rna3p_pyr': 13} Link IDs: {'rna2p': 19, 'rna3p': 14} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 676 SG CYS B 88 90.553 35.311 38.173 1.00 33.30 S ATOM 947 SG CYS B 121 94.678 33.022 37.660 1.00 41.85 S ATOM 993 SG CYS B 127 94.923 36.292 40.080 1.00 31.93 S ATOM 1017 SG CYS B 130 92.866 33.583 41.273 1.00 29.20 S ATOM 3755 SG CYS B 491 64.651 52.396 51.436 1.00 34.19 S ATOM 3837 SG CYS B 503 66.139 54.198 48.666 1.00 31.01 S ATOM 3859 SG CYS B 506 69.366 52.378 51.448 1.00 29.73 S ATOM 5830 SG CYS B 750 41.081 64.124 69.071 1.00 47.55 S ATOM 5843 SG CYS B 752 42.051 68.235 68.440 1.00 40.60 S ATOM 5865 SG CYS B 755 44.819 66.200 69.641 1.00 34.26 S ATOM 7868 SG CYS B1018 35.862 82.640 102.441 1.00 31.62 S ATOM 8039 SG CYS B1406 35.145 79.400 100.591 1.00 35.05 S ATOM 8090 SG CYS B1414 33.705 83.417 98.992 1.00 31.82 S ATOM 8107 SG CYS B1417 37.109 82.215 98.694 1.00 28.08 S Time building chain proxies: 3.05, per 1000 atoms: 0.18 Number of scatterers: 16907 At special positions: 0 Unit cell: (118.845, 136.8, 143.64, 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 4 29.99 S 57 16.00 P 49 15.00 O 3305 8.00 N 2934 7.00 C 10558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 575.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B1801 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 127 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 130 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 121 " pdb="ZN ZN B1801 " - pdb=" SG CYS B 88 " pdb=" ZN B1802 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 506 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 503 " pdb="ZN ZN B1802 " - pdb=" SG CYS B 491 " pdb=" ZN B1803 " pdb="ZN ZN B1803 " - pdb=" ND1 HIS B 747 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 752 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 750 " pdb="ZN ZN B1803 " - pdb=" SG CYS B 755 " pdb=" ZN B1804 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1406 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1414 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1018 " pdb="ZN ZN B1804 " - pdb=" SG CYS B1417 " Number of angles added : 15 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 20 sheets defined 39.3% alpha, 17.3% beta 5 base pairs and 13 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'B' and resid 27 through 32 Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 59 through 78 removed outlier: 3.786A pdb=" N VAL B 63 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 267 through 287 removed outlier: 3.871A pdb=" N ASN B 287 " --> pdb=" O ALA B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 291 through 303 removed outlier: 4.331A pdb=" N ILE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'B' and resid 338 through 350 Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 354 through 375 removed outlier: 3.508A pdb=" N PHE B 358 " --> pdb=" O GLY B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 488 removed outlier: 3.614A pdb=" N LEU B 475 " --> pdb=" O PRO B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 510 Processing helix chain 'B' and resid 569 through 580 Processing helix chain 'B' and resid 595 through 598 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'B' and resid 626 through 628 No H-bonds generated for 'chain 'B' and resid 626 through 628' Processing helix chain 'B' and resid 630 through 637 removed outlier: 3.792A pdb=" N LEU B 634 " --> pdb=" O LYS B 630 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU B 636 " --> pdb=" O LYS B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.724A pdb=" N LEU B 658 " --> pdb=" O ARG B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 693 Processing helix chain 'B' and resid 723 through 740 removed outlier: 3.770A pdb=" N HIS B 727 " --> pdb=" O LYS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 759 Processing helix chain 'B' and resid 831 through 848 Processing helix chain 'B' and resid 855 through 859 Processing helix chain 'B' and resid 873 through 883 Processing helix chain 'B' and resid 999 through 1015 removed outlier: 3.802A pdb=" N LEU B1003 " --> pdb=" O PRO B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1400 through 1404 removed outlier: 3.720A pdb=" N HIS B1404 " --> pdb=" O LYS B1401 " (cutoff:3.500A) Processing helix chain 'B' and resid 1414 through 1420 Processing helix chain 'B' and resid 1463 through 1468 removed outlier: 4.212A pdb=" N SER B1467 " --> pdb=" O ARG B1463 " (cutoff:3.500A) Processing helix chain 'B' and resid 1486 through 1493 removed outlier: 3.942A pdb=" N ILE B1490 " --> pdb=" O GLY B1486 " (cutoff:3.500A) Processing helix chain 'B' and resid 1494 through 1499 Processing helix chain 'B' and resid 1528 through 1540 Processing helix chain 'B' and resid 1583 through 1603 removed outlier: 3.505A pdb=" N ILE B1587 " --> pdb=" O PRO B1583 " (cutoff:3.500A) Processing helix chain 'B' and resid 1615 through 1618 removed outlier: 3.659A pdb=" N VAL B1618 " --> pdb=" O GLN B1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1615 through 1618' Processing helix chain 'B' and resid 1619 through 1629 Processing helix chain 'B' and resid 1673 through 1683 removed outlier: 3.570A pdb=" N THR B1683 " --> pdb=" O LYS B1679 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 33 Processing helix chain 'C' and resid 37 through 59 Processing helix chain 'C' and resid 64 through 81 removed outlier: 3.757A pdb=" N PHE C 68 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 81 " --> pdb=" O LEU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 109 removed outlier: 3.811A pdb=" N LYS C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 136 Processing helix chain 'C' and resid 141 through 156 Processing helix chain 'C' and resid 163 through 177 removed outlier: 4.107A pdb=" N ILE C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 Processing helix chain 'C' and resid 194 through 205 Processing helix chain 'C' and resid 209 through 223 Processing helix chain 'C' and resid 230 through 246 removed outlier: 4.258A pdb=" N ASP C 234 " --> pdb=" O HIS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.982A pdb=" N ILE C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 298 Processing helix chain 'C' and resid 302 through 322 removed outlier: 3.845A pdb=" N LYS C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 340 through 362 removed outlier: 3.975A pdb=" N TYR C 360 " --> pdb=" O TYR C 356 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 451 removed outlier: 3.517A pdb=" N PHE C 437 " --> pdb=" O TYR C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 469 Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 490 through 494 Processing helix chain 'C' and resid 509 through 513 removed outlier: 3.688A pdb=" N GLU C 512 " --> pdb=" O LEU C 509 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 513 " --> pdb=" O PHE C 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 509 through 513' Processing helix chain 'C' and resid 521 through 525 Processing helix chain 'C' and resid 547 through 552 Processing helix chain 'C' and resid 566 through 571 Processing helix chain 'C' and resid 592 through 596 removed outlier: 3.710A pdb=" N SER C 596 " --> pdb=" O PRO C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 613 Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 644 through 653 removed outlier: 3.851A pdb=" N ALA C 648 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 679 removed outlier: 3.849A pdb=" N THR C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 691 removed outlier: 4.032A pdb=" N TRP C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 707 removed outlier: 3.718A pdb=" N PHE C 703 " --> pdb=" O HIS C 699 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE C 707 " --> pdb=" O PHE C 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 151 through 153 removed outlier: 3.748A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG B 19 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N TRP B 44 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 21 " --> pdb=" O TRP B 44 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N TRP B 46 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TRP B 195 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N GLU B 22 " --> pdb=" O ARG B 193 " (cutoff:3.500A) removed outlier: 13.887A pdb=" N ARG B 193 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP B 190 " --> pdb=" O ARG B 180 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE B 192 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 167 through 168 removed outlier: 3.922A pdb=" N LEU B 167 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N SER B 56 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU B 158 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR B 9 " --> pdb=" O ILE B 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.627A pdb=" N VAL B 85 " --> pdb=" O TRP B 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.355A pdb=" N THR B 110 " --> pdb=" O VAL B 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.753A pdb=" N GLU B 415 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 611 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 417 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 609 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 419 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE B 607 " --> pdb=" O VAL B 419 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLY B 600 " --> pdb=" O LEU B 591 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 512 through 513 removed outlier: 6.753A pdb=" N GLU B 415 " --> pdb=" O GLU B 611 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLU B 611 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ILE B 417 " --> pdb=" O ILE B 609 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 609 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 419 " --> pdb=" O ILE B 607 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ILE B 607 " --> pdb=" O VAL B 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 431 through 432 removed outlier: 3.693A pdb=" N VAL B 432 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ASN B 459 " --> pdb=" O VAL B 432 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AA9, first strand: chain 'B' and resid 526 through 530 Processing sheet with id=AB1, first strand: chain 'B' and resid 533 through 534 removed outlier: 3.726A pdb=" N THR B 539 " --> pdb=" O ASN B 534 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 703 through 704 removed outlier: 3.542A pdb=" N ARG B 719 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 703 through 704 removed outlier: 3.542A pdb=" N ARG B 719 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE B 720 " --> pdb=" O LEU B 774 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 699 through 700 removed outlier: 6.942A pdb=" N ALA B 699 " --> pdb=" O TYR B 808 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ALA B 803 " --> pdb=" O ALA B 791 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 924 through 927 Processing sheet with id=AB6, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.975A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 991 through 992 removed outlier: 6.975A pdb=" N LEU B 996 " --> pdb=" O TYR B1436 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B1436 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL B1517 " --> pdb=" O GLU B1437 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU B 950 " --> pdb=" O ASN B1526 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS B 957 " --> pdb=" O ILE B1564 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE B1564 " --> pdb=" O LYS B 957 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N GLU B 959 " --> pdb=" O ILE B1562 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE B1562 " --> pdb=" O GLU B 959 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 985 through 986 removed outlier: 6.469A pdb=" N LYS B 985 " --> pdb=" O THR B1508 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 425 through 431 removed outlier: 3.588A pdb=" N PHE C 405 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 562 through 563 removed outlier: 7.961A pdb=" N LYS C 562 " --> pdb=" O TYR C 536 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU C 538 " --> pdb=" O LYS C 562 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR C 660 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 586 through 587 666 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 13 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3255 1.33 - 1.45: 4542 1.45 - 1.57: 9445 1.57 - 1.69: 62 1.69 - 1.81: 80 Bond restraints: 17384 Sorted by residual: bond pdb=" O3' G A 27 " pdb=" P C A 28 " ideal model delta sigma weight residual 1.607 1.475 0.132 1.50e-02 4.44e+03 7.70e+01 bond pdb=" O3' C D 9 " pdb=" P U D 10 " ideal model delta sigma weight residual 1.607 1.481 0.126 1.50e-02 4.44e+03 7.03e+01 bond pdb=" O3' U D 8 " pdb=" P C D 9 " ideal model delta sigma weight residual 1.607 1.488 0.119 1.50e-02 4.44e+03 6.31e+01 bond pdb=" O3' U D -2 " pdb=" P A D -1 " ideal model delta sigma weight residual 1.607 1.491 0.116 1.50e-02 4.44e+03 6.03e+01 bond pdb=" O3' G D -9 " pdb=" P U D -8 " ideal model delta sigma weight residual 1.607 1.493 0.114 1.50e-02 4.44e+03 5.77e+01 ... (remaining 17379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 23409 3.76 - 7.52: 236 7.52 - 11.29: 23 11.29 - 15.05: 2 15.05 - 18.81: 3 Bond angle restraints: 23673 Sorted by residual: angle pdb=" O3' C D 13 " pdb=" C3' C D 13 " pdb=" C2' C D 13 " ideal model delta sigma weight residual 113.70 132.27 -18.57 1.50e+00 4.44e-01 1.53e+02 angle pdb=" O2' C D 1 " pdb=" C2' C D 1 " pdb=" C1' C D 1 " ideal model delta sigma weight residual 108.40 91.70 16.70 1.50e+00 4.44e-01 1.24e+02 angle pdb=" O2' U D -2 " pdb=" C2' U D -2 " pdb=" C1' U D -2 " ideal model delta sigma weight residual 111.80 100.28 11.52 1.50e+00 4.44e-01 5.89e+01 angle pdb=" O4' A D -1 " pdb=" C1' A D -1 " pdb=" C2' A D -1 " ideal model delta sigma weight residual 105.80 99.29 6.51 1.00e+00 1.00e+00 4.23e+01 angle pdb=" O2' C D -7 " pdb=" C2' C D -7 " pdb=" C1' C D -7 " ideal model delta sigma weight residual 108.40 117.85 -9.45 1.50e+00 4.44e-01 3.97e+01 ... (remaining 23668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 9914 33.72 - 67.43: 404 67.43 - 101.15: 26 101.15 - 134.87: 2 134.87 - 168.58: 4 Dihedral angle restraints: 10350 sinusoidal: 4691 harmonic: 5659 Sorted by residual: dihedral pdb=" O4' U D -13 " pdb=" C1' U D -13 " pdb=" N1 U D -13 " pdb=" C2 U D -13 " ideal model delta sinusoidal sigma weight residual -160.00 5.71 -165.71 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' C D -7 " pdb=" C1' C D -7 " pdb=" N1 C D -7 " pdb=" C2 C D -7 " ideal model delta sinusoidal sigma weight residual 200.00 50.53 149.47 1 1.50e+01 4.44e-03 7.94e+01 dihedral pdb=" O4' U D -8 " pdb=" C1' U D -8 " pdb=" N1 U D -8 " pdb=" C2 U D -8 " ideal model delta sinusoidal sigma weight residual -128.00 40.58 -168.58 1 1.70e+01 3.46e-03 6.58e+01 ... (remaining 10347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 2518 0.181 - 0.363: 40 0.363 - 0.544: 3 0.544 - 0.725: 1 0.725 - 0.907: 1 Chirality restraints: 2563 Sorted by residual: chirality pdb=" C3' C D 13 " pdb=" C4' C D 13 " pdb=" O3' C D 13 " pdb=" C2' C D 13 " both_signs ideal model delta sigma weight residual False -2.48 -1.57 -0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" C2' C D -7 " pdb=" C3' C D -7 " pdb=" O2' C D -7 " pdb=" C1' C D -7 " both_signs ideal model delta sigma weight residual False -2.75 -2.19 -0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C2' C D 13 " pdb=" C3' C D 13 " pdb=" O2' C D 13 " pdb=" C1' C D 13 " both_signs ideal model delta sigma weight residual False -2.75 -2.32 -0.43 2.00e-01 2.50e+01 4.60e+00 ... (remaining 2560 not shown) Planarity restraints: 2873 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D -1 " 0.093 2.00e-02 2.50e+03 4.23e-02 4.93e+01 pdb=" N9 A D -1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 A D -1 " 0.008 2.00e-02 2.50e+03 pdb=" N7 A D -1 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A D -1 " -0.010 2.00e-02 2.50e+03 pdb=" C6 A D -1 " 0.029 2.00e-02 2.50e+03 pdb=" N6 A D -1 " 0.013 2.00e-02 2.50e+03 pdb=" N1 A D -1 " 0.020 2.00e-02 2.50e+03 pdb=" C2 A D -1 " -0.006 2.00e-02 2.50e+03 pdb=" N3 A D -1 " -0.021 2.00e-02 2.50e+03 pdb=" C4 A D -1 " -0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 34 " 0.077 2.00e-02 2.50e+03 3.25e-02 2.90e+01 pdb=" N9 A A 34 " -0.048 2.00e-02 2.50e+03 pdb=" C8 A A 34 " -0.008 2.00e-02 2.50e+03 pdb=" N7 A A 34 " -0.009 2.00e-02 2.50e+03 pdb=" C5 A A 34 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A A 34 " 0.017 2.00e-02 2.50e+03 pdb=" N6 A A 34 " 0.014 2.00e-02 2.50e+03 pdb=" N1 A A 34 " 0.027 2.00e-02 2.50e+03 pdb=" C2 A A 34 " -0.008 2.00e-02 2.50e+03 pdb=" N3 A A 34 " -0.032 2.00e-02 2.50e+03 pdb=" C4 A A 34 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 442 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C LYS B 442 " 0.068 2.00e-02 2.50e+03 pdb=" O LYS B 442 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU B 443 " -0.023 2.00e-02 2.50e+03 ... (remaining 2870 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4099 2.79 - 3.32: 13688 3.32 - 3.85: 26543 3.85 - 4.37: 30891 4.37 - 4.90: 54969 Nonbonded interactions: 130190 Sorted by model distance: nonbonded pdb=" OG SER B 378 " pdb=" OD1 ASN B 453 " model vdw 2.268 3.040 nonbonded pdb=" O ASN B 179 " pdb=" O2' G D -3 " model vdw 2.282 3.040 nonbonded pdb=" OH TYR B1645 " pdb=" OP1 C D 14 " model vdw 2.328 3.040 nonbonded pdb=" O THR C 702 " pdb=" OG SER C 706 " model vdw 2.329 3.040 nonbonded pdb=" OH TYR B 191 " pdb=" OD1 ASP B 386 " model vdw 2.333 3.040 ... (remaining 130185 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.890 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 : 0.010 0.486 17399 Z= 0.481 Angle : 1.027 27.530 23688 Z= 0.572 Chirality : 0.066 0.907 2563 Planarity : 0.008 0.088 2873 Dihedral : 17.322 168.585 6714 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 3.94 % Allowed : 12.64 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.15), residues: 1951 helix: -1.57 (0.15), residues: 692 sheet: 0.06 (0.31), residues: 267 loop : -2.35 (0.15), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 21 TYR 0.022 0.002 TYR C 75 PHE 0.025 0.002 PHE B 805 TRP 0.017 0.002 TRP C 443 HIS 0.006 0.001 HIS B 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.41 (17384) covalent geometry : angle 0.96864 / 0.57 (23673) hydrogen bonds : bond 0.16205 / 10.29 ( 645) hydrogen bonds : angle 5.80955 / 3.91 ( 1914) metal coordination : bond 0.25129 / 14.02 ( 15) metal coordination : angle 13.65040 / 7.35 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 414 time to evaluate : 0.649 Fit side-chains revert: symmetry clash REVERT: B 184 ASP cc_start: 0.7111 (m-30) cc_final: 0.6911 (m-30) REVERT: B 315 GLU cc_start: 0.7349 (tt0) cc_final: 0.7135 (mt-10) REVERT: B 318 ASP cc_start: 0.6904 (t0) cc_final: 0.6654 (t0) REVERT: B 351 LYS cc_start: 0.8446 (ttmm) cc_final: 0.8234 (tttt) REVERT: B 401 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8339 (mp) REVERT: B 516 ASP cc_start: 0.6923 (OUTLIER) cc_final: 0.6715 (p0) REVERT: B 547 ASP cc_start: 0.7474 (p0) cc_final: 0.7230 (p0) REVERT: B 651 PHE cc_start: 0.8405 (m-80) cc_final: 0.8188 (m-80) REVERT: B 698 ASP cc_start: 0.7080 (m-30) cc_final: 0.6833 (m-30) REVERT: B 807 THR cc_start: 0.8431 (p) cc_final: 0.8181 (m) REVERT: B 918 LYS cc_start: 0.5955 (mptt) cc_final: 0.5167 (mppt) REVERT: B 1400 ASP cc_start: 0.7527 (m-30) cc_final: 0.7319 (m-30) REVERT: B 1436 TYR cc_start: 0.8182 (t80) cc_final: 0.7922 (t80) REVERT: B 1565 ASP cc_start: 0.7212 (t0) cc_final: 0.6914 (m-30) REVERT: B 1660 ASP cc_start: 0.6454 (m-30) cc_final: 0.6123 (m-30) REVERT: B 1665 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7685 (mtpt) REVERT: B 1666 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7980 (mp) REVERT: C 167 ILE cc_start: 0.8093 (mt) cc_final: 0.7790 (mt) REVERT: C 267 LYS cc_start: 0.7937 (tttm) cc_final: 0.7646 (tttt) REVERT: C 352 CYS cc_start: 0.6977 (m) cc_final: 0.6451 (m) REVERT: C 483 ASP cc_start: 0.7792 (OUTLIER) cc_final: 0.7125 (m-30) REVERT: C 613 SER cc_start: 0.7965 (m) cc_final: 0.7743 (m) outliers start: 68 outliers final: 15 residues processed: 466 average time/residue: 0.5831 time to fit residues: 300.9229 Evaluate side-chains 365 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 346 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 401 LEU Chi-restraints excluded: chain B residue 473 SER Chi-restraints excluded: chain B residue 516 ASP Chi-restraints excluded: chain B residue 724 SER Chi-restraints excluded: chain B residue 831 SER Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 1424 ASP Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 129 SER Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 483 ASP Chi-restraints excluded: chain C residue 680 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN B 434 GLN B 453 ASN B 881 ASN B 900 ASN B 908 HIS B 917 ASN B 919 ASN B 924 HIS B1404 HIS B1438 ASN B1544 ASN B1596 GLN B1604 ASN C 147 ASN C 183 HIS C 513 ASN C 552 ASN C 572 ASN C 592 ASN C 602 ASN C 642 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107505 restraints weight = 23319.326| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.95 r_work: 0.3167 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17399 Z= 0.134 Angle : 0.588 11.691 23688 Z= 0.308 Chirality : 0.042 0.223 2563 Planarity : 0.005 0.071 2873 Dihedral : 11.785 176.391 2738 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.59 % Favored : 94.31 % Rotamer: Outliers : 4.12 % Allowed : 20.70 % Favored : 75.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.17), residues: 1951 helix: 0.66 (0.19), residues: 696 sheet: 0.33 (0.31), residues: 259 loop : -1.87 (0.16), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 260 TYR 0.013 0.001 TYR C 607 PHE 0.017 0.001 PHE B 546 TRP 0.013 0.001 TRP C 278 HIS 0.010 0.001 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (17384) covalent geometry : angle 0.58421 / 0.31 (23673) hydrogen bonds : bond 0.04159 / 2.76 ( 645) hydrogen bonds : angle 4.21150 / 2.85 ( 1914) metal coordination : bond 0.01003 / 0.53 ( 15) metal coordination : angle 2.60720 / 1.32 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 357 time to evaluate : 0.477 Fit side-chains REVERT: B 15 PHE cc_start: 0.8908 (m-80) cc_final: 0.8446 (m-80) REVERT: B 82 TRP cc_start: 0.8634 (t-100) cc_final: 0.8414 (t-100) REVERT: B 174 SER cc_start: 0.8601 (t) cc_final: 0.8362 (m) REVERT: B 315 GLU cc_start: 0.8331 (tt0) cc_final: 0.8034 (mt-10) REVERT: B 318 ASP cc_start: 0.7831 (t0) cc_final: 0.7631 (t0) REVERT: B 348 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.7449 (mp10) REVERT: B 351 LYS cc_start: 0.8646 (ttmm) cc_final: 0.8407 (tttt) REVERT: B 453 ASN cc_start: 0.7117 (OUTLIER) cc_final: 0.6888 (p0) REVERT: B 454 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7212 (mm-30) REVERT: B 547 ASP cc_start: 0.8193 (p0) cc_final: 0.7932 (p0) REVERT: B 624 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7608 (mm-30) REVERT: B 651 PHE cc_start: 0.8583 (m-80) cc_final: 0.8354 (m-80) REVERT: B 807 THR cc_start: 0.8545 (p) cc_final: 0.8300 (m) REVERT: B 918 LYS cc_start: 0.6178 (mptt) cc_final: 0.5225 (mppt) REVERT: B 932 LYS cc_start: 0.8076 (ptmm) cc_final: 0.7869 (pttp) REVERT: B 1436 TYR cc_start: 0.8597 (t80) cc_final: 0.8334 (t80) REVERT: B 1565 ASP cc_start: 0.7975 (t0) cc_final: 0.7431 (m-30) REVERT: B 1660 ASP cc_start: 0.7581 (m-30) cc_final: 0.7181 (m-30) REVERT: B 1665 LYS cc_start: 0.8527 (mtpt) cc_final: 0.8257 (mtpt) REVERT: C 102 GLU cc_start: 0.7457 (tt0) cc_final: 0.7139 (tt0) REVERT: C 148 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6778 (tt) REVERT: C 155 LYS cc_start: 0.6445 (tmmt) cc_final: 0.6198 (tmtt) REVERT: C 174 CYS cc_start: 0.7682 (m) cc_final: 0.7310 (p) REVERT: C 217 ASP cc_start: 0.7520 (t0) cc_final: 0.7266 (t0) REVERT: C 267 LYS cc_start: 0.8025 (tttm) cc_final: 0.7752 (tttt) REVERT: C 286 ASP cc_start: 0.7122 (m-30) cc_final: 0.6911 (m-30) REVERT: C 323 ARG cc_start: 0.8384 (mpt180) cc_final: 0.8076 (mtt90) REVERT: C 393 LEU cc_start: 0.8736 (mm) cc_final: 0.8441 (mt) REVERT: C 483 ASP cc_start: 0.8248 (m-30) cc_final: 0.7669 (m-30) outliers start: 71 outliers final: 26 residues processed: 400 average time/residue: 0.5673 time to fit residues: 251.8204 Evaluate side-chains 371 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 342 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 160 HIS Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 453 ASN Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1506 ASN Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 490 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 683 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 113 optimal weight: 4.9990 chunk 175 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN B 112 GLN B 453 ASN B 498 GLN B 673 GLN B 871 ASN B 908 HIS B 919 ASN B 986 ASN B1544 ASN B1573 ASN B1584 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.124214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.102995 restraints weight = 23637.011| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.95 r_work: 0.3088 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 17399 Z= 0.250 Angle : 0.686 11.179 23688 Z= 0.356 Chirality : 0.047 0.225 2563 Planarity : 0.006 0.070 2873 Dihedral : 11.783 175.142 2716 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.75 % Rotamer: Outliers : 5.68 % Allowed : 21.57 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.18), residues: 1951 helix: 1.08 (0.19), residues: 702 sheet: 0.46 (0.31), residues: 263 loop : -1.80 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 301 TYR 0.021 0.002 TYR B 149 PHE 0.024 0.002 PHE B 153 TRP 0.017 0.002 TRP C 278 HIS 0.010 0.002 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.25 (17384) covalent geometry : angle 0.68251 / 0.36 (23673) hydrogen bonds : bond 0.05648 / 3.75 ( 645) hydrogen bonds : angle 4.33442 / 2.96 ( 1914) metal coordination : bond 0.00557 / 0.33 ( 15) metal coordination : angle 2.75484 / 1.43 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 372 time to evaluate : 0.628 Fit side-chains REVERT: B 55 LYS cc_start: 0.8370 (OUTLIER) cc_final: 0.7906 (ptpt) REVERT: B 56 SER cc_start: 0.8715 (OUTLIER) cc_final: 0.8456 (t) REVERT: B 91 SER cc_start: 0.8581 (p) cc_final: 0.8361 (t) REVERT: B 174 SER cc_start: 0.8735 (t) cc_final: 0.8405 (p) REVERT: B 313 LYS cc_start: 0.8530 (mtpt) cc_final: 0.8302 (mtpp) REVERT: B 315 GLU cc_start: 0.8406 (tt0) cc_final: 0.8072 (mt-10) REVERT: B 348 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7343 (mp10) REVERT: B 421 ARG cc_start: 0.8067 (mtt-85) cc_final: 0.7851 (mtt-85) REVERT: B 454 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7287 (mm-30) REVERT: B 547 ASP cc_start: 0.8224 (p0) cc_final: 0.7972 (p0) REVERT: B 666 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8462 (tttm) REVERT: B 705 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7919 (mtp85) REVERT: B 836 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7877 (mt) REVERT: B 869 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7295 (t70) REVERT: B 879 MET cc_start: 0.7136 (mtp) cc_final: 0.6921 (mtt) REVERT: B 918 LYS cc_start: 0.6373 (mptt) cc_final: 0.5566 (mppt) REVERT: B 932 LYS cc_start: 0.8231 (ptmm) cc_final: 0.7987 (ptmm) REVERT: B 972 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6877 (tp30) REVERT: B 1436 TYR cc_start: 0.8776 (t80) cc_final: 0.8372 (t80) REVERT: B 1444 ILE cc_start: 0.8442 (mm) cc_final: 0.8203 (mp) REVERT: B 1459 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7547 (pt) REVERT: B 1491 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.8152 (ttp-170) REVERT: B 1504 GLU cc_start: 0.7901 (mp0) cc_final: 0.7605 (mp0) REVERT: B 1565 ASP cc_start: 0.7974 (t0) cc_final: 0.7560 (m-30) REVERT: B 1596 GLN cc_start: 0.8024 (mt0) cc_final: 0.7792 (mm110) REVERT: B 1665 LYS cc_start: 0.8673 (mtpt) cc_final: 0.8414 (mtpm) REVERT: B 1666 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8361 (mp) REVERT: C 42 LYS cc_start: 0.7417 (mttt) cc_final: 0.7147 (mtpp) REVERT: C 102 GLU cc_start: 0.7428 (tt0) cc_final: 0.7077 (tt0) REVERT: C 151 GLU cc_start: 0.7227 (mp0) cc_final: 0.6826 (mp0) REVERT: C 155 LYS cc_start: 0.6596 (tmmt) cc_final: 0.6345 (tmtt) REVERT: C 217 ASP cc_start: 0.7538 (t0) cc_final: 0.7297 (t0) REVERT: C 234 ASP cc_start: 0.7618 (t70) cc_final: 0.7168 (t0) REVERT: C 318 ASP cc_start: 0.8221 (t70) cc_final: 0.7982 (t0) REVERT: C 323 ARG cc_start: 0.8451 (mpt180) cc_final: 0.7936 (mtt-85) REVERT: C 352 CYS cc_start: 0.7518 (m) cc_final: 0.7144 (m) REVERT: C 472 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7957 (pp) REVERT: C 569 ASP cc_start: 0.7695 (t0) cc_final: 0.7411 (m-30) REVERT: C 628 GLU cc_start: 0.7669 (tt0) cc_final: 0.7446 (mt-10) outliers start: 98 outliers final: 40 residues processed: 422 average time/residue: 0.5930 time to fit residues: 276.8946 Evaluate side-chains 409 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 357 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 348 GLN Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 580 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 972 GLU Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1544 ASN Chi-restraints excluded: chain B residue 1573 ASN Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain B residue 1675 LYS Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 652 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 163 optimal weight: 0.0770 chunk 29 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 498 GLN B 615 ASN B 908 HIS B 919 ASN C 295 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 642 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.127187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105881 restraints weight = 23352.536| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.95 r_work: 0.3141 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17399 Z= 0.120 Angle : 0.559 11.039 23688 Z= 0.293 Chirality : 0.041 0.188 2563 Planarity : 0.005 0.066 2873 Dihedral : 11.536 176.628 2710 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.18 % Favored : 94.72 % Rotamer: Outliers : 4.35 % Allowed : 24.46 % Favored : 71.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 1951 helix: 1.64 (0.20), residues: 695 sheet: 0.40 (0.31), residues: 266 loop : -1.64 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 260 TYR 0.015 0.001 TYR C 607 PHE 0.013 0.001 PHE B 824 TRP 0.014 0.001 TRP C 443 HIS 0.013 0.001 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (17384) covalent geometry : angle 0.55615 / 0.29 (23673) hydrogen bonds : bond 0.03861 / 2.57 ( 645) hydrogen bonds : angle 4.07443 / 2.78 ( 1914) metal coordination : bond 0.00239 / 0.13 ( 15) metal coordination : angle 2.15660 / 1.13 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 352 time to evaluate : 0.393 Fit side-chains REVERT: B 7 ASN cc_start: 0.7675 (OUTLIER) cc_final: 0.7429 (m110) REVERT: B 91 SER cc_start: 0.8570 (p) cc_final: 0.8359 (t) REVERT: B 174 SER cc_start: 0.8637 (t) cc_final: 0.8317 (p) REVERT: B 313 LYS cc_start: 0.8497 (mtpt) cc_final: 0.8237 (mtpp) REVERT: B 454 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7208 (mm-30) REVERT: B 547 ASP cc_start: 0.8184 (p0) cc_final: 0.7947 (p0) REVERT: B 666 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8361 (tttm) REVERT: B 705 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7880 (mtp85) REVERT: B 788 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7986 (p0) REVERT: B 869 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7267 (t70) REVERT: B 918 LYS cc_start: 0.6380 (mptt) cc_final: 0.5537 (mppt) REVERT: B 932 LYS cc_start: 0.8249 (ptmm) cc_final: 0.8007 (ptmm) REVERT: B 1436 TYR cc_start: 0.8597 (t80) cc_final: 0.8327 (t80) REVERT: B 1444 ILE cc_start: 0.8348 (mm) cc_final: 0.8124 (mp) REVERT: B 1491 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.8107 (ttp-170) REVERT: B 1504 GLU cc_start: 0.7843 (mp0) cc_final: 0.7479 (mp0) REVERT: B 1565 ASP cc_start: 0.7900 (t0) cc_final: 0.7444 (m-30) REVERT: B 1660 ASP cc_start: 0.7827 (m-30) cc_final: 0.7587 (m-30) REVERT: B 1665 LYS cc_start: 0.8573 (mtpt) cc_final: 0.8336 (mtpt) REVERT: B 1668 ASP cc_start: 0.5809 (OUTLIER) cc_final: 0.5404 (t70) REVERT: C 42 LYS cc_start: 0.7426 (mttt) cc_final: 0.7150 (mtpp) REVERT: C 102 GLU cc_start: 0.7413 (tt0) cc_final: 0.7152 (mt-10) REVERT: C 151 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6905 (mp0) REVERT: C 217 ASP cc_start: 0.7471 (t0) cc_final: 0.7224 (t0) REVERT: C 224 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7817 (tmmm) REVERT: C 234 ASP cc_start: 0.7530 (t70) cc_final: 0.7095 (t0) REVERT: C 318 ASP cc_start: 0.8184 (t70) cc_final: 0.7933 (t0) REVERT: C 323 ARG cc_start: 0.8339 (mpt180) cc_final: 0.7976 (mtt-85) REVERT: C 413 MET cc_start: 0.8023 (mmp) cc_final: 0.7820 (tpt) REVERT: C 569 ASP cc_start: 0.7718 (t0) cc_final: 0.7456 (m-30) REVERT: C 628 GLU cc_start: 0.7665 (tt0) cc_final: 0.7453 (mt-10) outliers start: 75 outliers final: 37 residues processed: 388 average time/residue: 0.5621 time to fit residues: 241.1546 Evaluate side-chains 381 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 336 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 79 ASN Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1445 THR Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1509 THR Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 563 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 166 optimal weight: 3.9990 chunk 174 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 71 optimal weight: 0.0570 overall best weight: 1.9102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 498 GLN B 615 ASN B 871 ASN B 908 HIS B 919 ASN B1596 GLN C 46 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 642 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.121628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.100481 restraints weight = 23352.770| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.93 r_work: 0.3093 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 17399 Z= 0.238 Angle : 0.666 14.068 23688 Z= 0.344 Chirality : 0.047 0.202 2563 Planarity : 0.005 0.066 2873 Dihedral : 11.690 175.342 2710 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.30 % Favored : 93.64 % Rotamer: Outliers : 4.93 % Allowed : 24.00 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.18), residues: 1951 helix: 1.49 (0.20), residues: 699 sheet: 0.47 (0.31), residues: 266 loop : -1.72 (0.17), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 260 TYR 0.019 0.002 TYR B 149 PHE 0.019 0.002 PHE B 153 TRP 0.015 0.002 TRP B1530 HIS 0.017 0.002 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.24 (17384) covalent geometry : angle 0.66329 / 0.34 (23673) hydrogen bonds : bond 0.05329 / 3.57 ( 645) hydrogen bonds : angle 4.26494 / 2.91 ( 1914) metal coordination : bond 0.00564 / 0.33 ( 15) metal coordination : angle 2.44480 / 1.30 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 353 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: B 7 ASN cc_start: 0.7749 (OUTLIER) cc_final: 0.7453 (m110) REVERT: B 55 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7981 (ptpt) REVERT: B 56 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8486 (t) REVERT: B 313 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8227 (mtpp) REVERT: B 315 GLU cc_start: 0.8451 (tt0) cc_final: 0.8173 (mt-10) REVERT: B 454 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 663 GLU cc_start: 0.7931 (tp30) cc_final: 0.7636 (tp30) REVERT: B 666 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8415 (tttm) REVERT: B 687 THR cc_start: 0.8044 (m) cc_final: 0.7651 (p) REVERT: B 705 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7908 (mtp85) REVERT: B 788 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.8000 (p0) REVERT: B 836 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7858 (mt) REVERT: B 869 ASP cc_start: 0.7499 (OUTLIER) cc_final: 0.7298 (t0) REVERT: B 908 HIS cc_start: 0.8258 (t-90) cc_final: 0.8017 (t70) REVERT: B 918 LYS cc_start: 0.6498 (mptt) cc_final: 0.5580 (mppt) REVERT: B 932 LYS cc_start: 0.8325 (ptmm) cc_final: 0.8097 (ptmm) REVERT: B 1436 TYR cc_start: 0.8761 (t80) cc_final: 0.8349 (t80) REVERT: B 1444 ILE cc_start: 0.8484 (mm) cc_final: 0.8239 (mp) REVERT: B 1491 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8222 (ttp-170) REVERT: B 1504 GLU cc_start: 0.7949 (mp0) cc_final: 0.7561 (mp0) REVERT: B 1565 ASP cc_start: 0.7991 (t0) cc_final: 0.7548 (m-30) REVERT: B 1644 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8300 (ptm-80) REVERT: B 1666 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8507 (mp) REVERT: C 42 LYS cc_start: 0.7469 (mttt) cc_final: 0.7158 (mtpp) REVERT: C 102 GLU cc_start: 0.7453 (tt0) cc_final: 0.7206 (mt-10) REVERT: C 151 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: C 174 CYS cc_start: 0.7853 (m) cc_final: 0.7452 (p) REVERT: C 175 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7370 (mt-10) REVERT: C 217 ASP cc_start: 0.7517 (t0) cc_final: 0.7273 (t0) REVERT: C 224 LYS cc_start: 0.8259 (OUTLIER) cc_final: 0.7804 (tmmm) REVERT: C 234 ASP cc_start: 0.7616 (t70) cc_final: 0.7166 (t0) REVERT: C 318 ASP cc_start: 0.8159 (t70) cc_final: 0.7951 (t0) REVERT: C 323 ARG cc_start: 0.8440 (mpt180) cc_final: 0.7962 (mtt-85) REVERT: C 569 ASP cc_start: 0.7720 (t0) cc_final: 0.7512 (m-30) REVERT: C 628 GLU cc_start: 0.7684 (tt0) cc_final: 0.7447 (mt-10) outliers start: 85 outliers final: 48 residues processed: 396 average time/residue: 0.5792 time to fit residues: 253.1998 Evaluate side-chains 395 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 334 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 836 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 869 ASP Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1445 THR Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1490 ILE Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1514 LYS Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1644 ARG Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 699 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 112 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 86 optimal weight: 0.0020 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 498 GLN B 615 ASN B 919 ASN B 986 ASN B1596 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 642 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.126319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.105340 restraints weight = 23426.267| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.94 r_work: 0.3133 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17399 Z= 0.130 Angle : 0.577 13.983 23688 Z= 0.299 Chirality : 0.042 0.197 2563 Planarity : 0.005 0.064 2873 Dihedral : 11.567 175.975 2710 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 4.35 % Allowed : 25.62 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.18), residues: 1951 helix: 1.75 (0.20), residues: 698 sheet: 0.49 (0.31), residues: 266 loop : -1.64 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 260 TYR 0.015 0.001 TYR C 607 PHE 0.014 0.001 PHE B 824 TRP 0.013 0.001 TRP C 443 HIS 0.006 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (17384) covalent geometry : angle 0.57508 / 0.30 (23673) hydrogen bonds : bond 0.04064 / 2.72 ( 645) hydrogen bonds : angle 4.10192 / 2.80 ( 1914) metal coordination : bond 0.00248 / 0.14 ( 15) metal coordination : angle 2.16191 / 1.14 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 343 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: B 7 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.7459 (m110) REVERT: B 56 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8488 (t) REVERT: B 174 SER cc_start: 0.8654 (t) cc_final: 0.8348 (p) REVERT: B 313 LYS cc_start: 0.8441 (mtpt) cc_final: 0.8231 (mtmm) REVERT: B 315 GLU cc_start: 0.8463 (tt0) cc_final: 0.8113 (mt-10) REVERT: B 454 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7305 (mm-30) REVERT: B 547 ASP cc_start: 0.8181 (p0) cc_final: 0.7938 (p0) REVERT: B 625 ARG cc_start: 0.8522 (mpt180) cc_final: 0.8287 (mpt180) REVERT: B 663 GLU cc_start: 0.7920 (tp30) cc_final: 0.7632 (tp30) REVERT: B 666 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8384 (tttm) REVERT: B 687 THR cc_start: 0.7971 (m) cc_final: 0.7578 (p) REVERT: B 705 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7896 (mtp85) REVERT: B 788 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7997 (p0) REVERT: B 836 LEU cc_start: 0.8044 (mm) cc_final: 0.7755 (mt) REVERT: B 918 LYS cc_start: 0.6457 (mptt) cc_final: 0.5534 (mppt) REVERT: B 932 LYS cc_start: 0.8318 (ptmm) cc_final: 0.8081 (ptmm) REVERT: B 985 LYS cc_start: 0.8357 (mttp) cc_final: 0.8118 (mttm) REVERT: B 1436 TYR cc_start: 0.8669 (t80) cc_final: 0.8383 (t80) REVERT: B 1444 ILE cc_start: 0.8403 (mm) cc_final: 0.8162 (mp) REVERT: B 1491 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.8167 (ttp-170) REVERT: B 1504 GLU cc_start: 0.7903 (mp0) cc_final: 0.7512 (mp0) REVERT: B 1565 ASP cc_start: 0.7949 (t0) cc_final: 0.7480 (m-30) REVERT: B 1644 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8312 (ptm-80) REVERT: C 42 LYS cc_start: 0.7457 (mttt) cc_final: 0.7191 (mtpp) REVERT: C 102 GLU cc_start: 0.7392 (tt0) cc_final: 0.7136 (mt-10) REVERT: C 151 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: C 174 CYS cc_start: 0.7756 (m) cc_final: 0.7380 (p) REVERT: C 175 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7331 (mt-10) REVERT: C 217 ASP cc_start: 0.7472 (t0) cc_final: 0.7236 (t0) REVERT: C 224 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7754 (tmmm) REVERT: C 234 ASP cc_start: 0.7573 (t70) cc_final: 0.7087 (t0) REVERT: C 318 ASP cc_start: 0.8168 (t70) cc_final: 0.7917 (t0) REVERT: C 323 ARG cc_start: 0.8317 (mpt180) cc_final: 0.7876 (mtt90) REVERT: C 413 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7801 (tpt) REVERT: C 569 ASP cc_start: 0.7667 (t0) cc_final: 0.7398 (m-30) REVERT: C 628 GLU cc_start: 0.7660 (tt0) cc_final: 0.7430 (mt-10) outliers start: 75 outliers final: 44 residues processed: 381 average time/residue: 0.6017 time to fit residues: 253.2505 Evaluate side-chains 401 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 346 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 123 LYS Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 830 PHE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1445 THR Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1613 LEU Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1644 ARG Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1656 ILE Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 224 LYS Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 685 ASN Chi-restraints excluded: chain C residue 699 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 111 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 63 optimal weight: 0.3980 chunk 85 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 106 optimal weight: 0.1980 chunk 46 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN B 871 ASN B 908 HIS B 919 ASN B1596 GLN C 46 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.125321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.104309 restraints weight = 23480.441| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.94 r_work: 0.3110 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17399 Z= 0.175 Angle : 0.610 13.981 23688 Z= 0.315 Chirality : 0.044 0.179 2563 Planarity : 0.005 0.064 2873 Dihedral : 11.575 175.744 2710 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.74 % Favored : 94.21 % Rotamer: Outliers : 4.64 % Allowed : 25.28 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.18), residues: 1951 helix: 1.72 (0.20), residues: 699 sheet: 0.53 (0.31), residues: 256 loop : -1.66 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 260 TYR 0.016 0.002 TYR C 607 PHE 0.015 0.002 PHE B 546 TRP 0.013 0.001 TRP B1530 HIS 0.014 0.001 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.17 (17384) covalent geometry : angle 0.60768 / 0.31 (23673) hydrogen bonds : bond 0.04537 / 3.04 ( 645) hydrogen bonds : angle 4.11479 / 2.82 ( 1914) metal coordination : bond 0.00409 / 0.24 ( 15) metal coordination : angle 2.28187 / 1.21 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 343 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: B 7 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7482 (m110) REVERT: B 55 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7979 (ptpt) REVERT: B 56 SER cc_start: 0.8736 (OUTLIER) cc_final: 0.8490 (t) REVERT: B 313 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8220 (mtmm) REVERT: B 315 GLU cc_start: 0.8460 (tt0) cc_final: 0.8097 (mt-10) REVERT: B 454 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7301 (mm-30) REVERT: B 547 ASP cc_start: 0.8173 (p0) cc_final: 0.7934 (p0) REVERT: B 663 GLU cc_start: 0.7887 (tp30) cc_final: 0.7593 (tp30) REVERT: B 666 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8394 (tttm) REVERT: B 687 THR cc_start: 0.8006 (m) cc_final: 0.7607 (p) REVERT: B 705 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7899 (mtp85) REVERT: B 788 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7981 (p0) REVERT: B 836 LEU cc_start: 0.8084 (mm) cc_final: 0.7802 (mt) REVERT: B 908 HIS cc_start: 0.8352 (t-90) cc_final: 0.8047 (t-90) REVERT: B 918 LYS cc_start: 0.6410 (mptt) cc_final: 0.5426 (mppt) REVERT: B 932 LYS cc_start: 0.8331 (ptmm) cc_final: 0.8081 (ptmm) REVERT: B 968 ASP cc_start: 0.8097 (t0) cc_final: 0.7889 (t0) REVERT: B 1436 TYR cc_start: 0.8704 (t80) cc_final: 0.8380 (t80) REVERT: B 1444 ILE cc_start: 0.8404 (mm) cc_final: 0.8188 (mp) REVERT: B 1451 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7222 (tp30) REVERT: B 1491 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8213 (ttp-170) REVERT: B 1504 GLU cc_start: 0.7951 (mp0) cc_final: 0.7582 (mp0) REVERT: B 1565 ASP cc_start: 0.7984 (t0) cc_final: 0.7476 (m-30) REVERT: B 1644 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8302 (ptm-80) REVERT: B 1666 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8239 (mp) REVERT: C 30 GLU cc_start: 0.7326 (tt0) cc_final: 0.6918 (pt0) REVERT: C 102 GLU cc_start: 0.7430 (tt0) cc_final: 0.7186 (mt-10) REVERT: C 151 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: C 174 CYS cc_start: 0.7744 (m) cc_final: 0.7374 (p) REVERT: C 175 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: C 217 ASP cc_start: 0.7476 (t0) cc_final: 0.7250 (t0) REVERT: C 318 ASP cc_start: 0.8170 (t70) cc_final: 0.7914 (t0) REVERT: C 323 ARG cc_start: 0.8377 (mpt180) cc_final: 0.7919 (mtt-85) REVERT: C 413 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.7831 (tpt) REVERT: C 569 ASP cc_start: 0.7704 (t0) cc_final: 0.7471 (m-30) REVERT: C 628 GLU cc_start: 0.7661 (tt0) cc_final: 0.7436 (mt-10) outliers start: 80 outliers final: 47 residues processed: 382 average time/residue: 0.5884 time to fit residues: 247.9103 Evaluate side-chains 397 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 337 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 464 LYS Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1445 THR Chi-restraints excluded: chain B residue 1451 GLU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1599 ILE Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1644 ARG Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 685 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 112 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 498 GLN B 919 ASN B1573 ASN B1596 GLN C 119 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105298 restraints weight = 23554.515| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.94 r_work: 0.3130 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17399 Z= 0.139 Angle : 0.585 13.872 23688 Z= 0.302 Chirality : 0.042 0.197 2563 Planarity : 0.005 0.063 2873 Dihedral : 11.525 176.024 2710 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.31 % Rotamer: Outliers : 4.75 % Allowed : 25.45 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.18), residues: 1951 helix: 1.82 (0.20), residues: 699 sheet: 0.55 (0.31), residues: 256 loop : -1.61 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 260 TYR 0.016 0.001 TYR C 428 PHE 0.014 0.001 PHE B 824 TRP 0.012 0.001 TRP C 443 HIS 0.006 0.001 HIS B 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (17384) covalent geometry : angle 0.58294 / 0.30 (23673) hydrogen bonds : bond 0.04053 / 2.72 ( 645) hydrogen bonds : angle 4.04472 / 2.77 ( 1914) metal coordination : bond 0.00300 / 0.17 ( 15) metal coordination : angle 2.21806 / 1.18 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 331 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: B 7 ASN cc_start: 0.7708 (OUTLIER) cc_final: 0.7444 (m110) REVERT: B 55 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7970 (ptpt) REVERT: B 56 SER cc_start: 0.8734 (OUTLIER) cc_final: 0.8485 (t) REVERT: B 313 LYS cc_start: 0.8425 (mtpt) cc_final: 0.8212 (mtmm) REVERT: B 315 GLU cc_start: 0.8457 (tt0) cc_final: 0.8088 (mt-10) REVERT: B 454 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7250 (mm-30) REVERT: B 503 CYS cc_start: 0.6964 (OUTLIER) cc_final: 0.6713 (p) REVERT: B 547 ASP cc_start: 0.8162 (p0) cc_final: 0.7926 (p0) REVERT: B 663 GLU cc_start: 0.7911 (tp30) cc_final: 0.7610 (tp30) REVERT: B 666 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8354 (tttm) REVERT: B 687 THR cc_start: 0.7998 (m) cc_final: 0.7591 (p) REVERT: B 705 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7896 (mtp85) REVERT: B 788 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7994 (p0) REVERT: B 908 HIS cc_start: 0.8405 (t-90) cc_final: 0.8085 (t-90) REVERT: B 918 LYS cc_start: 0.6409 (mptt) cc_final: 0.5455 (mppt) REVERT: B 932 LYS cc_start: 0.8317 (ptmm) cc_final: 0.8069 (ptmm) REVERT: B 1436 TYR cc_start: 0.8638 (t80) cc_final: 0.8306 (t80) REVERT: B 1444 ILE cc_start: 0.8384 (mm) cc_final: 0.8166 (mp) REVERT: B 1491 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.8174 (ttp-170) REVERT: B 1504 GLU cc_start: 0.7900 (mp0) cc_final: 0.7541 (mp0) REVERT: B 1512 MET cc_start: 0.8401 (mtm) cc_final: 0.8097 (ttt) REVERT: B 1565 ASP cc_start: 0.7977 (t0) cc_final: 0.7434 (m-30) REVERT: B 1666 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8227 (mp) REVERT: B 1668 ASP cc_start: 0.5877 (OUTLIER) cc_final: 0.5438 (t70) REVERT: B 1691 PHE cc_start: 0.7953 (t80) cc_final: 0.7587 (t80) REVERT: C 30 GLU cc_start: 0.7335 (tt0) cc_final: 0.6975 (pt0) REVERT: C 102 GLU cc_start: 0.7423 (tt0) cc_final: 0.7171 (mt-10) REVERT: C 151 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: C 174 CYS cc_start: 0.7745 (m) cc_final: 0.7385 (p) REVERT: C 175 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7317 (mt-10) REVERT: C 217 ASP cc_start: 0.7464 (t0) cc_final: 0.7236 (t0) REVERT: C 234 ASP cc_start: 0.7560 (t70) cc_final: 0.7154 (t0) REVERT: C 318 ASP cc_start: 0.8159 (t70) cc_final: 0.7911 (t0) REVERT: C 323 ARG cc_start: 0.8319 (mpt180) cc_final: 0.7870 (mtt90) REVERT: C 413 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7822 (tpt) REVERT: C 569 ASP cc_start: 0.7680 (t0) cc_final: 0.7442 (m-30) REVERT: C 641 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6804 (pt0) outliers start: 82 outliers final: 48 residues processed: 376 average time/residue: 0.6369 time to fit residues: 264.1465 Evaluate side-chains 393 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 331 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1445 THR Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1573 ASN Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 685 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 68 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 168 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN B 348 GLN B 498 GLN B 919 ASN B1596 GLN C 46 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.123934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.102933 restraints weight = 23501.669| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.95 r_work: 0.3092 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2935 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 17399 Z= 0.228 Angle : 0.670 13.910 23688 Z= 0.345 Chirality : 0.046 0.203 2563 Planarity : 0.005 0.063 2873 Dihedral : 11.621 175.274 2710 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.20 % Favored : 93.75 % Rotamer: Outliers : 4.81 % Allowed : 25.39 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.18), residues: 1951 helix: 1.63 (0.19), residues: 699 sheet: 0.53 (0.31), residues: 256 loop : -1.68 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 260 TYR 0.019 0.002 TYR B 149 PHE 0.018 0.002 PHE B 153 TRP 0.013 0.002 TRP B1530 HIS 0.008 0.002 HIS B 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.23 (17384) covalent geometry : angle 0.66812 / 0.34 (23673) hydrogen bonds : bond 0.05110 / 3.43 ( 645) hydrogen bonds : angle 4.19392 / 2.87 ( 1914) metal coordination : bond 0.00634 / 0.37 ( 15) metal coordination : angle 2.27524 / 1.22 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 339 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: B 7 ASN cc_start: 0.7702 (OUTLIER) cc_final: 0.7422 (m110) REVERT: B 55 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7998 (ptpt) REVERT: B 56 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8477 (t) REVERT: B 313 LYS cc_start: 0.8453 (mtpt) cc_final: 0.8226 (mtmm) REVERT: B 315 GLU cc_start: 0.8414 (tt0) cc_final: 0.8043 (mt-10) REVERT: B 454 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7321 (mm-30) REVERT: B 503 CYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6892 (p) REVERT: B 547 ASP cc_start: 0.8216 (p0) cc_final: 0.7981 (p0) REVERT: B 666 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8431 (tttm) REVERT: B 687 THR cc_start: 0.8031 (m) cc_final: 0.7610 (p) REVERT: B 705 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7907 (mtp85) REVERT: B 788 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7998 (p0) REVERT: B 836 LEU cc_start: 0.8148 (mm) cc_final: 0.7921 (mt) REVERT: B 908 HIS cc_start: 0.8493 (t-90) cc_final: 0.8068 (t-90) REVERT: B 918 LYS cc_start: 0.6451 (mptt) cc_final: 0.5386 (mppt) REVERT: B 932 LYS cc_start: 0.8395 (ptmm) cc_final: 0.8159 (ptmm) REVERT: B 985 LYS cc_start: 0.8424 (mttp) cc_final: 0.8176 (mttm) REVERT: B 1436 TYR cc_start: 0.8777 (t80) cc_final: 0.8375 (t80) REVERT: B 1444 ILE cc_start: 0.8473 (mm) cc_final: 0.8226 (mp) REVERT: B 1491 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8229 (ttp-170) REVERT: B 1492 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7216 (mp-120) REVERT: B 1504 GLU cc_start: 0.7964 (mp0) cc_final: 0.7596 (mp0) REVERT: B 1512 MET cc_start: 0.8415 (mtm) cc_final: 0.8052 (ttt) REVERT: B 1565 ASP cc_start: 0.8005 (t0) cc_final: 0.7534 (m-30) REVERT: B 1666 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8367 (mp) REVERT: C 30 GLU cc_start: 0.7357 (tt0) cc_final: 0.6978 (pt0) REVERT: C 102 GLU cc_start: 0.7458 (tt0) cc_final: 0.7202 (mt-10) REVERT: C 151 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: C 174 CYS cc_start: 0.7802 (m) cc_final: 0.7395 (p) REVERT: C 175 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7332 (mt-10) REVERT: C 217 ASP cc_start: 0.7546 (t0) cc_final: 0.7306 (t0) REVERT: C 234 ASP cc_start: 0.7546 (t70) cc_final: 0.7168 (t0) REVERT: C 318 ASP cc_start: 0.8140 (t70) cc_final: 0.7892 (t0) REVERT: C 323 ARG cc_start: 0.8419 (mpt180) cc_final: 0.8116 (mtt90) REVERT: C 413 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7806 (tpt) REVERT: C 452 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7594 (tp30) REVERT: C 628 GLU cc_start: 0.7665 (tt0) cc_final: 0.7396 (mt-10) REVERT: C 641 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6943 (pt0) outliers start: 83 outliers final: 49 residues processed: 382 average time/residue: 0.6170 time to fit residues: 260.8967 Evaluate side-chains 396 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 333 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 329 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1445 THR Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1492 GLN Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 303 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 685 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 31 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 197 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 192 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 498 GLN B 871 ASN B 919 ASN B1573 ASN B1596 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.126591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105555 restraints weight = 23587.903| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.96 r_work: 0.3137 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17399 Z= 0.124 Angle : 0.588 13.921 23688 Z= 0.303 Chirality : 0.042 0.196 2563 Planarity : 0.005 0.062 2873 Dihedral : 11.501 176.022 2710 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.64 % Favored : 94.31 % Rotamer: Outliers : 3.71 % Allowed : 26.49 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.18), residues: 1951 helix: 1.89 (0.20), residues: 699 sheet: 0.64 (0.31), residues: 261 loop : -1.59 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 260 TYR 0.017 0.001 TYR C 428 PHE 0.015 0.001 PHE B 824 TRP 0.015 0.001 TRP C 443 HIS 0.006 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (17384) covalent geometry : angle 0.58559 / 0.30 (23673) hydrogen bonds : bond 0.03874 / 2.59 ( 645) hydrogen bonds : angle 4.02371 / 2.76 ( 1914) metal coordination : bond 0.00234 / 0.13 ( 15) metal coordination : angle 2.33952 / 1.25 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3902 Ramachandran restraints generated. 1951 Oldfield, 0 Emsley, 1951 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 331 time to evaluate : 0.633 Fit side-chains REVERT: B 7 ASN cc_start: 0.7676 (OUTLIER) cc_final: 0.7426 (m110) REVERT: B 55 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7954 (ptpt) REVERT: B 56 SER cc_start: 0.8721 (OUTLIER) cc_final: 0.8484 (t) REVERT: B 132 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8516 (mt) REVERT: B 313 LYS cc_start: 0.8428 (mtpt) cc_final: 0.8221 (mtmm) REVERT: B 315 GLU cc_start: 0.8427 (tt0) cc_final: 0.8056 (mt-10) REVERT: B 434 GLN cc_start: 0.8207 (pt0) cc_final: 0.7973 (pt0) REVERT: B 454 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7172 (mm-30) REVERT: B 503 CYS cc_start: 0.6876 (OUTLIER) cc_final: 0.6649 (p) REVERT: B 547 ASP cc_start: 0.8201 (p0) cc_final: 0.7967 (p0) REVERT: B 666 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8359 (tttm) REVERT: B 687 THR cc_start: 0.8000 (m) cc_final: 0.7579 (p) REVERT: B 705 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7904 (mtp85) REVERT: B 788 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7991 (p0) REVERT: B 836 LEU cc_start: 0.8035 (mm) cc_final: 0.7802 (mt) REVERT: B 918 LYS cc_start: 0.6385 (mptt) cc_final: 0.4977 (tppp) REVERT: B 932 LYS cc_start: 0.8372 (ptmm) cc_final: 0.8133 (ptmm) REVERT: B 1436 TYR cc_start: 0.8628 (t80) cc_final: 0.8329 (t80) REVERT: B 1444 ILE cc_start: 0.8394 (mm) cc_final: 0.8161 (mp) REVERT: B 1458 VAL cc_start: 0.8371 (OUTLIER) cc_final: 0.8166 (t) REVERT: B 1491 ARG cc_start: 0.8463 (ttp-170) cc_final: 0.8200 (ttp-170) REVERT: B 1512 MET cc_start: 0.8378 (mtm) cc_final: 0.8048 (ttt) REVERT: B 1565 ASP cc_start: 0.7938 (t0) cc_final: 0.7439 (m-30) REVERT: B 1666 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8221 (mp) REVERT: C 30 GLU cc_start: 0.7305 (tt0) cc_final: 0.6930 (pt0) REVERT: C 102 GLU cc_start: 0.7391 (tt0) cc_final: 0.7130 (mt-10) REVERT: C 151 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: C 155 LYS cc_start: 0.6181 (tmmt) cc_final: 0.5702 (tmtt) REVERT: C 174 CYS cc_start: 0.7811 (m) cc_final: 0.7455 (p) REVERT: C 175 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7353 (mt-10) REVERT: C 217 ASP cc_start: 0.7503 (t0) cc_final: 0.7271 (t0) REVERT: C 234 ASP cc_start: 0.7539 (t70) cc_final: 0.7136 (t0) REVERT: C 318 ASP cc_start: 0.8126 (t70) cc_final: 0.7861 (t0) REVERT: C 323 ARG cc_start: 0.8285 (mpt180) cc_final: 0.7838 (mtt90) REVERT: C 413 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7831 (tpt) REVERT: C 641 GLU cc_start: 0.7087 (OUTLIER) cc_final: 0.6864 (pt0) outliers start: 64 outliers final: 42 residues processed: 364 average time/residue: 0.6625 time to fit residues: 266.5978 Evaluate side-chains 379 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 323 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 318 ASP Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 409 GLU Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 503 CYS Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 581 GLU Chi-restraints excluded: chain B residue 596 SER Chi-restraints excluded: chain B residue 605 LYS Chi-restraints excluded: chain B residue 666 LYS Chi-restraints excluded: chain B residue 705 ARG Chi-restraints excluded: chain B residue 711 ASN Chi-restraints excluded: chain B residue 763 GLU Chi-restraints excluded: chain B residue 788 ASP Chi-restraints excluded: chain B residue 826 ILE Chi-restraints excluded: chain B residue 842 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1445 THR Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1474 GLU Chi-restraints excluded: chain B residue 1573 ASN Chi-restraints excluded: chain B residue 1643 VAL Chi-restraints excluded: chain B residue 1647 VAL Chi-restraints excluded: chain B residue 1666 LEU Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain C residue 45 ILE Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 246 ASP Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 413 MET Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 683 LYS Chi-restraints excluded: chain C residue 685 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 21 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 433 GLN B 498 GLN B 919 ASN B1573 ASN B1596 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 476 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105485 restraints weight = 23592.374| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.96 r_work: 0.3133 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 17399 Z= 0.174 Angle : 0.811 58.948 23688 Z= 0.466 Chirality : 0.043 0.228 2563 Planarity : 0.005 0.064 2873 Dihedral : 11.500 176.013 2710 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 3.59 % Allowed : 26.78 % Favored : 69.62 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.18), residues: 1951 helix: 1.89 (0.20), residues: 699 sheet: 0.65 (0.31), residues: 261 loop : -1.59 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 260 TYR 0.015 0.001 TYR C 428 PHE 0.015 0.001 PHE B 824 TRP 0.013 0.001 TRP C 443 HIS 0.006 0.001 HIS B 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (17384) covalent geometry : angle 0.80908 / 0.47 (23673) hydrogen bonds : bond 0.03937 / 2.63 ( 645) hydrogen bonds : angle 4.02351 / 2.76 ( 1914) metal coordination : bond 0.00291 / 0.17 ( 15) metal coordination : angle 2.33657 / 1.25 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5954.51 seconds wall clock time: 102 minutes 4.77 seconds (6124.77 seconds total)