Starting phenix.real_space_refine on Sat Sep 12 16:49:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xsr_33432/09_2026/7xsr_33432.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xsr_33432/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7xsr_33432/09_2026/7xsr_33432.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xsr_33432/09_2026/7xsr_33432.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xsr_33432/09_2026/7xsr_33432.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xsr_33432/09_2026/7xsr_33432.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xsr_33432/09_2026/7xsr_33432.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xsr_33432/09_2026/7xsr_33432.map" } 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-2.2.1-6174/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: {'RNAv2': 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: {'RNAv2': 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: 3.00, 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: 1.47 Conformation dependent library (CDL) restraints added in 655.2 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: 1.48 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: 3.75 Time building geometry restraints manager: 1.91 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 1.20e-02 6.94e+03 1.20e+02 bond pdb=" O3' C D 9 " pdb=" P U D 10 " ideal model delta sigma weight residual 1.607 1.481 0.126 1.20e-02 6.94e+03 1.10e+02 bond pdb=" O3' U D 8 " pdb=" P C D 9 " ideal model delta sigma weight residual 1.607 1.488 0.119 1.20e-02 6.94e+03 9.85e+01 bond pdb=" O3' U D -2 " pdb=" P A D -1 " ideal model delta sigma weight residual 1.607 1.491 0.116 1.20e-02 6.94e+03 9.42e+01 bond pdb=" O3' G D -9 " pdb=" P U D -8 " ideal model delta sigma weight residual 1.607 1.493 0.114 1.20e-02 6.94e+03 9.01e+01 ... (remaining 17379 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 23365 3.76 - 7.52: 272 7.52 - 11.29: 29 11.29 - 15.05: 4 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 113.80 132.27 -18.47 3.00e+00 1.11e-01 3.79e+01 angle pdb=" O3' G A 38 " pdb=" C3' G A 38 " pdb=" C2' G A 38 " ideal model delta sigma weight residual 113.80 101.73 12.07 2.00e+00 2.50e-01 3.64e+01 angle pdb=" C ILE B1656 " pdb=" N GLU B1657 " pdb=" CA GLU B1657 " ideal model delta sigma weight residual 120.79 129.17 -8.38 1.39e+00 5.18e-01 3.64e+01 angle pdb=" C LYS C 59 " pdb=" N LYS C 60 " pdb=" CA LYS C 60 " ideal model delta sigma weight residual 120.82 129.68 -8.86 1.50e+00 4.44e-01 3.49e+01 angle pdb=" O2' C D 1 " pdb=" C2' C D 1 " pdb=" C1' C D 1 " ideal model delta sigma weight residual 108.20 91.70 16.50 3.00e+00 1.11e-01 3.03e+01 ... (remaining 23668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8834 17.94 - 35.89: 1050 35.89 - 53.83: 333 53.83 - 71.77: 106 71.77 - 89.72: 27 Dihedral angle restraints: 10350 sinusoidal: 4691 harmonic: 5659 Sorted by residual: dihedral pdb=" C4' G D -17 " pdb=" C3' G D -17 " pdb=" C2' G D -17 " pdb=" C1' G D -17 " ideal model delta sinusoidal sigma weight residual 36.34 -40.50 76.85 1 3.10e+00 1.04e-01 7.72e+02 dihedral pdb=" C4' A D -12 " pdb=" C3' A D -12 " pdb=" C2' A D -12 " pdb=" C1' A D -12 " ideal model delta sinusoidal sigma weight residual 36.35 -39.60 75.94 1 3.10e+00 1.04e-01 7.56e+02 dihedral pdb=" C4' G A 38 " pdb=" C3' G A 38 " pdb=" C2' G A 38 " pdb=" C1' G A 38 " ideal model delta sinusoidal sigma weight residual 36.35 -38.43 74.77 1 3.10e+00 1.04e-01 7.37e+02 ... (remaining 10347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.186: 2492 0.186 - 0.371: 67 0.371 - 0.557: 2 0.557 - 0.742: 1 0.742 - 0.928: 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 -2.50 -1.57 -0.93 2.00e-01 2.50e+01 2.15e+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 -2.79 -2.19 -0.60 2.00e-01 2.50e+01 8.96e+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 -2.79 -2.32 -0.47 2.00e-01 2.50e+01 5.41e+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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.280 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.570 ------------------------------------------------------------------------------- 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= 0.498 Angle : 1.066 27.530 23688 Z= 0.534 Chirality : 0.071 0.928 2563 Planarity : 0.008 0.088 2873 Dihedral : 18.166 89.715 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 0.00744 / 0.43 (17384) covalent geometry : angle 1.00997 / 0.53 (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 : 0.550 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: 0.6124 time to fit residues: 315.5492 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 : 0.597 ------------------------------------------------------------------------------- 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: 0.9990 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.130180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109528 restraints weight = 23436.620| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.93 r_work: 0.3204 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17399 Z= 0.162 Angle : 0.887 18.366 23688 Z= 0.399 Chirality : 0.088 1.127 2563 Planarity : 0.006 0.072 2873 Dihedral : 11.810 143.822 2738 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.84 % Favored : 94.05 % Rotamer: Outliers : 4.06 % Allowed : 20.87 % Favored : 75.07 % 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: -1.01 (0.17), residues: 1951 helix: 0.56 (0.19), residues: 696 sheet: 0.34 (0.31), residues: 259 loop : -1.92 (0.16), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 476 TYR 0.014 0.001 TYR C 607 PHE 0.018 0.001 PHE B 546 TRP 0.013 0.001 TRP C 278 HIS 0.008 0.001 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (17384) covalent geometry : angle 0.88457 / 0.40 (23673) hydrogen bonds : bond 0.04582 / 3.04 ( 645) hydrogen bonds : angle 4.28532 / 2.90 ( 1914) metal coordination : bond 0.01001 / 0.53 ( 15) metal coordination : angle 2.98691 / 1.49 ( 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 425 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 355 time to evaluate : 0.613 Fit side-chains REVERT: B 15 PHE cc_start: 0.8906 (m-80) cc_final: 0.8410 (m-80) REVERT: B 174 SER cc_start: 0.8619 (t) cc_final: 0.8384 (m) REVERT: B 315 GLU cc_start: 0.8361 (tt0) cc_final: 0.8070 (mt-10) REVERT: B 348 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7428 (mp10) REVERT: B 351 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8425 (tttt) REVERT: B 509 MET cc_start: 0.8780 (mmm) cc_final: 0.8519 (mmp) REVERT: B 547 ASP cc_start: 0.8168 (p0) cc_final: 0.7907 (p0) REVERT: B 581 GLU cc_start: 0.7603 (pt0) cc_final: 0.7362 (pt0) REVERT: B 624 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7654 (mm-30) REVERT: B 651 PHE cc_start: 0.8586 (m-80) cc_final: 0.8355 (m-80) REVERT: B 653 GLU cc_start: 0.7461 (tp30) cc_final: 0.7222 (tp30) REVERT: B 698 ASP cc_start: 0.7458 (m-30) cc_final: 0.7243 (m-30) REVERT: B 807 THR cc_start: 0.8528 (p) cc_final: 0.8288 (m) REVERT: B 918 LYS cc_start: 0.6152 (mptt) cc_final: 0.5263 (mppt) REVERT: B 932 LYS cc_start: 0.8092 (ptmm) cc_final: 0.7882 (pttp) REVERT: B 1436 TYR cc_start: 0.8630 (t80) cc_final: 0.8357 (t80) REVERT: B 1491 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7128 (ttt180) REVERT: B 1504 GLU cc_start: 0.7743 (mp0) cc_final: 0.7441 (mp0) REVERT: B 1565 ASP cc_start: 0.8003 (t0) cc_final: 0.7463 (m-30) REVERT: B 1660 ASP cc_start: 0.7562 (m-30) cc_final: 0.7151 (m-30) REVERT: B 1665 LYS cc_start: 0.8523 (mtpt) cc_final: 0.8223 (mtpt) REVERT: B 1666 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8390 (mp) REVERT: C 148 LEU cc_start: 0.7029 (OUTLIER) cc_final: 0.6817 (tt) REVERT: C 174 CYS cc_start: 0.7641 (m) cc_final: 0.7306 (p) REVERT: C 217 ASP cc_start: 0.7526 (t0) cc_final: 0.7265 (t0) REVERT: C 267 LYS cc_start: 0.8037 (tttm) cc_final: 0.7759 (tttt) REVERT: C 286 ASP cc_start: 0.7090 (m-30) cc_final: 0.6875 (m-30) REVERT: C 393 LEU cc_start: 0.8741 (mm) cc_final: 0.8448 (mt) REVERT: C 483 ASP cc_start: 0.8253 (m-30) cc_final: 0.7685 (m-30) outliers start: 70 outliers final: 24 residues processed: 398 average time/residue: 0.6159 time to fit residues: 271.9257 Evaluate side-chains 367 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 339 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASP 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 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 969 THR Chi-restraints excluded: chain B residue 1458 VAL Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1506 ASN Chi-restraints excluded: chain B residue 1666 LEU 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 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: 0.9990 chunk 175 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 673 GLN B 908 HIS B 919 ASN B1544 ASN B1573 ASN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107473 restraints weight = 23521.398| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.94 r_work: 0.3164 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 17399 Z= 0.198 Angle : 0.812 12.432 23688 Z= 0.376 Chirality : 0.073 0.845 2563 Planarity : 0.005 0.069 2873 Dihedral : 11.713 160.488 2717 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.69 % Favored : 94.21 % Rotamer: Outliers : 4.81 % Allowed : 22.03 % Favored : 73.16 % 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: -0.50 (0.18), residues: 1951 helix: 1.18 (0.20), residues: 702 sheet: 0.43 (0.31), residues: 261 loop : -1.75 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 260 TYR 0.017 0.002 TYR B 149 PHE 0.020 0.002 PHE B 546 TRP 0.015 0.002 TRP C 278 HIS 0.010 0.002 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (17384) covalent geometry : angle 0.80948 / 0.38 (23673) hydrogen bonds : bond 0.04987 / 3.30 ( 645) hydrogen bonds : angle 4.23366 / 2.88 ( 1914) metal coordination : bond 0.00420 / 0.24 ( 15) metal coordination : angle 2.55796 / 1.32 ( 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 447 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 364 time to evaluate : 0.609 Fit side-chains REVERT: B 15 PHE cc_start: 0.8891 (m-80) cc_final: 0.8454 (m-80) REVERT: B 55 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.7897 (ptpt) REVERT: B 147 LYS cc_start: 0.8012 (ttmm) cc_final: 0.7788 (mtpp) REVERT: B 174 SER cc_start: 0.8681 (t) cc_final: 0.8342 (p) REVERT: B 229 LYS cc_start: 0.8247 (mtpt) cc_final: 0.8014 (mtmp) REVERT: B 315 GLU cc_start: 0.8441 (tt0) cc_final: 0.8073 (mt-10) REVERT: B 348 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7338 (mp10) REVERT: B 547 ASP cc_start: 0.8174 (p0) cc_final: 0.7927 (p0) REVERT: B 624 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7752 (mm-30) REVERT: B 651 PHE cc_start: 0.8647 (m-80) cc_final: 0.8363 (m-80) REVERT: B 666 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8424 (tttm) REVERT: B 698 ASP cc_start: 0.7531 (m-30) cc_final: 0.7314 (m-30) REVERT: B 705 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7916 (mtp85) REVERT: B 869 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7268 (t70) REVERT: B 918 LYS cc_start: 0.6298 (mptt) cc_final: 0.5476 (mppt) REVERT: B 932 LYS cc_start: 0.8232 (ptmm) cc_final: 0.7979 (ptmm) REVERT: B 1436 TYR cc_start: 0.8712 (t80) cc_final: 0.8333 (t80) REVERT: B 1444 ILE cc_start: 0.8382 (mm) cc_final: 0.8134 (mp) REVERT: B 1491 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7186 (ttt180) REVERT: B 1539 LEU cc_start: 0.8125 (mt) cc_final: 0.7904 (mp) REVERT: B 1565 ASP cc_start: 0.7923 (t0) cc_final: 0.7507 (m-30) REVERT: B 1596 GLN cc_start: 0.8012 (mt0) cc_final: 0.7811 (mm110) REVERT: B 1665 LYS cc_start: 0.8623 (mtpt) cc_final: 0.8386 (mtpm) REVERT: B 1671 ASN cc_start: 0.7732 (p0) cc_final: 0.7529 (p0) REVERT: C 42 LYS cc_start: 0.7387 (mttt) cc_final: 0.7120 (mtpp) REVERT: C 102 GLU cc_start: 0.7418 (tt0) cc_final: 0.7067 (tt0) REVERT: C 151 GLU cc_start: 0.7179 (mp0) cc_final: 0.6773 (mp0) REVERT: C 174 CYS cc_start: 0.7833 (m) cc_final: 0.7499 (p) REVERT: C 217 ASP cc_start: 0.7505 (t0) cc_final: 0.7241 (t0) REVERT: C 224 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7876 (tmmm) REVERT: C 234 ASP cc_start: 0.7580 (t70) cc_final: 0.7147 (t0) REVERT: C 286 ASP cc_start: 0.7139 (m-30) cc_final: 0.6921 (m-30) REVERT: C 318 ASP cc_start: 0.8186 (t70) cc_final: 0.7922 (t0) REVERT: C 393 LEU cc_start: 0.8761 (mm) cc_final: 0.8549 (mt) REVERT: C 413 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7838 (tpt) REVERT: C 472 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7863 (pp) REVERT: C 569 ASP cc_start: 0.7742 (t0) cc_final: 0.7487 (m-30) REVERT: C 628 GLU cc_start: 0.7664 (tt0) cc_final: 0.7445 (mt-10) outliers start: 83 outliers final: 39 residues processed: 408 average time/residue: 0.6457 time to fit residues: 291.1592 Evaluate side-chains 397 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 349 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 55 LYS 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 348 GLN 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 553 GLU Chi-restraints excluded: chain B residue 612 TRP Chi-restraints excluded: chain B residue 636 GLU 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 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 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 1497 ILE 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 1672 LEU Chi-restraints excluded: chain B residue 1679 LYS Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 145 LEU 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 413 MET Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 563 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 163 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 154 optimal weight: 0.3980 chunk 56 optimal weight: 0.4980 chunk 85 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 498 GLN B 908 HIS B 919 ASN ** B1544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1584 GLN C 295 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 642 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.129354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.108641 restraints weight = 23343.821| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.93 r_work: 0.3189 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17399 Z= 0.150 Angle : 0.744 11.469 23688 Z= 0.346 Chirality : 0.068 0.781 2563 Planarity : 0.005 0.067 2873 Dihedral : 11.495 161.758 2711 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 4.70 % Allowed : 24.17 % Favored : 71.13 % 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: -0.21 (0.18), residues: 1951 helix: 1.60 (0.20), residues: 696 sheet: 0.38 (0.31), residues: 266 loop : -1.65 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1644 TYR 0.014 0.001 TYR C 607 PHE 0.014 0.001 PHE B 546 TRP 0.012 0.001 TRP C 443 HIS 0.013 0.001 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (17384) covalent geometry : angle 0.74258 / 0.35 (23673) hydrogen bonds : bond 0.04175 / 2.77 ( 645) hydrogen bonds : angle 4.10172 / 2.80 ( 1914) metal coordination : bond 0.00289 / 0.16 ( 15) metal coordination : angle 2.16515 / 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 430 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 349 time to evaluate : 0.662 Fit side-chains REVERT: B 7 ASN cc_start: 0.7680 (OUTLIER) cc_final: 0.7430 (m110) REVERT: B 509 MET cc_start: 0.8776 (mmm) cc_final: 0.8554 (mmp) REVERT: B 547 ASP cc_start: 0.8146 (p0) cc_final: 0.7901 (p0) REVERT: B 651 PHE cc_start: 0.8644 (m-80) cc_final: 0.8440 (m-80) REVERT: B 666 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8389 (tttm) REVERT: B 687 THR cc_start: 0.7941 (m) cc_final: 0.7548 (p) REVERT: B 698 ASP cc_start: 0.7551 (m-30) cc_final: 0.7349 (m-30) REVERT: B 705 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7880 (mtp85) REVERT: B 788 ASP cc_start: 0.8189 (OUTLIER) cc_final: 0.7971 (p0) REVERT: B 869 ASP cc_start: 0.7457 (OUTLIER) cc_final: 0.7241 (t70) REVERT: B 918 LYS cc_start: 0.6355 (mptt) cc_final: 0.5548 (mppt) REVERT: B 932 LYS cc_start: 0.8259 (ptmm) cc_final: 0.8008 (ptmm) REVERT: B 968 ASP cc_start: 0.8031 (t0) cc_final: 0.7778 (t0) REVERT: B 1436 TYR cc_start: 0.8635 (t80) cc_final: 0.8374 (t80) REVERT: B 1444 ILE cc_start: 0.8335 (mm) cc_final: 0.8091 (mp) REVERT: B 1491 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7056 (ttt180) REVERT: B 1504 GLU cc_start: 0.7798 (mp0) cc_final: 0.7563 (mp0) REVERT: B 1565 ASP cc_start: 0.7907 (t0) cc_final: 0.7461 (m-30) REVERT: B 1660 ASP cc_start: 0.7760 (m-30) cc_final: 0.7242 (m-30) REVERT: B 1665 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8110 (mtpt) REVERT: B 1668 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.5378 (t70) REVERT: C 42 LYS cc_start: 0.7426 (mttt) cc_final: 0.7142 (mtpp) REVERT: C 102 GLU cc_start: 0.7394 (tt0) cc_final: 0.7129 (mt-10) REVERT: C 151 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: C 174 CYS cc_start: 0.7803 (m) cc_final: 0.7523 (p) REVERT: C 217 ASP cc_start: 0.7475 (t0) cc_final: 0.7225 (t0) REVERT: C 224 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7896 (tmmm) REVERT: C 234 ASP cc_start: 0.7550 (t70) cc_final: 0.7117 (t0) REVERT: C 286 ASP cc_start: 0.7107 (m-30) cc_final: 0.6886 (m-30) REVERT: C 318 ASP cc_start: 0.8186 (t70) cc_final: 0.7950 (t0) REVERT: C 393 LEU cc_start: 0.8746 (mm) cc_final: 0.8534 (mt) REVERT: C 413 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7857 (tpt) REVERT: C 628 GLU cc_start: 0.7687 (tt0) cc_final: 0.7471 (mt-10) outliers start: 81 outliers final: 44 residues processed: 393 average time/residue: 0.6534 time to fit residues: 284.7453 Evaluate side-chains 388 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 334 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 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 349 SER 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 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 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 1468 ILE Chi-restraints excluded: chain B residue 1471 ASP 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 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 B residue 1679 LYS 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 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 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 555 ILE Chi-restraints excluded: chain C residue 652 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 166 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 135 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 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 B 986 ASN B1573 ASN B1596 GLN 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.128991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108266 restraints weight = 23282.097| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.92 r_work: 0.3184 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17399 Z= 0.159 Angle : 0.748 13.903 23688 Z= 0.348 Chirality : 0.067 0.775 2563 Planarity : 0.005 0.066 2873 Dihedral : 11.518 162.469 2711 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.41 % Rotamer: Outliers : 4.99 % Allowed : 24.12 % Favored : 70.90 % 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: -0.09 (0.18), residues: 1951 helix: 1.73 (0.20), residues: 695 sheet: 0.44 (0.31), residues: 266 loop : -1.61 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 260 TYR 0.014 0.001 TYR C 607 PHE 0.014 0.001 PHE B 153 TRP 0.012 0.001 TRP B1530 HIS 0.013 0.001 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (17384) covalent geometry : angle 0.74676 / 0.35 (23673) hydrogen bonds : bond 0.04239 / 2.82 ( 645) hydrogen bonds : angle 4.06097 / 2.78 ( 1914) metal coordination : bond 0.00302 / 0.17 ( 15) metal coordination : angle 2.16057 / 1.15 ( 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 424 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 338 time to evaluate : 0.691 Fit side-chains REVERT: B 7 ASN cc_start: 0.7674 (OUTLIER) cc_final: 0.7428 (m110) REVERT: B 55 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7936 (ptpt) REVERT: B 291 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7502 (mm-30) REVERT: B 315 GLU cc_start: 0.8443 (tt0) cc_final: 0.8180 (mt-10) REVERT: B 454 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7129 (mm-30) REVERT: B 547 ASP cc_start: 0.8153 (p0) cc_final: 0.7917 (p0) REVERT: B 651 PHE cc_start: 0.8634 (m-80) cc_final: 0.8430 (m-80) REVERT: B 666 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8365 (tttm) REVERT: B 698 ASP cc_start: 0.7548 (m-30) cc_final: 0.7341 (m-30) REVERT: B 705 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7869 (mtp85) REVERT: B 727 HIS cc_start: 0.6502 (OUTLIER) cc_final: 0.5763 (p90) REVERT: B 788 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7965 (p0) REVERT: B 918 LYS cc_start: 0.6411 (mptt) cc_final: 0.5550 (mppt) REVERT: B 932 LYS cc_start: 0.8289 (ptmm) cc_final: 0.8060 (ptmm) REVERT: B 968 ASP cc_start: 0.8033 (t0) cc_final: 0.7777 (t0) REVERT: B 985 LYS cc_start: 0.8314 (mttp) cc_final: 0.8105 (mttm) REVERT: B 1436 TYR cc_start: 0.8642 (t80) cc_final: 0.8344 (t80) REVERT: B 1444 ILE cc_start: 0.8355 (mm) cc_final: 0.8112 (mp) REVERT: B 1458 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8234 (t) REVERT: B 1491 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8163 (ttp-170) REVERT: B 1504 GLU cc_start: 0.7826 (mp0) cc_final: 0.7532 (mp0) REVERT: B 1565 ASP cc_start: 0.7930 (t0) cc_final: 0.7485 (m-30) REVERT: B 1665 LYS cc_start: 0.8543 (mtpt) cc_final: 0.8342 (mtmt) REVERT: B 1668 ASP cc_start: 0.5799 (OUTLIER) cc_final: 0.5362 (t70) REVERT: C 42 LYS cc_start: 0.7432 (mttt) cc_final: 0.7138 (mtpp) REVERT: C 102 GLU cc_start: 0.7379 (tt0) cc_final: 0.7122 (mt-10) REVERT: C 151 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6793 (mp0) REVERT: C 174 CYS cc_start: 0.7817 (m) cc_final: 0.7563 (p) REVERT: C 175 GLU cc_start: 0.7710 (tt0) cc_final: 0.7438 (mt-10) REVERT: C 217 ASP cc_start: 0.7482 (t0) cc_final: 0.7237 (t0) REVERT: C 224 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7838 (tmmm) REVERT: C 234 ASP cc_start: 0.7534 (t70) cc_final: 0.7099 (t0) REVERT: C 286 ASP cc_start: 0.7083 (m-30) cc_final: 0.6858 (m-30) REVERT: C 318 ASP cc_start: 0.8182 (t70) cc_final: 0.7948 (t0) REVERT: C 413 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7848 (tpt) REVERT: C 628 GLU cc_start: 0.7641 (tt0) cc_final: 0.7407 (mt-10) REVERT: C 641 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6821 (pt0) outliers start: 86 outliers final: 48 residues processed: 391 average time/residue: 0.6496 time to fit residues: 280.6589 Evaluate side-chains 396 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 335 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 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 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 518 VAL 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 727 HIS 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 929 SER 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 1467 SER Chi-restraints excluded: chain B residue 1468 ILE Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1509 THR 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 1656 ILE Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain B residue 1679 LYS 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 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 391 LEU 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 517 CYS Chi-restraints excluded: chain C residue 555 ILE Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 652 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 112 optimal weight: 3.9990 chunk 104 optimal weight: 0.0980 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 153 optimal weight: 0.0030 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 0.0570 chunk 23 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 198 optimal weight: 2.9990 overall best weight: 1.0312 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 498 GLN B 615 ASN B 908 HIS B 919 ASN B1573 ASN B1596 GLN C 357 GLN C 476 ASN C 541 ASN C 642 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.106171 restraints weight = 23490.690| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.94 r_work: 0.3190 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17399 Z= 0.156 Angle : 0.738 14.046 23688 Z= 0.344 Chirality : 0.066 0.768 2563 Planarity : 0.005 0.065 2873 Dihedral : 11.498 163.116 2711 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 4.70 % Allowed : 24.93 % Favored : 70.38 % 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: -0.03 (0.18), residues: 1951 helix: 1.78 (0.20), residues: 697 sheet: 0.49 (0.31), residues: 266 loop : -1.58 (0.17), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 260 TYR 0.014 0.001 TYR C 607 PHE 0.014 0.001 PHE B 557 TRP 0.012 0.001 TRP B1530 HIS 0.014 0.001 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 (17384) covalent geometry : angle 0.73670 / 0.34 (23673) hydrogen bonds : bond 0.04150 / 2.77 ( 645) hydrogen bonds : angle 4.03854 / 2.76 ( 1914) metal coordination : bond 0.00304 / 0.18 ( 15) metal coordination : angle 2.12444 / 1.13 ( 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 426 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 345 time to evaluate : 0.620 Fit side-chains REVERT: B 7 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7477 (m110) REVERT: B 15 PHE cc_start: 0.8855 (m-80) cc_final: 0.8450 (m-80) REVERT: B 291 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7503 (mm-30) REVERT: B 315 GLU cc_start: 0.8462 (tt0) cc_final: 0.8177 (mt-10) REVERT: B 378 SER cc_start: 0.6610 (OUTLIER) cc_final: 0.6321 (p) REVERT: B 452 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7188 (mt) REVERT: B 454 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7134 (mm-30) REVERT: B 547 ASP cc_start: 0.8159 (p0) cc_final: 0.7921 (p0) REVERT: B 651 PHE cc_start: 0.8644 (m-80) cc_final: 0.8417 (m-80) REVERT: B 666 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8364 (tttm) REVERT: B 698 ASP cc_start: 0.7540 (m-30) cc_final: 0.7324 (m-30) REVERT: B 705 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7887 (mtp85) REVERT: B 788 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7963 (p0) REVERT: B 908 HIS cc_start: 0.8181 (t-90) cc_final: 0.7722 (t70) REVERT: B 918 LYS cc_start: 0.6459 (mptt) cc_final: 0.5565 (mppt) REVERT: B 932 LYS cc_start: 0.8336 (ptmm) cc_final: 0.8088 (ptmm) REVERT: B 968 ASP cc_start: 0.7995 (t0) cc_final: 0.7782 (t0) REVERT: B 1436 TYR cc_start: 0.8648 (t80) cc_final: 0.8347 (t80) REVERT: B 1444 ILE cc_start: 0.8378 (mm) cc_final: 0.8134 (mp) REVERT: B 1491 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7155 (ttt180) REVERT: B 1504 GLU cc_start: 0.7841 (mp0) cc_final: 0.7500 (mp0) REVERT: B 1565 ASP cc_start: 0.7939 (t0) cc_final: 0.7411 (m-30) REVERT: B 1668 ASP cc_start: 0.5754 (OUTLIER) cc_final: 0.5328 (t70) REVERT: C 41 ARG cc_start: 0.7219 (mtm-85) cc_final: 0.7000 (mtm-85) REVERT: C 102 GLU cc_start: 0.7408 (tt0) cc_final: 0.7169 (mt-10) REVERT: C 151 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6755 (mp0) REVERT: C 174 CYS cc_start: 0.7769 (m) cc_final: 0.7563 (p) REVERT: C 175 GLU cc_start: 0.7675 (tt0) cc_final: 0.7470 (mt-10) REVERT: C 217 ASP cc_start: 0.7484 (t0) cc_final: 0.7243 (t0) REVERT: C 224 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7820 (tmmm) REVERT: C 234 ASP cc_start: 0.7516 (t70) cc_final: 0.7046 (t0) REVERT: C 286 ASP cc_start: 0.7116 (m-30) cc_final: 0.6902 (m-30) REVERT: C 318 ASP cc_start: 0.8146 (t70) cc_final: 0.7916 (t0) REVERT: C 413 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7878 (tpt) REVERT: C 628 GLU cc_start: 0.7664 (tt0) cc_final: 0.7443 (mt-10) REVERT: C 641 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6791 (pt0) outliers start: 81 outliers final: 51 residues processed: 388 average time/residue: 0.6490 time to fit residues: 278.7828 Evaluate side-chains 404 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 341 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 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 329 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 518 VAL Chi-restraints excluded: chain B residue 548 ILE 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 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 1467 SER Chi-restraints excluded: chain B residue 1491 ARG Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1509 THR Chi-restraints excluded: chain B residue 1514 LYS Chi-restraints excluded: chain B residue 1573 ASN Chi-restraints excluded: chain B residue 1599 ILE 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 B residue 1672 LEU Chi-restraints excluded: chain B residue 1679 LYS 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 195 ASP 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 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 555 ILE Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 641 GLU Chi-restraints excluded: chain C residue 652 ILE Chi-restraints excluded: chain C residue 685 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 111 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 192 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 46 optimal weight: 0.0470 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 348 GLN B 498 GLN B 615 ASN B 871 ASN B 919 ASN B1596 GLN C 46 ASN C 197 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.130318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109671 restraints weight = 23453.073| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.94 r_work: 0.3206 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3199 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= 0.132 Angle : 0.708 14.015 23688 Z= 0.330 Chirality : 0.063 0.717 2563 Planarity : 0.005 0.064 2873 Dihedral : 11.438 163.690 2710 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.23 % Favored : 94.72 % Rotamer: Outliers : 4.41 % Allowed : 25.57 % 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: 1.92 (0.20), residues: 695 sheet: 0.50 (0.31), residues: 266 loop : -1.53 (0.17), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 120 TYR 0.015 0.001 TYR C 428 PHE 0.015 0.001 PHE B1570 TRP 0.012 0.001 TRP C 443 HIS 0.006 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (17384) covalent geometry : angle 0.70637 / 0.33 (23673) hydrogen bonds : bond 0.03810 / 2.54 ( 645) hydrogen bonds : angle 3.97836 / 2.73 ( 1914) metal coordination : bond 0.00266 / 0.15 ( 15) metal coordination : angle 2.06482 / 1.11 ( 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 416 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 340 time to evaluate : 0.602 Fit side-chains REVERT: B 7 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7469 (m110) REVERT: B 15 PHE cc_start: 0.8856 (m-80) cc_final: 0.8440 (m-80) REVERT: B 55 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7944 (ptpt) REVERT: B 291 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7505 (mm-30) REVERT: B 315 GLU cc_start: 0.8450 (tt0) cc_final: 0.8154 (mt-10) REVERT: B 378 SER cc_start: 0.6569 (OUTLIER) cc_final: 0.6293 (p) REVERT: B 452 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7132 (mt) REVERT: B 454 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7063 (mm-30) REVERT: B 509 MET cc_start: 0.8792 (mmm) cc_final: 0.8580 (mmp) REVERT: B 547 ASP cc_start: 0.8166 (p0) cc_final: 0.7928 (p0) REVERT: B 651 PHE cc_start: 0.8631 (m-80) cc_final: 0.8409 (m-80) REVERT: B 666 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8323 (tttm) REVERT: B 698 ASP cc_start: 0.7546 (m-30) cc_final: 0.7339 (m-30) REVERT: B 705 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.7878 (mtp85) REVERT: B 788 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7976 (p0) REVERT: B 908 HIS cc_start: 0.8265 (t-90) cc_final: 0.8040 (t70) REVERT: B 918 LYS cc_start: 0.6439 (mptt) cc_final: 0.5496 (mppt) REVERT: B 932 LYS cc_start: 0.8351 (ptmm) cc_final: 0.8086 (ptmm) REVERT: B 968 ASP cc_start: 0.7991 (t0) cc_final: 0.7788 (t0) REVERT: B 985 LYS cc_start: 0.8289 (mttp) cc_final: 0.8076 (mttm) REVERT: B 1436 TYR cc_start: 0.8579 (t80) cc_final: 0.8354 (t80) REVERT: B 1444 ILE cc_start: 0.8365 (mm) cc_final: 0.8140 (mp) REVERT: B 1491 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.8090 (ttp-170) REVERT: B 1504 GLU cc_start: 0.7828 (mp0) cc_final: 0.7518 (mp0) REVERT: B 1565 ASP cc_start: 0.7953 (t0) cc_final: 0.7395 (m-30) REVERT: B 1668 ASP cc_start: 0.5742 (OUTLIER) cc_final: 0.5316 (t70) REVERT: C 30 GLU cc_start: 0.7306 (tt0) cc_final: 0.7011 (pt0) REVERT: C 102 GLU cc_start: 0.7376 (tt0) cc_final: 0.7142 (mt-10) REVERT: C 151 GLU cc_start: 0.7195 (OUTLIER) cc_final: 0.6740 (mp0) REVERT: C 175 GLU cc_start: 0.7677 (tt0) cc_final: 0.7456 (mt-10) REVERT: C 217 ASP cc_start: 0.7480 (t0) cc_final: 0.7249 (t0) REVERT: C 224 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7793 (tmmm) REVERT: C 234 ASP cc_start: 0.7516 (t70) cc_final: 0.7051 (t0) REVERT: C 286 ASP cc_start: 0.7094 (m-30) cc_final: 0.6889 (m-30) REVERT: C 318 ASP cc_start: 0.8141 (t70) cc_final: 0.7900 (t0) REVERT: C 413 MET cc_start: 0.8086 (OUTLIER) cc_final: 0.7884 (tpt) REVERT: C 628 GLU cc_start: 0.7629 (tt0) cc_final: 0.7400 (mt-10) REVERT: C 641 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6758 (pt0) outliers start: 76 outliers final: 51 residues processed: 377 average time/residue: 0.6350 time to fit residues: 264.7343 Evaluate side-chains 405 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 341 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 74 LEU Chi-restraints excluded: chain B residue 79 ASN 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 337 THR Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 452 ILE 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 1454 LEU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1467 SER Chi-restraints excluded: chain B residue 1468 ILE 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 1509 THR Chi-restraints excluded: chain B residue 1514 LYS Chi-restraints excluded: chain B residue 1599 ILE 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 B residue 1672 LEU Chi-restraints excluded: chain B residue 1679 LYS 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 197 GLN 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 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 555 ILE Chi-restraints excluded: chain C residue 563 ASP Chi-restraints excluded: chain C residue 641 GLU 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: 4.9990 chunk 21 optimal weight: 0.5980 chunk 190 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 534 ASN B 615 ASN B 919 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.131522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.110757 restraints weight = 23333.341| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.93 r_work: 0.3225 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17399 Z= 0.121 Angle : 0.694 14.031 23688 Z= 0.324 Chirality : 0.061 0.674 2563 Planarity : 0.005 0.063 2873 Dihedral : 11.363 163.672 2710 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.07 % Favored : 94.87 % Rotamer: Outliers : 4.23 % Allowed : 25.74 % 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: 0.12 (0.18), residues: 1951 helix: 1.91 (0.20), residues: 703 sheet: 0.47 (0.31), residues: 266 loop : -1.48 (0.17), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 260 TYR 0.016 0.001 TYR C 428 PHE 0.016 0.001 PHE B1570 TRP 0.013 0.001 TRP C 443 HIS 0.006 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (17384) covalent geometry : angle 0.69251 / 0.32 (23673) hydrogen bonds : bond 0.03593 / 2.39 ( 645) hydrogen bonds : angle 3.90310 / 2.68 ( 1914) metal coordination : bond 0.00217 / 0.12 ( 15) metal coordination : angle 2.03169 / 1.09 ( 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 415 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 342 time to evaluate : 0.524 Fit side-chains REVERT: B 7 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.7395 (m110) REVERT: B 15 PHE cc_start: 0.8836 (m-80) cc_final: 0.8465 (m-80) REVERT: B 55 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7898 (ptpt) REVERT: B 291 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7490 (mm-30) REVERT: B 315 GLU cc_start: 0.8466 (tt0) cc_final: 0.8154 (mt-10) REVERT: B 378 SER cc_start: 0.6614 (OUTLIER) cc_final: 0.6345 (p) REVERT: B 452 ILE cc_start: 0.7621 (OUTLIER) cc_final: 0.7100 (mt) REVERT: B 454 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7052 (mm-30) REVERT: B 509 MET cc_start: 0.8772 (mmm) cc_final: 0.8547 (mmp) REVERT: B 547 ASP cc_start: 0.8162 (p0) cc_final: 0.7925 (p0) REVERT: B 651 PHE cc_start: 0.8608 (m-80) cc_final: 0.8402 (m-80) REVERT: B 666 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8328 (tttm) REVERT: B 698 ASP cc_start: 0.7541 (m-30) cc_final: 0.7332 (m-30) REVERT: B 705 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.7882 (mtp85) REVERT: B 788 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7995 (p0) REVERT: B 836 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7831 (mt) REVERT: B 918 LYS cc_start: 0.6394 (mptt) cc_final: 0.5504 (mppt) REVERT: B 932 LYS cc_start: 0.8323 (ptmm) cc_final: 0.8064 (ptmm) REVERT: B 985 LYS cc_start: 0.8249 (mttp) cc_final: 0.8040 (mttm) REVERT: B 1444 ILE cc_start: 0.8345 (mm) cc_final: 0.8108 (mp) REVERT: B 1565 ASP cc_start: 0.7932 (t0) cc_final: 0.7371 (m-30) REVERT: B 1668 ASP cc_start: 0.5670 (OUTLIER) cc_final: 0.5257 (t70) REVERT: B 1691 PHE cc_start: 0.7855 (t80) cc_final: 0.7496 (t80) REVERT: C 30 GLU cc_start: 0.7257 (tt0) cc_final: 0.6993 (pt0) REVERT: C 102 GLU cc_start: 0.7347 (tt0) cc_final: 0.7110 (mt-10) REVERT: C 151 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6661 (mp0) REVERT: C 155 LYS cc_start: 0.6175 (tmmt) cc_final: 0.5603 (tmtt) REVERT: C 217 ASP cc_start: 0.7451 (t0) cc_final: 0.7214 (t0) REVERT: C 224 LYS cc_start: 0.8185 (OUTLIER) cc_final: 0.7780 (tmmm) REVERT: C 234 ASP cc_start: 0.7494 (t70) cc_final: 0.7032 (t0) REVERT: C 286 ASP cc_start: 0.7060 (m-30) cc_final: 0.6848 (m-30) REVERT: C 318 ASP cc_start: 0.8170 (t70) cc_final: 0.7918 (t0) REVERT: C 340 GLU cc_start: 0.5049 (OUTLIER) cc_final: 0.4773 (pm20) REVERT: C 628 GLU cc_start: 0.7629 (tt0) cc_final: 0.7412 (mt-10) REVERT: C 641 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6674 (pt0) outliers start: 73 outliers final: 42 residues processed: 377 average time/residue: 0.6446 time to fit residues: 268.8136 Evaluate side-chains 386 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 331 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 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 337 THR Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 475 LEU 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 836 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 1454 LEU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1467 SER 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 1514 LYS 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 B residue 1672 LEU Chi-restraints excluded: chain B residue 1679 LYS 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 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 340 GLU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 641 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 68 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 8 optimal weight: 0.0000 chunk 158 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 871 ASN B 908 HIS B 919 ASN B1573 ASN B1596 GLN C 357 GLN C 476 ASN 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 = 0.3597 r_free = 0.3597 target = 0.126581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.105640 restraints weight = 23361.222| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.94 r_work: 0.3181 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17399 Z= 0.181 Angle : 0.768 14.137 23688 Z= 0.359 Chirality : 0.067 0.821 2563 Planarity : 0.005 0.063 2873 Dihedral : 11.550 162.996 2710 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.16 % Rotamer: Outliers : 4.17 % Allowed : 25.57 % Favored : 70.26 % 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: 0.04 (0.18), residues: 1951 helix: 1.82 (0.20), residues: 698 sheet: 0.50 (0.31), residues: 266 loop : -1.52 (0.17), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 260 TYR 0.016 0.002 TYR C 428 PHE 0.017 0.002 PHE B 557 TRP 0.011 0.001 TRP B1530 HIS 0.018 0.002 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.18 (17384) covalent geometry : angle 0.76660 / 0.36 (23673) hydrogen bonds : bond 0.04471 / 2.99 ( 645) hydrogen bonds : angle 4.03878 / 2.77 ( 1914) metal coordination : bond 0.00417 / 0.24 ( 15) metal coordination : angle 2.20109 / 1.18 ( 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 416 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 344 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: B 7 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7465 (m110) REVERT: B 15 PHE cc_start: 0.8884 (m-80) cc_final: 0.8477 (m-80) REVERT: B 55 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7949 (ptpt) REVERT: B 291 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7506 (mm-30) REVERT: B 315 GLU cc_start: 0.8438 (tt0) cc_final: 0.8132 (mt-10) REVERT: B 378 SER cc_start: 0.6564 (OUTLIER) cc_final: 0.6282 (p) REVERT: B 452 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7129 (mt) REVERT: B 454 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7148 (mm-30) REVERT: B 473 SER cc_start: 0.8487 (OUTLIER) cc_final: 0.8217 (m) REVERT: B 547 ASP cc_start: 0.8145 (p0) cc_final: 0.7900 (p0) REVERT: B 651 PHE cc_start: 0.8647 (m-80) cc_final: 0.8422 (m-80) REVERT: B 666 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8372 (tttm) REVERT: B 698 ASP cc_start: 0.7531 (m-30) cc_final: 0.7321 (m-30) REVERT: B 705 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7889 (mtp85) REVERT: B 788 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7981 (p0) REVERT: B 836 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7854 (mt) REVERT: B 918 LYS cc_start: 0.6461 (mptt) cc_final: 0.5061 (mppt) REVERT: B 932 LYS cc_start: 0.8342 (ptmm) cc_final: 0.8093 (ptmm) REVERT: B 985 LYS cc_start: 0.8396 (mttp) cc_final: 0.8161 (mttm) REVERT: B 1565 ASP cc_start: 0.7962 (t0) cc_final: 0.7467 (m-30) REVERT: B 1668 ASP cc_start: 0.5823 (OUTLIER) cc_final: 0.5388 (t70) REVERT: C 30 GLU cc_start: 0.7309 (tt0) cc_final: 0.7031 (pt0) REVERT: C 102 GLU cc_start: 0.7424 (tt0) cc_final: 0.7165 (mt-10) REVERT: C 151 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6691 (mp0) REVERT: C 155 LYS cc_start: 0.6314 (tmmt) cc_final: 0.5838 (tmtt) REVERT: C 217 ASP cc_start: 0.7484 (t0) cc_final: 0.7253 (t0) REVERT: C 234 ASP cc_start: 0.7509 (t70) cc_final: 0.7041 (t0) REVERT: C 318 ASP cc_start: 0.8133 (t70) cc_final: 0.7892 (t0) REVERT: C 628 GLU cc_start: 0.7632 (tt0) cc_final: 0.7393 (mt-10) outliers start: 72 outliers final: 50 residues processed: 381 average time/residue: 0.6374 time to fit residues: 269.2001 Evaluate side-chains 399 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 338 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 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 329 LEU Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 378 SER 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 452 ILE Chi-restraints excluded: chain B residue 473 SER 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 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 836 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 866 ILE Chi-restraints excluded: chain B residue 929 SER Chi-restraints excluded: chain B residue 969 THR Chi-restraints excluded: chain B residue 975 LEU Chi-restraints excluded: chain B residue 1454 LEU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1467 SER Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1509 THR Chi-restraints excluded: chain B residue 1514 LYS 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 1656 ILE Chi-restraints excluded: chain B residue 1668 ASP Chi-restraints excluded: chain B residue 1672 LEU Chi-restraints excluded: chain B residue 1675 LYS Chi-restraints excluded: chain B residue 1679 LYS 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 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 340 GLU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 517 CYS 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: 0.6980 chunk 185 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 101 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1596 GLN C 46 ASN C 197 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.129518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108823 restraints weight = 23231.301| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.92 r_work: 0.3196 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17399 Z= 0.153 Angle : 0.746 14.043 23688 Z= 0.349 Chirality : 0.063 0.759 2563 Planarity : 0.005 0.063 2873 Dihedral : 11.555 164.094 2710 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.33 % Favored : 94.62 % Rotamer: Outliers : 3.59 % Allowed : 26.14 % Favored : 70.26 % 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: 0.04 (0.18), residues: 1951 helix: 1.79 (0.20), residues: 706 sheet: 0.55 (0.31), residues: 256 loop : -1.53 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 260 TYR 0.016 0.001 TYR C 428 PHE 0.013 0.001 PHE B 824 TRP 0.011 0.001 TRP B1530 HIS 0.010 0.001 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (17384) covalent geometry : angle 0.74423 / 0.35 (23673) hydrogen bonds : bond 0.04111 / 2.74 ( 645) hydrogen bonds : angle 4.01192 / 2.75 ( 1914) metal coordination : bond 0.00320 / 0.18 ( 15) metal coordination : angle 2.06801 / 1.10 ( 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 405 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 343 time to evaluate : 0.515 Fit side-chains REVERT: B 7 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7415 (m110) REVERT: B 15 PHE cc_start: 0.8873 (m-80) cc_final: 0.8449 (m-80) REVERT: B 55 LYS cc_start: 0.8316 (OUTLIER) cc_final: 0.7832 (ptpt) REVERT: B 291 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7489 (mm-30) REVERT: B 315 GLU cc_start: 0.8436 (tt0) cc_final: 0.8126 (mt-10) REVERT: B 378 SER cc_start: 0.6573 (OUTLIER) cc_final: 0.6292 (p) REVERT: B 452 ILE cc_start: 0.7673 (OUTLIER) cc_final: 0.7063 (mt) REVERT: B 454 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7128 (mm-30) REVERT: B 473 SER cc_start: 0.8452 (OUTLIER) cc_final: 0.8187 (m) REVERT: B 547 ASP cc_start: 0.8179 (p0) cc_final: 0.7930 (p0) REVERT: B 651 PHE cc_start: 0.8629 (m-80) cc_final: 0.8378 (m-80) REVERT: B 666 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8370 (tttm) REVERT: B 698 ASP cc_start: 0.7530 (m-30) cc_final: 0.7320 (m-30) REVERT: B 705 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7885 (mtp85) REVERT: B 788 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7995 (p0) REVERT: B 918 LYS cc_start: 0.6430 (mptt) cc_final: 0.5500 (mppt) REVERT: B 932 LYS cc_start: 0.8317 (ptmm) cc_final: 0.8075 (ptmm) REVERT: B 985 LYS cc_start: 0.8337 (mttp) cc_final: 0.8117 (mttm) REVERT: B 1444 ILE cc_start: 0.8398 (mm) cc_final: 0.8173 (mp) REVERT: B 1565 ASP cc_start: 0.7943 (t0) cc_final: 0.7408 (m-30) REVERT: B 1668 ASP cc_start: 0.5753 (OUTLIER) cc_final: 0.5338 (t70) REVERT: B 1691 PHE cc_start: 0.7963 (t80) cc_final: 0.7555 (t80) REVERT: C 30 GLU cc_start: 0.7283 (tt0) cc_final: 0.7027 (pt0) REVERT: C 42 LYS cc_start: 0.7443 (mttt) cc_final: 0.7175 (mtpp) REVERT: C 102 GLU cc_start: 0.7382 (tt0) cc_final: 0.7124 (mt-10) REVERT: C 151 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6662 (mp0) REVERT: C 155 LYS cc_start: 0.6196 (tmmt) cc_final: 0.5745 (tmtt) REVERT: C 217 ASP cc_start: 0.7444 (t0) cc_final: 0.7207 (t0) REVERT: C 234 ASP cc_start: 0.7500 (t70) cc_final: 0.7031 (t0) REVERT: C 318 ASP cc_start: 0.8152 (t70) cc_final: 0.7905 (t0) REVERT: C 340 GLU cc_start: 0.5112 (OUTLIER) cc_final: 0.4844 (pm20) REVERT: C 628 GLU cc_start: 0.7608 (tt0) cc_final: 0.7366 (mt-10) outliers start: 62 outliers final: 45 residues processed: 378 average time/residue: 0.6487 time to fit residues: 272.6456 Evaluate side-chains 394 residues out of total 1725 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 338 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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 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 329 LEU Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 413 THR Chi-restraints excluded: chain B residue 426 THR Chi-restraints excluded: chain B residue 452 ILE Chi-restraints excluded: chain B residue 473 SER 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 1454 LEU Chi-restraints excluded: chain B residue 1459 LEU Chi-restraints excluded: chain B residue 1467 SER Chi-restraints excluded: chain B residue 1497 ILE Chi-restraints excluded: chain B residue 1509 THR Chi-restraints excluded: chain B residue 1514 LYS 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 B residue 1672 LEU Chi-restraints excluded: chain B residue 1679 LYS 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 197 GLN 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 340 GLU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 VAL Chi-restraints excluded: chain C residue 475 ASP Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 567 SER 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: 0.7980 chunk 104 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 79 ASN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN B 498 GLN ** B 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 919 ASN B1596 GLN C 46 ASN C 357 GLN C 415 ASN C 476 ASN 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 = 0.3624 r_free = 0.3624 target = 0.129560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.108882 restraints weight = 23203.780| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.92 r_work: 0.3198 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 17399 Z= 0.189 Angle : 0.902 59.188 23688 Z= 0.483 Chirality : 0.064 0.756 2563 Planarity : 0.005 0.074 2873 Dihedral : 11.552 164.113 2710 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.43 % Favored : 94.52 % Rotamer: Outliers : 3.65 % Allowed : 26.49 % Favored : 69.86 % 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: 0.02 (0.18), residues: 1951 helix: 1.77 (0.20), residues: 706 sheet: 0.55 (0.31), residues: 256 loop : -1.53 (0.17), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1644 TYR 0.014 0.001 TYR C 607 PHE 0.013 0.001 PHE B 824 TRP 0.011 0.001 TRP B1530 HIS 0.007 0.001 HIS B 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.19 (17384) covalent geometry : angle 0.90106 / 0.48 (23673) hydrogen bonds : bond 0.04096 / 2.73 ( 645) hydrogen bonds : angle 4.01615 / 2.75 ( 1914) metal coordination : bond 0.00297 / 0.17 ( 15) metal coordination : angle 2.06639 / 1.10 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6699.88 seconds wall clock time: 114 minutes 41.04 seconds (6881.04 seconds total)