Starting phenix.real_space_refine on Sat Sep 12 14:28:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y84_33680/09_2026/7y84_33680.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y84_33680/09_2026/7y84_33680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y84_33680/09_2026/7y84_33680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y84_33680/09_2026/7y84_33680.map" model { file = "/net/cci-nas-00/data/ceres_data/7y84_33680/09_2026/7y84_33680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y84_33680/09_2026/7y84_33680.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7y84_33680/09_2026/7y84_33680.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y84_33680/09_2026/7y84_33680.cif" } resolution = 2.61 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= -0.001 sd= 0.294 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 35 5.49 5 Mg 1 5.21 5 S 57 5.16 5 C 10122 2.51 5 N 2779 2.21 5 O 3083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 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: 16081 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1242, 10032 Classifications: {'peptide': 1242} Link IDs: {'PTRANS': 59, 'TRANS': 1182} Chain breaks: 10 Chain: "B" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 735 Classifications: {'RNAv2': 35} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 10, 'rna3p_pur': 3, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 14} Chain: "C" Number of atoms: 5309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5309 Classifications: {'peptide': 652} Link IDs: {'PTRANS': 18, 'TRANS': 633} Chain breaks: 6 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 1, ' ZN': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 668 SG CYS A 88 56.467 26.583 134.850 1.00 39.23 S ATOM 939 SG CYS A 121 57.946 23.883 137.148 1.00 48.35 S ATOM 985 SG CYS A 127 56.874 22.982 133.570 1.00 34.53 S ATOM 1009 SG CYS A 130 59.715 25.502 134.142 1.00 37.08 S ATOM 3566 SG CYS A 491 50.184 45.764 108.913 1.00 36.08 S ATOM 3634 SG CYS A 501 49.607 45.302 112.434 1.00 29.52 S ATOM 3648 SG CYS A 503 46.864 44.102 110.424 1.00 30.84 S ATOM 3670 SG CYS A 506 50.124 42.202 110.117 1.00 38.32 S ATOM 5641 SG CYS A 750 50.605 62.762 84.789 1.00 46.28 S ATOM 5654 SG CYS A 752 47.531 61.305 83.035 1.00 42.05 S ATOM 5676 SG CYS A 755 50.120 58.934 84.638 1.00 33.91 S ATOM 7635 SG CYS A1018 57.774 61.020 48.850 1.00 48.41 S ATOM 7831 SG CYS A1406 58.393 62.937 52.100 1.00 42.50 S ATOM 7882 SG CYS A1414 55.055 63.264 50.358 1.00 42.72 S ATOM 7899 SG CYS A1417 55.855 60.064 51.993 1.00 47.60 S Time building chain proxies: 2.93, per 1000 atoms: 0.18 Number of scatterers: 16081 At special positions: 0 Unit cell: (101.2, 95.7, 157.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 57 16.00 P 35 15.00 Mg 1 11.99 O 3083 8.00 N 2779 7.00 C 10122 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: 1.40 Conformation dependent library (CDL) restraints added in 548.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 121 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 506 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 491 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1803 " - pdb=" SG CYS A 755 " pdb=" ZN A1804 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1804 " - pdb=" SG CYS A1406 " Number of angles added : 21 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3510 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 23 sheets defined 44.2% alpha, 18.8% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.002A pdb=" N LYS A 30 " --> pdb=" O TRP A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 Processing helix chain 'A' and resid 59 through 78 Processing helix chain 'A' and resid 127 through 134 Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 169 through 172 No H-bonds generated for 'chain 'A' and resid 169 through 172' Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.275A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 removed outlier: 4.250A pdb=" N GLY A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 307' Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 354 through 375 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 511 removed outlier: 3.856A pdb=" N ARG A 511 " --> pdb=" O ILE A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 638 through 642 Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 664 Processing helix chain 'A' and resid 665 through 667 No H-bonds generated for 'chain 'A' and resid 665 through 667' Processing helix chain 'A' and resid 686 through 693 removed outlier: 3.557A pdb=" N LEU A 691 " --> pdb=" O THR A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.511A pdb=" N PHE A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 738 " --> pdb=" O ALA A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 744 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 776 through 780 Processing helix chain 'A' and resid 831 through 847 Processing helix chain 'A' and resid 855 through 859 Processing helix chain 'A' and resid 873 through 879 removed outlier: 3.591A pdb=" N MET A 879 " --> pdb=" O ASP A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 914 Processing helix chain 'A' and resid 999 through 1015 Processing helix chain 'A' and resid 1394 through 1399 Processing helix chain 'A' and resid 1400 through 1404 Processing helix chain 'A' and resid 1414 through 1420 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.908A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1486 through 1493 Processing helix chain 'A' and resid 1493 through 1501 removed outlier: 3.701A pdb=" N ARG A1498 " --> pdb=" O GLN A1494 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU A1499 " --> pdb=" O LEU A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1540 Processing helix chain 'A' and resid 1552 through 1556 Processing helix chain 'A' and resid 1583 through 1603 Processing helix chain 'A' and resid 1615 through 1618 removed outlier: 3.590A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1662 through 1668 removed outlier: 3.529A pdb=" N ASP A1668 " --> pdb=" O LYS A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1682 Processing helix chain 'C' and resid 16 through 32 Processing helix chain 'C' and resid 37 through 60 removed outlier: 3.823A pdb=" N LYS C 43 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 63 No H-bonds generated for 'chain 'C' and resid 61 through 63' Processing helix chain 'C' and resid 64 through 82 Processing helix chain 'C' and resid 90 through 110 removed outlier: 3.713A pdb=" N ARG C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA C 107 " --> pdb=" O PHE C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 136 Processing helix chain 'C' and resid 141 through 154 Processing helix chain 'C' and resid 163 through 176 removed outlier: 4.235A pdb=" N ILE C 167 " --> pdb=" O TYR C 163 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN C 168 " --> pdb=" O GLU C 164 " (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 208 through 224 removed outlier: 3.769A pdb=" N ALA C 212 " --> pdb=" O ASP C 208 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS C 224 " --> pdb=" O THR C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 246 removed outlier: 3.903A pdb=" N ASP C 234 " --> pdb=" O HIS C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 267 removed outlier: 4.309A pdb=" N ASP C 253 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 295 removed outlier: 4.569A pdb=" N VAL C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 323 removed outlier: 4.281A pdb=" N ARG C 323 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 333 Processing helix chain 'C' and resid 340 through 359 removed outlier: 3.728A pdb=" N GLY C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 451 Processing helix chain 'C' and resid 454 through 469 Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 489 through 495 Processing helix chain 'C' and resid 496 through 500 Processing helix 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 removed outlier: 3.692A pdb=" N ASN C 552 " --> pdb=" O GLU C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 573 removed outlier: 3.614A pdb=" N ILE C 573 " --> pdb=" O ASP C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 595 Processing helix chain 'C' and resid 607 through 614 Processing helix chain 'C' and resid 627 through 632 Processing helix chain 'C' and resid 644 through 652 removed outlier: 3.628A pdb=" N ALA C 648 " --> pdb=" O SER C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 678 removed outlier: 3.543A pdb=" N THR C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU C 678 " --> pdb=" O GLU C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 691 removed outlier: 3.611A pdb=" N TRP C 687 " --> pdb=" O LYS C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 708 removed outlier: 3.576A pdb=" N ALA C 708 " --> pdb=" O TYR C 704 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.621A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 18 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP A 195 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 12.996A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP A 190 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.953A pdb=" N LEU A 167 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 111 removed outlier: 5.901A pdb=" N THR A 110 " --> pdb=" O VAL A 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.062A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.062A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.090A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ILE A 460 " --> pdb=" O GLU A 549 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB1, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.524A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.524A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.990A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB5, first strand: chain 'A' and resid 920 through 921 Processing sheet with id=AB6, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AB7, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.333A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ALA A1434 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ASP A1521 " --> pdb=" O ALA A1434 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N TYR A1436 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER A1519 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 5.232A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 985 through 987 removed outlier: 6.277A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N GLU A1510 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N TYR A 987 " --> pdb=" O GLU A1510 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1421 through 1422 Processing sheet with id=AC2, first strand: chain 'C' and resid 274 through 276 removed outlier: 6.713A pdb=" N ARG C 275 " --> pdb=" O LEU C 326 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 425 through 432 removed outlier: 6.469A pdb=" N VAL C 401 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL C 487 " --> pdb=" O VAL C 401 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 403 " --> pdb=" O VAL C 487 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 536 through 540 removed outlier: 6.526A pdb=" N VAL C 537 " --> pdb=" O THR C 581 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU C 583 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU C 539 " --> pdb=" O LEU C 583 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N THR C 660 " --> pdb=" O LEU C 624 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 585 through 587 removed outlier: 4.124A pdb=" N HIS C 585 " --> pdb=" O LYS C 599 " (cutoff:3.500A) 709 hydrogen bonds defined for protein. 1956 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 3.78 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2608 1.29 - 1.42: 4401 1.42 - 1.55: 9341 1.55 - 1.68: 73 1.68 - 1.81: 80 Bond restraints: 16503 Sorted by residual: bond pdb=" C GLU A 654 " pdb=" O GLU A 654 " ideal model delta sigma weight residual 1.234 1.157 0.077 1.35e-02 5.49e+03 3.23e+01 bond pdb=" C PHE A 652 " pdb=" O PHE A 652 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.20e-02 6.94e+03 1.39e+01 bond pdb=" C LEU C 449 " pdb=" O LEU C 449 " ideal model delta sigma weight residual 1.234 1.184 0.050 1.35e-02 5.49e+03 1.37e+01 bond pdb=" C LYS C 451 " pdb=" O LYS C 451 " ideal model delta sigma weight residual 1.235 1.191 0.044 1.26e-02 6.30e+03 1.23e+01 bond pdb=" C GLU C 452 " pdb=" O GLU C 452 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.17e-02 7.31e+03 1.16e+01 ... (remaining 16498 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.14: 21862 2.14 - 4.28: 441 4.28 - 6.42: 83 6.42 - 8.56: 5 8.56 - 10.69: 5 Bond angle restraints: 22396 Sorted by residual: angle pdb=" C LYS C 94 " pdb=" N GLU C 95 " pdb=" CA GLU C 95 " ideal model delta sigma weight residual 120.28 129.81 -9.53 1.34e+00 5.57e-01 5.05e+01 angle pdb=" C LYS A 815 " pdb=" CA LYS A 815 " pdb=" CB LYS A 815 " ideal model delta sigma weight residual 110.85 119.54 -8.69 1.70e+00 3.46e-01 2.61e+01 angle pdb=" CA PHE A 651 " pdb=" CB PHE A 651 " pdb=" CG PHE A 651 " ideal model delta sigma weight residual 113.80 108.83 4.97 1.00e+00 1.00e+00 2.47e+01 angle pdb=" C TYR C 450 " pdb=" CA TYR C 450 " pdb=" CB TYR C 450 " ideal model delta sigma weight residual 109.55 117.32 -7.77 1.68e+00 3.54e-01 2.14e+01 angle pdb=" C3' C B 45 " pdb=" O3' C B 45 " pdb=" P U B 46 " ideal model delta sigma weight residual 119.70 124.72 -5.02 1.20e+00 6.94e-01 1.75e+01 ... (remaining 22391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8150 17.98 - 35.96: 1143 35.96 - 53.95: 381 53.95 - 71.93: 128 71.93 - 89.91: 35 Dihedral angle restraints: 9837 sinusoidal: 4385 harmonic: 5452 Sorted by residual: dihedral pdb=" C4' G B 33 " pdb=" C3' G B 33 " pdb=" C2' G B 33 " pdb=" C1' G B 33 " ideal model delta sinusoidal sigma weight residual 36.34 -38.61 74.95 1 3.10e+00 1.04e-01 7.40e+02 dihedral pdb=" C4' G B 27 " pdb=" C3' G B 27 " pdb=" C2' G B 27 " pdb=" C1' G B 27 " ideal model delta sinusoidal sigma weight residual 36.34 -38.38 74.73 1 3.10e+00 1.04e-01 7.36e+02 dihedral pdb=" C4' U B 41 " pdb=" C3' U B 41 " pdb=" C2' U B 41 " pdb=" C1' U B 41 " ideal model delta sinusoidal sigma weight residual 36.34 -38.26 74.61 1 3.10e+00 1.04e-01 7.34e+02 ... (remaining 9834 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 2323 0.133 - 0.266: 68 0.266 - 0.398: 25 0.398 - 0.531: 2 0.531 - 0.664: 2 Chirality restraints: 2420 Sorted by residual: chirality pdb=" C1' C B 45 " pdb=" O4' C B 45 " pdb=" C2' C B 45 " pdb=" N1 C B 45 " both_signs ideal model delta sigma weight residual False 2.46 1.79 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" C2' C B 45 " pdb=" C3' C B 45 " pdb=" O2' C B 45 " pdb=" C1' C B 45 " both_signs ideal model delta sigma weight residual False -2.79 -2.20 -0.59 2.00e-01 2.50e+01 8.56e+00 chirality pdb=" CA LYS A 815 " pdb=" N LYS A 815 " pdb=" C LYS A 815 " pdb=" CB LYS A 815 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.10e+00 ... (remaining 2417 not shown) Planarity restraints: 2745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 651 " -0.044 2.00e-02 2.50e+03 2.80e-02 1.37e+01 pdb=" CG PHE A 651 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE A 651 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 651 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE A 651 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 651 " -0.015 2.00e-02 2.50e+03 pdb=" CZ PHE A 651 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 23 " -0.045 2.00e-02 2.50e+03 2.35e-02 1.25e+01 pdb=" N1 U B 23 " 0.051 2.00e-02 2.50e+03 pdb=" C2 U B 23 " 0.002 2.00e-02 2.50e+03 pdb=" O2 U B 23 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U B 23 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B 23 " -0.005 2.00e-02 2.50e+03 pdb=" O4 U B 23 " -0.013 2.00e-02 2.50e+03 pdb=" C5 U B 23 " -0.002 2.00e-02 2.50e+03 pdb=" C6 U B 23 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 45 " -0.045 2.00e-02 2.50e+03 2.20e-02 1.09e+01 pdb=" N1 C B 45 " 0.040 2.00e-02 2.50e+03 pdb=" C2 C B 45 " 0.006 2.00e-02 2.50e+03 pdb=" O2 C B 45 " 0.012 2.00e-02 2.50e+03 pdb=" N3 C B 45 " -0.015 2.00e-02 2.50e+03 pdb=" C4 C B 45 " 0.000 2.00e-02 2.50e+03 pdb=" N4 C B 45 " -0.014 2.00e-02 2.50e+03 pdb=" C5 C B 45 " 0.004 2.00e-02 2.50e+03 pdb=" C6 C B 45 " 0.012 2.00e-02 2.50e+03 ... (remaining 2742 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 10 2.14 - 2.83: 5249 2.83 - 3.52: 22924 3.52 - 4.21: 45699 4.21 - 4.90: 76003 Nonbonded interactions: 149885 Sorted by model distance: nonbonded pdb=" NE ARG A 145 " pdb=" NZ LYS A 147 " model vdw 1.448 3.200 nonbonded pdb=" CZ ARG A 145 " pdb=" NZ LYS A 147 " model vdw 1.872 3.350 nonbonded pdb=" NH2 ARG A 145 " pdb=" NZ LYS A 147 " model vdw 1.921 3.200 nonbonded pdb=" OD1 ASP A 137 " pdb="MG MG A1805 " model vdw 1.961 2.170 nonbonded pdb=" O GLY A 134 " pdb="MG MG A1805 " model vdw 1.963 2.170 ... (remaining 149880 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: 1.100 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.220 Find NCS groups from input model: 0.060 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 : 0.007 0.077 16519 Z= 0.295 Angle : 0.769 11.363 22417 Z= 0.398 Chirality : 0.066 0.664 2420 Planarity : 0.005 0.074 2745 Dihedral : 19.672 89.912 6327 Min Nonbonded Distance : 1.448 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.92 % Allowed : 26.74 % Favored : 71.33 % Cbeta Deviations : 0.11 % 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: -0.44 (0.18), residues: 1858 helix: -0.36 (0.18), residues: 698 sheet: -0.47 (0.28), residues: 271 loop : 0.03 (0.20), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 578 TYR 0.031 0.002 TYR C 450 PHE 0.044 0.003 PHE A 651 TRP 0.012 0.002 TRP C 400 HIS 0.008 0.001 HIS C 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.29 (16503) covalent geometry : angle 0.75712 / 0.40 (22396) hydrogen bonds : bond 0.21000 / 13.81 ( 667) hydrogen bonds : angle 8.12254 / 5.67 ( 1956) metal coordination : bond 0.01122 / 0.63 ( 16) metal coordination : angle 4.50272 / 2.83 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 209 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 815 LYS cc_start: 0.8515 (mttp) cc_final: 0.8027 (mppt) REVERT: A 1565 ASP cc_start: 0.7949 (t70) cc_final: 0.7569 (t0) REVERT: C 95 GLU cc_start: 0.7664 (tt0) cc_final: 0.7426 (tt0) REVERT: C 327 ARG cc_start: 0.6976 (mtt180) cc_final: 0.6735 (mmt-90) REVERT: C 430 GLU cc_start: 0.8213 (mt-10) cc_final: 0.8001 (mt-10) REVERT: C 637 ASP cc_start: 0.7694 (t0) cc_final: 0.7315 (t0) outliers start: 32 outliers final: 22 residues processed: 231 average time/residue: 0.6447 time to fit residues: 164.2445 Evaluate side-chains 210 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1627 LYS Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 711 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 335 GLN A 348 GLN A 664 ASN A 696 ASN A 708 ASN A 905 HIS ** A 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 973 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN A 993 ASN A1010 HIS A1484 HIS A1485 ASN A1492 GLN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1592 ASN A1617 HIS C 304 ASN C 559 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.166627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.133618 restraints weight = 15605.781| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.44 r_work: 0.3320 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 16519 Z= 0.196 Angle : 1.031 31.064 22417 Z= 0.437 Chirality : 0.094 1.242 2420 Planarity : 0.005 0.063 2745 Dihedral : 12.513 157.330 2494 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.06 % Allowed : 24.82 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.19), residues: 1858 helix: 0.53 (0.19), residues: 714 sheet: -0.64 (0.29), residues: 248 loop : 0.09 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 64 TYR 0.018 0.002 TYR C 704 PHE 0.016 0.002 PHE A1518 TRP 0.013 0.002 TRP A 82 HIS 0.005 0.001 HIS C 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 (16503) covalent geometry : angle 1.02620 / 0.44 (22396) hydrogen bonds : bond 0.04981 / 3.31 ( 667) hydrogen bonds : angle 5.83758 / 4.05 ( 1956) metal coordination : bond 0.00555 / 0.32 ( 16) metal coordination : angle 3.53094 / 2.05 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 0.439 Fit side-chains REVERT: A 100 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7768 (ttpt) REVERT: A 815 LYS cc_start: 0.8407 (mttp) cc_final: 0.7876 (mppt) REVERT: A 869 ASP cc_start: 0.6352 (OUTLIER) cc_final: 0.5834 (m-30) REVERT: A 944 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7632 (pp20) REVERT: A 1493 LYS cc_start: 0.6661 (mttt) cc_final: 0.6088 (mmtm) REVERT: A 1543 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7676 (mmmm) REVERT: A 1692 GLN cc_start: 0.4916 (OUTLIER) cc_final: 0.4348 (pt0) REVERT: C 290 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8131 (tt) REVERT: C 327 ARG cc_start: 0.7488 (mtt180) cc_final: 0.6813 (mmt-90) REVERT: C 435 GLU cc_start: 0.8634 (tt0) cc_final: 0.7818 (mp0) REVERT: C 508 LYS cc_start: 0.7882 (pttp) cc_final: 0.7418 (mmtp) REVERT: C 595 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7723 (mtt-85) REVERT: C 637 ASP cc_start: 0.7771 (t0) cc_final: 0.7428 (t0) outliers start: 51 outliers final: 22 residues processed: 250 average time/residue: 0.5981 time to fit residues: 165.2420 Evaluate side-chains 229 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 201 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1543 LYS Chi-restraints excluded: chain A residue 1692 GLN Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 699 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 74 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 287 ASN A 335 GLN A 348 GLN A 913 GLN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 973 ASN A 986 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1516 ASN A1617 HIS C 281 HIS C 304 ASN C 559 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.159612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.124972 restraints weight = 15631.767| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.55 r_work: 0.3189 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.068 16519 Z= 0.382 Angle : 1.077 32.443 22417 Z= 0.468 Chirality : 0.091 1.094 2420 Planarity : 0.006 0.052 2745 Dihedral : 13.518 175.991 2474 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 4.75 % Allowed : 22.06 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.19), residues: 1858 helix: 0.37 (0.19), residues: 712 sheet: -0.81 (0.28), residues: 270 loop : 0.06 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 64 TYR 0.025 0.003 TYR C 277 PHE 0.023 0.003 PHE C 440 TRP 0.015 0.003 TRP A 612 HIS 0.012 0.002 HIS C 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00888 / 0.38 (16503) covalent geometry : angle 1.06924 / 0.47 (22396) hydrogen bonds : bond 0.05375 / 3.54 ( 667) hydrogen bonds : angle 5.90302 / 4.11 ( 1956) metal coordination : bond 0.01322 / 0.84 ( 16) metal coordination : angle 4.35828 / 2.54 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 219 time to evaluate : 0.622 Fit side-chains REVERT: A 96 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6883 (mm-30) REVERT: A 291 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7079 (pp20) REVERT: A 357 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8242 (ttpp) REVERT: A 698 ASP cc_start: 0.8584 (m-30) cc_final: 0.8270 (m-30) REVERT: A 815 LYS cc_start: 0.8521 (mttp) cc_final: 0.7972 (mppt) REVERT: A 944 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.7770 (pp20) REVERT: A 955 ASN cc_start: 0.8589 (m-40) cc_final: 0.8342 (m110) REVERT: A 985 LYS cc_start: 0.8292 (mptm) cc_final: 0.7852 (mttt) REVERT: A 1493 LYS cc_start: 0.6895 (mttt) cc_final: 0.6242 (mmtt) REVERT: A 1587 ILE cc_start: 0.7981 (mt) cc_final: 0.7765 (mt) REVERT: A 1629 LEU cc_start: 0.7965 (mt) cc_final: 0.7701 (mt) REVERT: A 1692 GLN cc_start: 0.4988 (OUTLIER) cc_final: 0.4645 (pt0) REVERT: C 22 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6637 (mmtm) REVERT: C 161 ASP cc_start: 0.7798 (m-30) cc_final: 0.7315 (m-30) REVERT: C 327 ARG cc_start: 0.7567 (mtt180) cc_final: 0.6854 (mmt-90) REVERT: C 409 LYS cc_start: 0.8368 (mtmm) cc_final: 0.7962 (mtpt) REVERT: C 508 LYS cc_start: 0.8221 (pttp) cc_final: 0.7736 (mmtp) REVERT: C 595 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7902 (mtt-85) REVERT: C 637 ASP cc_start: 0.7985 (t0) cc_final: 0.7705 (t0) outliers start: 79 outliers final: 40 residues processed: 270 average time/residue: 0.6277 time to fit residues: 186.4050 Evaluate side-chains 257 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 212 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LYS Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1675 LYS Chi-restraints excluded: chain A residue 1692 GLN Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 411 GLU Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 699 HIS Chi-restraints excluded: chain C residue 711 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 113 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 129 optimal weight: 0.3980 chunk 156 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 178 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN A 348 GLN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS C 304 ASN C 559 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.168051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.133155 restraints weight = 15559.139| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.38 r_work: 0.3351 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16519 Z= 0.168 Angle : 0.800 26.680 22417 Z= 0.355 Chirality : 0.069 0.887 2420 Planarity : 0.005 0.051 2745 Dihedral : 13.561 175.650 2474 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.37 % Allowed : 23.44 % Favored : 73.20 % 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: 0.32 (0.19), residues: 1858 helix: 0.97 (0.20), residues: 710 sheet: -0.86 (0.28), residues: 259 loop : 0.07 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 382 TYR 0.016 0.002 TYR C 607 PHE 0.014 0.002 PHE A 192 TRP 0.015 0.001 TRP A 612 HIS 0.005 0.001 HIS A1010 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.17 (16503) covalent geometry : angle 0.79338 / 0.36 (22396) hydrogen bonds : bond 0.04170 / 2.78 ( 667) hydrogen bonds : angle 5.41749 / 3.77 ( 1956) metal coordination : bond 0.00481 / 0.27 ( 16) metal coordination : angle 3.47157 / 2.02 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 220 time to evaluate : 0.618 Fit side-chains REVERT: A 100 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7722 (ttpt) REVERT: A 291 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.6961 (pp20) REVERT: A 357 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8210 (ttpp) REVERT: A 382 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7300 (ttm110) REVERT: A 581 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7724 (pt0) REVERT: A 815 LYS cc_start: 0.8427 (mttp) cc_final: 0.7916 (mppt) REVERT: A 869 ASP cc_start: 0.6307 (OUTLIER) cc_final: 0.5927 (m-30) REVERT: A 944 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7613 (pp20) REVERT: A 955 ASN cc_start: 0.8521 (m-40) cc_final: 0.8246 (m110) REVERT: A 1493 LYS cc_start: 0.6614 (mttt) cc_final: 0.6013 (mmtt) REVERT: A 1587 ILE cc_start: 0.7993 (mt) cc_final: 0.7781 (mt) REVERT: A 1692 GLN cc_start: 0.5037 (OUTLIER) cc_final: 0.4607 (pt0) REVERT: C 55 LEU cc_start: 0.7684 (tp) cc_final: 0.7001 (mp) REVERT: C 95 GLU cc_start: 0.7773 (tt0) cc_final: 0.7291 (tt0) REVERT: C 290 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8136 (tt) REVERT: C 327 ARG cc_start: 0.7522 (mtt180) cc_final: 0.6910 (mmt-90) REVERT: C 409 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7874 (mtpt) REVERT: C 435 GLU cc_start: 0.8652 (tt0) cc_final: 0.7860 (mp0) REVERT: C 508 LYS cc_start: 0.8003 (pttp) cc_final: 0.7550 (mmtp) REVERT: C 595 ARG cc_start: 0.8265 (mtp85) cc_final: 0.7871 (mtt-85) REVERT: C 637 ASP cc_start: 0.7888 (t0) cc_final: 0.7572 (t0) outliers start: 56 outliers final: 25 residues processed: 256 average time/residue: 0.6162 time to fit residues: 174.2207 Evaluate side-chains 238 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 382 ARG Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1675 LYS Chi-restraints excluded: chain A residue 1692 GLN Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 699 HIS Chi-restraints excluded: chain C residue 702 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 286 GLN A 348 GLN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS C 304 ASN C 559 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.161524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.127486 restraints weight = 15585.097| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.48 r_work: 0.3250 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 16519 Z= 0.300 Angle : 0.896 21.859 22417 Z= 0.401 Chirality : 0.076 0.906 2420 Planarity : 0.005 0.055 2745 Dihedral : 13.923 173.159 2471 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 4.63 % Allowed : 22.60 % Favored : 72.78 % 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 (0.19), residues: 1858 helix: 0.72 (0.19), residues: 714 sheet: -1.04 (0.27), residues: 271 loop : 0.04 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 382 TYR 0.022 0.002 TYR C 277 PHE 0.020 0.002 PHE C 440 TRP 0.017 0.002 TRP A 612 HIS 0.009 0.001 HIS C 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.30 (16503) covalent geometry : angle 0.88824 / 0.40 (22396) hydrogen bonds : bond 0.04697 / 3.09 ( 667) hydrogen bonds : angle 5.55200 / 3.86 ( 1956) metal coordination : bond 0.01039 / 0.62 ( 16) metal coordination : angle 3.98648 / 2.26 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 219 time to evaluate : 0.585 Fit side-chains REVERT: A 147 LYS cc_start: 0.8621 (mppt) cc_final: 0.8090 (ttpp) REVERT: A 151 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8211 (tp) REVERT: A 291 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6960 (pp20) REVERT: A 357 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.8212 (ttpp) REVERT: A 511 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8684 (mtt90) REVERT: A 545 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8859 (tm) REVERT: A 581 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7771 (pt0) REVERT: A 693 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7409 (mm-30) REVERT: A 815 LYS cc_start: 0.8448 (mttp) cc_final: 0.7905 (mppt) REVERT: A 944 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7444 (pp20) REVERT: A 1493 LYS cc_start: 0.6790 (mttt) cc_final: 0.6086 (mmtm) REVERT: A 1587 ILE cc_start: 0.7917 (mt) cc_final: 0.7693 (mt) REVERT: A 1692 GLN cc_start: 0.5021 (OUTLIER) cc_final: 0.4589 (pt0) REVERT: C 22 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6397 (mmtt) REVERT: C 55 LEU cc_start: 0.7625 (tp) cc_final: 0.7056 (mp) REVERT: C 95 GLU cc_start: 0.7838 (tt0) cc_final: 0.7318 (tt0) REVERT: C 155 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.6214 (ttmp) REVERT: C 327 ARG cc_start: 0.7484 (mtt180) cc_final: 0.6775 (mmt-90) REVERT: C 409 LYS cc_start: 0.8281 (OUTLIER) cc_final: 0.7947 (mtpt) REVERT: C 435 GLU cc_start: 0.8596 (tt0) cc_final: 0.7793 (mp0) REVERT: C 508 LYS cc_start: 0.8061 (pttp) cc_final: 0.7601 (mmtp) REVERT: C 595 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7832 (mtt-85) REVERT: C 637 ASP cc_start: 0.8006 (t0) cc_final: 0.7710 (t0) outliers start: 77 outliers final: 43 residues processed: 266 average time/residue: 0.6004 time to fit residues: 176.8340 Evaluate side-chains 261 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 207 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1584 GLN Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1675 LYS Chi-restraints excluded: chain A residue 1692 GLN Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 549 THR Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 597 MET Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 699 HIS Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 711 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 91 optimal weight: 5.9990 chunk 166 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 122 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN A 348 GLN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 ASN A 986 ASN A1438 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS C 304 ASN C 559 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.166517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.133349 restraints weight = 15723.314| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.41 r_work: 0.3336 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16519 Z= 0.169 Angle : 0.749 13.022 22417 Z= 0.342 Chirality : 0.064 0.675 2420 Planarity : 0.005 0.056 2745 Dihedral : 13.874 179.740 2471 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.79 % Allowed : 23.74 % Favored : 72.48 % 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: 0.32 (0.19), residues: 1858 helix: 1.06 (0.20), residues: 710 sheet: -1.07 (0.27), residues: 269 loop : 0.09 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 382 TYR 0.016 0.002 TYR C 277 PHE 0.013 0.002 PHE A 824 TRP 0.015 0.001 TRP A 612 HIS 0.012 0.001 HIS A1617 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (16503) covalent geometry : angle 0.74207 / 0.34 (22396) hydrogen bonds : bond 0.04043 / 2.69 ( 667) hydrogen bonds : angle 5.30070 / 3.69 ( 1956) metal coordination : bond 0.00530 / 0.30 ( 16) metal coordination : angle 3.46078 / 1.98 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 0.625 Fit side-chains REVERT: A 100 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.7817 (ttpt) REVERT: A 147 LYS cc_start: 0.8596 (mppt) cc_final: 0.8042 (ttpp) REVERT: A 291 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.6993 (pp20) REVERT: A 357 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8168 (ttpp) REVERT: A 545 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8794 (tm) REVERT: A 581 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: A 693 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7500 (mm-30) REVERT: A 815 LYS cc_start: 0.8419 (mttp) cc_final: 0.7880 (mppt) REVERT: A 869 ASP cc_start: 0.6295 (OUTLIER) cc_final: 0.5878 (m-30) REVERT: A 944 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7426 (pp20) REVERT: A 955 ASN cc_start: 0.8495 (m110) cc_final: 0.8135 (m-40) REVERT: A 1493 LYS cc_start: 0.6719 (mttt) cc_final: 0.5990 (mmtm) REVERT: A 1587 ILE cc_start: 0.7940 (mt) cc_final: 0.7730 (mt) REVERT: A 1692 GLN cc_start: 0.4970 (OUTLIER) cc_final: 0.4644 (pt0) REVERT: C 55 LEU cc_start: 0.7647 (tp) cc_final: 0.7000 (mp) REVERT: C 95 GLU cc_start: 0.7737 (tt0) cc_final: 0.7235 (tt0) REVERT: C 155 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.5961 (ttmp) REVERT: C 290 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8078 (tp) REVERT: C 327 ARG cc_start: 0.7420 (mtt180) cc_final: 0.6762 (mmt-90) REVERT: C 347 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7069 (mppt) REVERT: C 409 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7889 (mtpt) REVERT: C 435 GLU cc_start: 0.8568 (tt0) cc_final: 0.7764 (mp0) REVERT: C 508 LYS cc_start: 0.7974 (pttp) cc_final: 0.7549 (mmtp) REVERT: C 595 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7818 (mtt-85) REVERT: C 637 ASP cc_start: 0.7934 (t0) cc_final: 0.7637 (t0) outliers start: 63 outliers final: 28 residues processed: 250 average time/residue: 0.6198 time to fit residues: 171.0144 Evaluate side-chains 238 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 198 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1675 LYS Chi-restraints excluded: chain A residue 1692 GLN Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 699 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 139 optimal weight: 0.9980 chunk 188 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 186 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 348 GLN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN A1438 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS C 304 ASN C 559 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.164672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.131094 restraints weight = 15527.717| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.40 r_work: 0.3306 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16519 Z= 0.208 Angle : 0.773 17.707 22417 Z= 0.350 Chirality : 0.065 0.721 2420 Planarity : 0.005 0.062 2745 Dihedral : 14.018 178.288 2471 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.15 % Allowed : 23.38 % Favored : 72.48 % 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: 0.27 (0.19), residues: 1858 helix: 1.04 (0.20), residues: 712 sheet: -1.13 (0.27), residues: 269 loop : 0.05 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 382 TYR 0.018 0.002 TYR C 277 PHE 0.016 0.002 PHE A 15 TRP 0.015 0.002 TRP A 612 HIS 0.006 0.001 HIS C 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.21 (16503) covalent geometry : angle 0.76612 / 0.35 (22396) hydrogen bonds : bond 0.04177 / 2.77 ( 667) hydrogen bonds : angle 5.29679 / 3.68 ( 1956) metal coordination : bond 0.00698 / 0.39 ( 16) metal coordination : angle 3.51187 / 1.99 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 0.565 Fit side-chains REVERT: A 100 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7932 (ttpt) REVERT: A 291 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.6966 (pp20) REVERT: A 357 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8194 (ttpp) REVERT: A 511 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8696 (mtt90) REVERT: A 545 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8747 (tm) REVERT: A 581 GLU cc_start: 0.8090 (pt0) cc_final: 0.7859 (pt0) REVERT: A 693 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7495 (mm-30) REVERT: A 815 LYS cc_start: 0.8486 (mttp) cc_final: 0.7961 (mppt) REVERT: A 869 ASP cc_start: 0.6330 (OUTLIER) cc_final: 0.5913 (m-30) REVERT: A 944 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7427 (pp20) REVERT: A 955 ASN cc_start: 0.8476 (m110) cc_final: 0.8083 (m110) REVERT: A 985 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8085 (mttt) REVERT: A 1493 LYS cc_start: 0.6755 (mttt) cc_final: 0.6012 (mmtm) REVERT: A 1587 ILE cc_start: 0.7976 (mt) cc_final: 0.7775 (mt) REVERT: A 1692 GLN cc_start: 0.4983 (OUTLIER) cc_final: 0.4579 (pt0) REVERT: C 22 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6341 (mmtm) REVERT: C 55 LEU cc_start: 0.7665 (tp) cc_final: 0.7007 (mp) REVERT: C 155 LYS cc_start: 0.7280 (OUTLIER) cc_final: 0.5920 (ttmp) REVERT: C 290 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8125 (tp) REVERT: C 327 ARG cc_start: 0.7441 (mtt180) cc_final: 0.6754 (mmt-90) REVERT: C 347 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7002 (mppt) REVERT: C 409 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7926 (mtpt) REVERT: C 435 GLU cc_start: 0.8575 (tt0) cc_final: 0.7788 (mp0) REVERT: C 508 LYS cc_start: 0.7996 (pttp) cc_final: 0.7537 (mmtp) REVERT: C 578 ARG cc_start: 0.7244 (tpt-90) cc_final: 0.6694 (tpt90) REVERT: C 595 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7829 (mtt-85) REVERT: C 637 ASP cc_start: 0.7885 (t0) cc_final: 0.7581 (t0) outliers start: 69 outliers final: 35 residues processed: 256 average time/residue: 0.6163 time to fit residues: 174.3645 Evaluate side-chains 250 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 985 LYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1501 VAL Chi-restraints excluded: chain A residue 1507 VAL Chi-restraints excluded: chain A residue 1675 LYS Chi-restraints excluded: chain A residue 1692 GLN Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 226 THR Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 699 HIS Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 711 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 82 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 348 GLN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN A1438 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS C 304 ASN C 559 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.167664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.133763 restraints weight = 15499.823| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.36 r_work: 0.3348 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16519 Z= 0.168 Angle : 0.723 15.856 22417 Z= 0.329 Chirality : 0.061 0.653 2420 Planarity : 0.005 0.058 2745 Dihedral : 14.063 179.651 2471 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.43 % Allowed : 24.28 % Favored : 72.30 % 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: 0.40 (0.19), residues: 1858 helix: 1.18 (0.20), residues: 710 sheet: -1.13 (0.27), residues: 269 loop : 0.11 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 382 TYR 0.015 0.002 TYR C 277 PHE 0.016 0.002 PHE C 254 TRP 0.014 0.001 TRP A 612 HIS 0.004 0.001 HIS C 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (16503) covalent geometry : angle 0.71625 / 0.33 (22396) hydrogen bonds : bond 0.03925 / 2.62 ( 667) hydrogen bonds : angle 5.16186 / 3.59 ( 1956) metal coordination : bond 0.00552 / 0.33 ( 16) metal coordination : angle 3.30791 / 1.86 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 215 time to evaluate : 0.620 Fit side-chains REVERT: A 95 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7222 (m-30) REVERT: A 100 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7819 (ttpt) REVERT: A 147 LYS cc_start: 0.8467 (mppt) cc_final: 0.7988 (ttpt) REVERT: A 291 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6885 (pp20) REVERT: A 357 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8154 (ttpp) REVERT: A 545 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8700 (tm) REVERT: A 581 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7697 (pt0) REVERT: A 653 GLU cc_start: 0.7434 (mp0) cc_final: 0.7171 (mp0) REVERT: A 693 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7473 (mm-30) REVERT: A 719 ARG cc_start: 0.8215 (mmt90) cc_final: 0.7856 (mtt90) REVERT: A 815 LYS cc_start: 0.8466 (mttp) cc_final: 0.7953 (mppt) REVERT: A 869 ASP cc_start: 0.6398 (OUTLIER) cc_final: 0.6038 (m-30) REVERT: A 944 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7472 (pp20) REVERT: A 955 ASN cc_start: 0.8483 (m110) cc_final: 0.8102 (m110) REVERT: A 985 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8061 (mttt) REVERT: A 1493 LYS cc_start: 0.6755 (mttt) cc_final: 0.6030 (mmtm) REVERT: A 1509 THR cc_start: 0.8402 (m) cc_final: 0.8158 (p) REVERT: A 1587 ILE cc_start: 0.7986 (mt) cc_final: 0.7764 (mt) REVERT: A 1692 GLN cc_start: 0.4980 (OUTLIER) cc_final: 0.4675 (pt0) REVERT: C 22 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.6345 (mmtm) REVERT: C 55 LEU cc_start: 0.7599 (tp) cc_final: 0.6915 (mp) REVERT: C 290 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8269 (mt) REVERT: C 327 ARG cc_start: 0.7459 (mtt180) cc_final: 0.6779 (mmt-90) REVERT: C 347 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.6954 (mppt) REVERT: C 409 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7885 (mtpt) REVERT: C 435 GLU cc_start: 0.8604 (tt0) cc_final: 0.7768 (mp0) REVERT: C 469 MET cc_start: 0.8960 (mtt) cc_final: 0.8736 (mtt) REVERT: C 508 LYS cc_start: 0.8005 (pttp) cc_final: 0.7512 (mmtp) REVERT: C 595 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7848 (mtt-85) REVERT: C 637 ASP cc_start: 0.7876 (t0) cc_final: 0.7564 (t0) outliers start: 57 outliers final: 30 residues processed: 251 average time/residue: 0.6154 time to fit residues: 170.5413 Evaluate side-chains 249 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 205 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 LYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1675 LYS Chi-restraints excluded: chain A residue 1692 GLN Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 699 HIS Chi-restraints excluded: chain C residue 711 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 152 optimal weight: 0.6980 chunk 186 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 130 optimal weight: 7.9990 chunk 120 optimal weight: 6.9990 chunk 27 optimal weight: 0.0570 overall best weight: 1.3504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 GLN A 348 GLN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN A1438 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS C 304 ASN C 559 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.165415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.131505 restraints weight = 15479.124| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.36 r_work: 0.3317 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16519 Z= 0.205 Angle : 0.758 17.459 22417 Z= 0.344 Chirality : 0.064 0.687 2420 Planarity : 0.005 0.061 2745 Dihedral : 14.043 178.956 2469 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.19 % Allowed : 24.70 % Favored : 72.12 % 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: 0.33 (0.19), residues: 1858 helix: 1.08 (0.20), residues: 713 sheet: -1.14 (0.27), residues: 269 loop : 0.09 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 382 TYR 0.018 0.002 TYR C 277 PHE 0.026 0.002 PHE C 254 TRP 0.014 0.002 TRP A 612 HIS 0.009 0.001 HIS C 699 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (16503) covalent geometry : angle 0.75077 / 0.34 (22396) hydrogen bonds : bond 0.04076 / 2.72 ( 667) hydrogen bonds : angle 5.18809 / 3.60 ( 1956) metal coordination : bond 0.00657 / 0.37 ( 16) metal coordination : angle 3.41731 / 1.91 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 207 time to evaluate : 0.613 Fit side-chains REVERT: A 95 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7250 (m-30) REVERT: A 100 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7895 (ttpt) REVERT: A 147 LYS cc_start: 0.8448 (mppt) cc_final: 0.7988 (ttpt) REVERT: A 291 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.6933 (pp20) REVERT: A 357 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8194 (ttpp) REVERT: A 511 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8699 (mtt90) REVERT: A 545 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8730 (tm) REVERT: A 581 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: A 693 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7502 (mm-30) REVERT: A 815 LYS cc_start: 0.8466 (mttp) cc_final: 0.7937 (mppt) REVERT: A 869 ASP cc_start: 0.6324 (OUTLIER) cc_final: 0.5959 (m-30) REVERT: A 944 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7437 (pp20) REVERT: A 955 ASN cc_start: 0.8491 (m110) cc_final: 0.8093 (m110) REVERT: A 985 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8077 (mttt) REVERT: A 1493 LYS cc_start: 0.6794 (mttt) cc_final: 0.6055 (mmtm) REVERT: A 1692 GLN cc_start: 0.5076 (OUTLIER) cc_final: 0.4730 (pt0) REVERT: C 22 LYS cc_start: 0.6897 (OUTLIER) cc_final: 0.6345 (mmtm) REVERT: C 55 LEU cc_start: 0.7633 (tp) cc_final: 0.7013 (mp) REVERT: C 290 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8294 (mt) REVERT: C 327 ARG cc_start: 0.7463 (mtt180) cc_final: 0.6762 (mmt-90) REVERT: C 347 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7004 (mppt) REVERT: C 409 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7876 (mtpt) REVERT: C 435 GLU cc_start: 0.8565 (tt0) cc_final: 0.7784 (mp0) REVERT: C 508 LYS cc_start: 0.7976 (pttp) cc_final: 0.7529 (mmtp) REVERT: C 595 ARG cc_start: 0.8209 (mtp85) cc_final: 0.7839 (mtt-85) REVERT: C 637 ASP cc_start: 0.7862 (t0) cc_final: 0.7573 (t0) outliers start: 53 outliers final: 29 residues processed: 242 average time/residue: 0.6340 time to fit residues: 169.4050 Evaluate side-chains 245 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 985 LYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1617 HIS Chi-restraints excluded: chain A residue 1675 LYS Chi-restraints excluded: chain A residue 1692 GLN Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 613 SER Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 134 optimal weight: 0.9990 chunk 96 optimal weight: 0.0470 chunk 189 optimal weight: 5.9990 chunk 60 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 179 ASN A 286 GLN A 348 GLN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN A1438 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS C 304 ASN C 559 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.166627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.132848 restraints weight = 15473.322| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.37 r_work: 0.3335 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16519 Z= 0.170 Angle : 0.730 16.567 22417 Z= 0.333 Chirality : 0.062 0.657 2420 Planarity : 0.005 0.060 2745 Dihedral : 14.042 179.863 2469 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.12 % Allowed : 25.00 % Favored : 71.88 % 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: 0.39 (0.19), residues: 1858 helix: 1.15 (0.20), residues: 712 sheet: -1.15 (0.27), residues: 269 loop : 0.13 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 382 TYR 0.016 0.002 TYR C 277 PHE 0.029 0.002 PHE C 254 TRP 0.014 0.001 TRP A 612 HIS 0.008 0.001 HIS C 699 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (16503) covalent geometry : angle 0.72280 / 0.33 (22396) hydrogen bonds : bond 0.03950 / 2.64 ( 667) hydrogen bonds : angle 5.15346 / 3.58 ( 1956) metal coordination : bond 0.00569 / 0.32 ( 16) metal coordination : angle 3.38568 / 1.90 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.445 Fit side-chains REVERT: A 95 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7246 (m-30) REVERT: A 100 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7831 (ttpt) REVERT: A 147 LYS cc_start: 0.8400 (mppt) cc_final: 0.7965 (ttpt) REVERT: A 291 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6918 (pp20) REVERT: A 357 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8199 (ttpp) REVERT: A 511 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8695 (mtt90) REVERT: A 545 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8694 (tm) REVERT: A 581 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7676 (pt0) REVERT: A 693 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7518 (mm-30) REVERT: A 815 LYS cc_start: 0.8461 (mttp) cc_final: 0.7932 (mppt) REVERT: A 869 ASP cc_start: 0.6399 (OUTLIER) cc_final: 0.6033 (m-30) REVERT: A 944 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7431 (pp20) REVERT: A 955 ASN cc_start: 0.8499 (m110) cc_final: 0.8094 (m110) REVERT: A 985 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8074 (mttt) REVERT: A 1493 LYS cc_start: 0.6758 (mttt) cc_final: 0.6038 (mmtm) REVERT: A 1509 THR cc_start: 0.8425 (m) cc_final: 0.8188 (p) REVERT: A 1692 GLN cc_start: 0.5043 (OUTLIER) cc_final: 0.4706 (pt0) REVERT: C 22 LYS cc_start: 0.6835 (OUTLIER) cc_final: 0.6327 (mmtm) REVERT: C 55 LEU cc_start: 0.7584 (tp) cc_final: 0.6945 (mp) REVERT: C 155 LYS cc_start: 0.7169 (OUTLIER) cc_final: 0.6347 (ttmp) REVERT: C 290 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8292 (mt) REVERT: C 327 ARG cc_start: 0.7461 (mtt180) cc_final: 0.6768 (mmt-90) REVERT: C 347 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.6918 (mppt) REVERT: C 435 GLU cc_start: 0.8550 (tt0) cc_final: 0.7764 (mp0) REVERT: C 595 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7824 (mtt-85) REVERT: C 637 ASP cc_start: 0.7851 (t0) cc_final: 0.7550 (t0) outliers start: 52 outliers final: 28 residues processed: 235 average time/residue: 0.6190 time to fit residues: 160.3071 Evaluate side-chains 245 residues out of total 1664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 202 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 100 LYS Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 357 LYS Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 511 ARG Chi-restraints excluded: chain A residue 518 VAL Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 581 GLU Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 869 ASP Chi-restraints excluded: chain A residue 944 GLU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 985 LYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1675 LYS Chi-restraints excluded: chain A residue 1692 GLN Chi-restraints excluded: chain C residue 22 LYS Chi-restraints excluded: chain C residue 80 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 155 LYS Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 253 ASP Chi-restraints excluded: chain C residue 254 PHE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 517 CYS Chi-restraints excluded: chain C residue 567 SER Chi-restraints excluded: chain C residue 645 VAL Chi-restraints excluded: chain C residue 664 VAL Chi-restraints excluded: chain C residue 671 SER Chi-restraints excluded: chain C residue 711 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 151 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 chunk 175 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 112 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN A 348 GLN ** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 986 ASN A1438 ASN ** A1506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1617 HIS C 119 GLN C 210 HIS C 304 ASN C 559 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.168898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.133893 restraints weight = 15494.163| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.36 r_work: 0.3368 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16519 Z= 0.147 Angle : 0.697 15.303 22417 Z= 0.319 Chirality : 0.059 0.611 2420 Planarity : 0.004 0.058 2745 Dihedral : 13.900 178.635 2469 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.70 % Allowed : 26.08 % Favored : 71.21 % 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: 0.51 (0.19), residues: 1858 helix: 1.28 (0.20), residues: 710 sheet: -1.07 (0.28), residues: 269 loop : 0.16 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 578 TYR 0.016 0.001 TYR C 704 PHE 0.026 0.001 PHE C 254 TRP 0.014 0.001 TRP A 612 HIS 0.010 0.001 HIS C 699 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (16503) covalent geometry : angle 0.69008 / 0.32 (22396) hydrogen bonds : bond 0.03803 / 2.55 ( 667) hydrogen bonds : angle 5.03549 / 3.49 ( 1956) metal coordination : bond 0.00545 / 0.34 ( 16) metal coordination : angle 3.21275 / 1.81 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5585.83 seconds wall clock time: 96 minutes 9.60 seconds (5769.60 seconds total)