Starting phenix.real_space_refine on Fri Jul 3 23:31:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y85_33681/07_2026/7y85_33681.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y85_33681/07_2026/7y85_33681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y85_33681/07_2026/7y85_33681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y85_33681/07_2026/7y85_33681.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7y85_33681/07_2026/7y85_33681.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y85_33681/07_2026/7y85_33681.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y85_33681/07_2026/7y85_33681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y85_33681/07_2026/7y85_33681.cif" } resolution = 2.73 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= 0.218 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 59 5.49 5 Mg 1 5.21 5 S 56 5.16 5 C 10284 2.51 5 N 2862 2.21 5 O 3236 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16502 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1232, 9941 Classifications: {'peptide': 1232} Link IDs: {'PTRANS': 58, 'TRANS': 1173} Chain breaks: 9 Chain: "B" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 757 Classifications: {'RNA': 36} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 10, 'rna3p_pur': 5, 'rna3p_pyr': 11} Link IDs: {'rna2p': 20, 'rna3p': 15} Chain: "C" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 496 Classifications: {'RNA': 23} Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 14, 'rna3p_pyr': 6} Link IDs: {'rna2p': 3, 'rna3p': 19} Chain: "D" Number of atoms: 5303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 652, 5303 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 5602 SG CYS A 750 47.049 32.564 71.788 1.00 94.79 S ATOM 5615 SG CYS A 752 44.045 33.881 73.684 1.00 81.51 S ATOM 5637 SG CYS A 755 46.744 36.305 72.550 1.00 83.83 S ATOM 3527 SG CYS A 491 48.404 50.205 48.362 1.00 96.92 S ATOM 3595 SG CYS A 501 48.817 50.090 44.835 1.00 81.08 S ATOM 3609 SG CYS A 503 45.580 51.529 46.224 1.00 80.61 S ATOM 3631 SG CYS A 506 48.792 53.564 46.794 1.00 77.65 S ATOM 7528 SG CYS A1018 52.973 34.547 108.275 1.00 92.82 S ATOM 7724 SG CYS A1406 53.817 32.771 105.027 1.00 87.47 S ATOM 7775 SG CYS A1414 50.452 32.245 106.711 1.00 92.36 S ATOM 7792 SG CYS A1417 51.062 35.493 105.093 1.00 95.26 S ATOM 668 SG CYS A 88 56.259 69.552 22.627 1.00 86.53 S ATOM 939 SG CYS A 121 58.076 72.372 20.716 1.00 93.44 S ATOM 985 SG CYS A 127 56.652 72.986 24.153 1.00 80.77 S ATOM 1009 SG CYS A 130 59.592 70.552 23.731 1.00 70.98 S Time building chain proxies: 3.43, per 1000 atoms: 0.21 Number of scatterers: 16502 At special positions: 0 Unit cell: (100.1, 96.8, 158.4, 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 56 16.00 P 59 15.00 Mg 1 11.99 O 3236 8.00 N 2862 7.00 C 10284 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: 1.49 Conformation dependent library (CDL) restraints added in 663.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 752 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 755 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 491 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 501 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 506 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1406 " pdb=" ZN A1805 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 130 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 88 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 127 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 121 " Number of angles added : 21 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3488 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 23 sheets defined 42.5% alpha, 19.6% beta 14 base pairs and 23 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 4.069A 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 removed outlier: 3.564A pdb=" N GLY A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 290 through 307 removed outlier: 4.248A pdb=" N ARG A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N HIS A 306 " --> pdb=" O THR A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 338 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: 3.647A pdb=" N GLU A 508 " --> pdb=" O LYS A 504 " (cutoff:3.500A) removed outlier: 3.660A 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 618 through 624 Processing helix chain 'A' and resid 625 through 628 Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.591A pdb=" N LEU A 642 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 665 removed outlier: 3.515A pdb=" N GLU A 663 " --> pdb=" O PHE A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 692 removed outlier: 3.689A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 740 removed outlier: 3.503A pdb=" N PHE A 731 " --> pdb=" O HIS A 727 " (cutoff:3.500A) removed outlier: 3.520A 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 831 through 847 Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.557A pdb=" N LYS A 912 " --> pdb=" O HIS A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1015 Processing helix chain 'A' and resid 1394 through 1399 Processing helix chain 'A' and resid 1414 through 1420 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 4.240A 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 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 Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1662 through 1668 Processing helix chain 'A' and resid 1673 through 1683 Processing helix chain 'D' and resid 16 through 33 removed outlier: 4.240A pdb=" N ARG D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP D 29 " --> pdb=" O GLU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 60 removed outlier: 3.721A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU D 55 " --> pdb=" O ILE D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 63 No H-bonds generated for 'chain 'D' and resid 61 through 63' Processing helix chain 'D' and resid 64 through 81 removed outlier: 3.875A pdb=" N ALA D 72 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG D 73 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE D 80 " --> pdb=" O TYR D 76 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 109 removed outlier: 3.508A pdb=" N PHE D 103 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN D 109 " --> pdb=" O ASP D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 136 Processing helix chain 'D' and resid 141 through 155 Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.832A pdb=" N ILE D 167 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU D 176 " --> pdb=" O ARG D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.685A pdb=" N LEU D 187 " --> pdb=" O HIS D 183 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE D 188 " --> pdb=" O PHE D 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 183 through 188' Processing helix chain 'D' and resid 194 through 202 Processing helix chain 'D' and resid 210 through 223 removed outlier: 4.348A pdb=" N GLU D 214 " --> pdb=" O HIS D 210 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 244 removed outlier: 3.772A pdb=" N ASP D 234 " --> pdb=" O HIS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.525A pdb=" N ILE D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 296 removed outlier: 4.325A pdb=" N ARG D 282 " --> pdb=" O TRP D 278 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL D 283 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 323 removed outlier: 3.819A pdb=" N ILE D 310 " --> pdb=" O LYS D 306 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA D 314 " --> pdb=" O ILE D 310 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG D 323 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 333 removed outlier: 3.785A pdb=" N LYS D 333 " --> pdb=" O SER D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 361 removed outlier: 4.446A pdb=" N TYR D 360 " --> pdb=" O TYR D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 451 removed outlier: 4.180A pdb=" N LEU D 436 " --> pdb=" O GLN D 432 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU D 438 " --> pdb=" O LYS D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 469 removed outlier: 3.503A pdb=" N THR D 460 " --> pdb=" O GLU D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 473 Processing helix chain 'D' and resid 489 through 494 Processing helix chain 'D' and resid 509 through 514 removed outlier: 4.048A pdb=" N ASN D 513 " --> pdb=" O LEU D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 521 through 525 Processing helix chain 'D' and resid 543 through 547 Processing helix chain 'D' and resid 566 through 573 removed outlier: 3.561A pdb=" N GLU D 571 " --> pdb=" O SER D 567 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE D 573 " --> pdb=" O ASP D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 595 Processing helix chain 'D' and resid 607 through 614 Processing helix chain 'D' and resid 627 through 632 Processing helix chain 'D' and resid 644 through 652 removed outlier: 3.656A pdb=" N ALA D 648 " --> pdb=" O SER D 644 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 679 removed outlier: 3.681A pdb=" N THR D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN D 679 " --> pdb=" O TRP D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 691 removed outlier: 3.892A pdb=" N TRP D 687 " --> pdb=" O LYS D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 708 removed outlier: 3.722A pdb=" N PHE D 703 " --> pdb=" O HIS D 699 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.718A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ARG A 19 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N TRP A 44 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N TRP A 46 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 12.985A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ARG A 180 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N TYR A 191 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU A 178 " --> pdb=" O TYR A 191 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ARG A 193 " --> pdb=" O ARG A 176 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A 176 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N TRP A 195 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER A 174 " --> pdb=" O TRP A 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 168 removed outlier: 3.749A pdb=" N LEU A 167 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 6.718A 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 110 through 111 removed outlier: 5.841A 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 512 through 514 removed outlier: 6.453A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.453A pdb=" N GLU A 415 " --> pdb=" O GLU A 611 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU A 611 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ILE A 417 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ILE A 609 " --> pdb=" O ILE A 417 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 432 removed outlier: 4.134A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AA9, first strand: chain 'A' and resid 526 through 533 removed outlier: 10.325A pdb=" N GLU A 526 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ASP A 547 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 10.727A pdb=" N ARG A 528 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 9.451A pdb=" N LEU A 545 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N ARG A 530 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N GLY A 543 " --> pdb=" O ARG A 530 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ALA A 532 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.519A 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: 5.519A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLN A 673 " --> pdb=" O ILE A 868 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ILE A 868 " --> pdb=" O GLN A 673 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR A 675 " --> pdb=" O ILE A 866 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE A 866 " --> pdb=" O THR A 675 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLU A 677 " --> pdb=" O ALA A 864 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.088A pdb=" N ALA A 699 " --> pdb=" O TYR A 808 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ALA A 803 " --> pdb=" O ALA A 791 " (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: 6.272A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N ALA A1434 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ASP A1521 " --> pdb=" O ALA A1434 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N TYR A1436 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N SER A1519 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A1438 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.728A 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: 6.860A pdb=" N VAL A1517 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N THR A 960 " --> pdb=" O VAL A1517 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER A1519 " --> pdb=" O LEU A 958 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU A 958 " --> pdb=" O SER A1519 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N ASP A1521 " --> pdb=" O CYS A 956 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N CYS A 956 " --> pdb=" O ASP A1521 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ARG A1523 " --> pdb=" O ILE A 954 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 954 " --> pdb=" O ARG A1523 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLU A1525 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLY A 952 " --> pdb=" O GLU A1525 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU A1567 " --> pdb=" O VAL A1582 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 967 through 968 removed outlier: 4.439A pdb=" N LYS A 988 " --> pdb=" O ASP A 968 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N PHE A 989 " --> 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 'D' and resid 274 through 276 removed outlier: 6.587A pdb=" N ARG D 275 " --> pdb=" O LEU D 326 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 425 through 431 Processing sheet with id=AC4, first strand: chain 'D' and resid 536 through 540 removed outlier: 6.180A pdb=" N LEU D 580 " --> pdb=" O ILE D 623 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL D 622 " --> pdb=" O VAL D 658 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N THR D 660 " --> pdb=" O VAL D 622 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N LEU D 624 " --> pdb=" O THR D 660 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 586 through 587 649 hydrogen bonds defined for protein. 1809 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 74 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 23 stacking parallelities Total time for adding SS restraints: 3.61 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2831 1.32 - 1.45: 4756 1.45 - 1.57: 9203 1.57 - 1.69: 116 1.69 - 1.82: 78 Bond restraints: 16984 Sorted by residual: bond pdb=" O3' C B 45 " pdb=" P U B 46 " ideal model delta sigma weight residual 1.607 1.537 0.070 1.50e-02 4.44e+03 2.16e+01 bond pdb=" C PRO A 911 " pdb=" O PRO A 911 " ideal model delta sigma weight residual 1.237 1.198 0.039 1.26e-02 6.30e+03 9.57e+00 bond pdb=" N SER A 910 " pdb=" CA SER A 910 " ideal model delta sigma weight residual 1.461 1.489 -0.028 9.20e-03 1.18e+04 9.41e+00 bond pdb=" C PRO A1614 " pdb=" O PRO A1614 " ideal model delta sigma weight residual 1.233 1.206 0.028 1.06e-02 8.90e+03 6.83e+00 bond pdb=" P U B 46 " pdb=" OP2 U B 46 " ideal model delta sigma weight residual 1.485 1.437 0.048 2.00e-02 2.50e+03 5.85e+00 ... (remaining 16979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 22771 1.84 - 3.68: 342 3.68 - 5.53: 44 5.53 - 7.37: 8 7.37 - 9.21: 5 Bond angle restraints: 23170 Sorted by residual: angle pdb=" C3' C B 45 " pdb=" O3' C B 45 " pdb=" P U B 46 " ideal model delta sigma weight residual 120.20 111.64 8.56 1.50e+00 4.44e-01 3.26e+01 angle pdb=" O3' U B 46 " pdb=" C3' U B 46 " pdb=" C2' U B 46 " ideal model delta sigma weight residual 109.50 101.58 7.92 1.50e+00 4.44e-01 2.79e+01 angle pdb=" C ALA D 601 " pdb=" CA ALA D 601 " pdb=" CB ALA D 601 " ideal model delta sigma weight residual 117.23 110.17 7.06 1.36e+00 5.41e-01 2.69e+01 angle pdb=" O4' G B 47 " pdb=" C1' G B 47 " pdb=" N9 G B 47 " ideal model delta sigma weight residual 108.20 115.76 -7.56 1.50e+00 4.44e-01 2.54e+01 angle pdb=" C3' U B 46 " pdb=" C2' U B 46 " pdb=" O2' U B 46 " ideal model delta sigma weight residual 114.60 121.66 -7.06 1.50e+00 4.44e-01 2.22e+01 ... (remaining 23165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.70: 9493 34.70 - 69.41: 532 69.41 - 104.11: 30 104.11 - 138.81: 1 138.81 - 173.52: 1 Dihedral angle restraints: 10057 sinusoidal: 4636 harmonic: 5421 Sorted by residual: dihedral pdb=" O4' U C 14 " pdb=" C1' U C 14 " pdb=" N1 U C 14 " pdb=" C2 U C 14 " ideal model delta sinusoidal sigma weight residual 232.00 58.48 173.52 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" CA CYS A 491 " pdb=" C CYS A 491 " pdb=" N ASN A 492 " pdb=" CA ASN A 492 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" C4' U B 46 " pdb=" C3' U B 46 " pdb=" C2' U B 46 " pdb=" C1' U B 46 " ideal model delta sinusoidal sigma weight residual -35.00 -7.95 -27.05 1 8.00e+00 1.56e-02 1.64e+01 ... (remaining 10054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2321 0.074 - 0.147: 195 0.147 - 0.221: 6 0.221 - 0.294: 2 0.294 - 0.368: 2 Chirality restraints: 2526 Sorted by residual: chirality pdb=" C1' G B 47 " pdb=" O4' G B 47 " pdb=" C2' G B 47 " pdb=" N9 G B 47 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" C2' U B 46 " pdb=" C3' U B 46 " pdb=" O2' U B 46 " pdb=" C1' U B 46 " both_signs ideal model delta sigma weight residual False -2.52 -2.17 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" P U B 46 " pdb=" OP1 U B 46 " pdb=" OP2 U B 46 " pdb=" O5' U B 46 " both_signs ideal model delta sigma weight residual True 2.41 -2.13 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2523 not shown) Planarity restraints: 2755 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 47 " 0.047 2.00e-02 2.50e+03 2.19e-02 1.44e+01 pdb=" N9 G B 47 " -0.057 2.00e-02 2.50e+03 pdb=" C8 G B 47 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G B 47 " 0.003 2.00e-02 2.50e+03 pdb=" C5 G B 47 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G B 47 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G B 47 " 0.013 2.00e-02 2.50e+03 pdb=" N1 G B 47 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 47 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G B 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G B 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G B 47 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 23 " 0.029 2.00e-02 2.50e+03 1.50e-02 5.09e+00 pdb=" N1 U B 23 " -0.033 2.00e-02 2.50e+03 pdb=" C2 U B 23 " -0.003 2.00e-02 2.50e+03 pdb=" O2 U B 23 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U B 23 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U B 23 " 0.002 2.00e-02 2.50e+03 pdb=" O4 U B 23 " 0.009 2.00e-02 2.50e+03 pdb=" C5 U B 23 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U B 23 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C B 45 " -0.029 2.00e-02 2.50e+03 1.49e-02 4.97e+00 pdb=" N1 C B 45 " 0.032 2.00e-02 2.50e+03 pdb=" C2 C B 45 " 0.002 2.00e-02 2.50e+03 pdb=" O2 C B 45 " 0.002 2.00e-02 2.50e+03 pdb=" N3 C B 45 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C B 45 " -0.003 2.00e-02 2.50e+03 pdb=" N4 C B 45 " -0.010 2.00e-02 2.50e+03 pdb=" C5 C B 45 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C B 45 " 0.005 2.00e-02 2.50e+03 ... (remaining 2752 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 180 2.53 - 3.12: 12223 3.12 - 3.72: 28935 3.72 - 4.31: 42608 4.31 - 4.90: 68535 Nonbonded interactions: 152481 Sorted by model distance: nonbonded pdb=" OP2 U B 26 " pdb="MG MG A1804 " model vdw 1.940 2.170 nonbonded pdb=" OD1 ASP A 137 " pdb="MG MG A1804 " model vdw 1.959 2.170 nonbonded pdb=" O GLY A 134 " pdb="MG MG A1804 " model vdw 2.060 2.170 nonbonded pdb=" O LYS D 321 " pdb=" OH TYR D 643 " model vdw 2.136 3.040 nonbonded pdb=" O ASP A 801 " pdb=" O2' C C 7 " model vdw 2.150 3.040 ... (remaining 152476 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: 1.240 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.240 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 17000 Z= 0.179 Angle : 0.576 9.372 23191 Z= 0.307 Chirality : 0.042 0.368 2526 Planarity : 0.004 0.047 2755 Dihedral : 18.767 173.518 6569 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.87 % Allowed : 30.01 % Favored : 66.12 % 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: -0.05 (0.19), residues: 1850 helix: 0.30 (0.20), residues: 660 sheet: -0.68 (0.28), residues: 268 loop : 0.09 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 252 TYR 0.022 0.002 TYR A 925 PHE 0.015 0.002 PHE D 204 TRP 0.036 0.001 TRP D 675 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (16984) covalent geometry : angle 0.56668 / 0.31 (23170) hydrogen bonds : bond 0.23553 / 15.45 ( 651) hydrogen bonds : angle 8.32052 / 5.79 ( 1883) metal coordination : bond 0.00908 / 0.55 ( 16) metal coordination : angle 3.55484 / 1.87 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 206 time to evaluate : 0.633 Fit side-chains REVERT: A 639 GLU cc_start: 0.6532 (mt-10) cc_final: 0.6057 (tm-30) REVERT: A 985 LYS cc_start: 0.7333 (mtmm) cc_final: 0.6748 (mtpt) REVERT: A 1022 PHE cc_start: 0.7649 (t80) cc_final: 0.7443 (t80) REVERT: A 1595 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.5465 (t80) REVERT: D 51 ILE cc_start: 0.6500 (mt) cc_final: 0.6292 (pt) REVERT: D 209 ASP cc_start: 0.6117 (m-30) cc_final: 0.5742 (p0) REVERT: D 263 ARG cc_start: 0.7188 (mtp85) cc_final: 0.6785 (mmm160) outliers start: 64 outliers final: 55 residues processed: 266 average time/residue: 0.5316 time to fit residues: 160.8032 Evaluate side-chains 253 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 197 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 97 SER Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 517 SER Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 765 SER Chi-restraints excluded: chain A residue 792 ILE Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1422 THR Chi-restraints excluded: chain A residue 1426 LYS Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1511 VAL Chi-restraints excluded: chain A residue 1531 GLU Chi-restraints excluded: chain A residue 1595 TYR Chi-restraints excluded: chain A residue 1613 LEU Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 186 ASN Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 279 SER Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 478 ILE Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 513 ASN Chi-restraints excluded: chain D residue 523 SER Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 615 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain D residue 706 SER Chi-restraints excluded: chain D residue 711 SER Chi-restraints excluded: chain D residue 714 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0870 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.0670 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 459 ASN A1516 ASN A1537 GLN A1584 GLN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 GLN D 427 GLN D 432 GLN D 621 GLN D 699 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.169281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.120341 restraints weight = 17447.440| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.85 r_work: 0.3291 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17000 Z= 0.142 Angle : 0.562 9.133 23191 Z= 0.295 Chirality : 0.042 0.426 2526 Planarity : 0.004 0.047 2755 Dihedral : 12.163 174.480 2833 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 5.08 % Allowed : 25.71 % Favored : 69.21 % 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: 0.20 (0.19), residues: 1850 helix: 0.73 (0.19), residues: 690 sheet: -0.61 (0.28), residues: 275 loop : 0.06 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 252 TYR 0.020 0.002 TYR D 704 PHE 0.016 0.001 PHE D 204 TRP 0.018 0.001 TRP D 675 HIS 0.006 0.001 HIS D 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (16984) covalent geometry : angle 0.55459 / 0.29 (23170) hydrogen bonds : bond 0.04822 / 3.22 ( 651) hydrogen bonds : angle 5.45592 / 3.78 ( 1883) metal coordination : bond 0.00653 / 0.40 ( 16) metal coordination : angle 3.15297 / 1.60 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 257 time to evaluate : 0.529 Fit side-chains REVERT: A 125 GLU cc_start: 0.7885 (tp30) cc_final: 0.6627 (pp20) REVERT: A 159 ASP cc_start: 0.8064 (m-30) cc_final: 0.7733 (m-30) REVERT: A 275 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6428 (mtpt) REVERT: A 703 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8280 (pttm) REVERT: A 802 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.6916 (mppt) REVERT: A 985 LYS cc_start: 0.7068 (mtmm) cc_final: 0.6630 (mttp) REVERT: A 1022 PHE cc_start: 0.7907 (t80) cc_final: 0.7554 (t80) REVERT: A 1395 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6666 (mp) REVERT: A 1474 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.7000 (pm20) REVERT: A 1488 ARG cc_start: 0.7152 (mtt90) cc_final: 0.6880 (mtt-85) REVERT: A 1528 ARG cc_start: 0.8557 (mpp80) cc_final: 0.8233 (mpp80) REVERT: A 1563 LYS cc_start: 0.7785 (tppt) cc_final: 0.7522 (tppt) REVERT: A 1630 TRP cc_start: 0.8134 (t60) cc_final: 0.7835 (t60) REVERT: D 23 GLU cc_start: 0.7218 (tp30) cc_final: 0.6857 (tp30) REVERT: D 26 ARG cc_start: 0.6672 (ppt170) cc_final: 0.6253 (ppt170) REVERT: D 181 GLU cc_start: 0.6600 (OUTLIER) cc_final: 0.6135 (mp0) REVERT: D 204 PHE cc_start: 0.6119 (OUTLIER) cc_final: 0.3929 (p90) REVERT: D 209 ASP cc_start: 0.6109 (m-30) cc_final: 0.5769 (p0) REVERT: D 260 ARG cc_start: 0.6930 (mtm-85) cc_final: 0.6711 (mtm-85) REVERT: D 267 LYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6774 (pttm) REVERT: D 513 ASN cc_start: 0.7980 (m-40) cc_final: 0.7745 (m-40) REVERT: D 548 GLU cc_start: 0.7548 (mm-30) cc_final: 0.7287 (mm-30) REVERT: D 671 SER cc_start: 0.7918 (t) cc_final: 0.7351 (m) outliers start: 84 outliers final: 20 residues processed: 323 average time/residue: 0.6160 time to fit residues: 222.5883 Evaluate side-chains 245 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 946 THR Chi-restraints excluded: chain A residue 1395 LEU Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 714 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 112 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 176 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN D 150 ASN D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 503 ASN D 621 GLN D 699 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.162923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112677 restraints weight = 17526.237| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.78 r_work: 0.3173 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 17000 Z= 0.273 Angle : 0.633 12.914 23191 Z= 0.326 Chirality : 0.045 0.406 2526 Planarity : 0.005 0.049 2755 Dihedral : 11.803 167.161 2762 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.63 % Allowed : 26.80 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.19), residues: 1850 helix: 0.52 (0.19), residues: 698 sheet: -0.84 (0.28), residues: 279 loop : 0.07 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 120 TYR 0.030 0.002 TYR A1595 PHE 0.023 0.002 PHE D 477 TRP 0.020 0.002 TRP D 675 HIS 0.006 0.001 HIS D 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00631 / 0.27 (16984) covalent geometry : angle 0.61853 / 0.32 (23170) hydrogen bonds : bond 0.04842 / 3.24 ( 651) hydrogen bonds : angle 5.36021 / 3.72 ( 1883) metal coordination : bond 0.01223 / 0.74 ( 16) metal coordination : angle 4.54134 / 2.46 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 230 time to evaluate : 0.668 Fit side-chains REVERT: A 125 GLU cc_start: 0.7823 (tp30) cc_final: 0.6528 (pp20) REVERT: A 138 ASN cc_start: 0.8337 (m-40) cc_final: 0.8072 (m-40) REVERT: A 159 ASP cc_start: 0.8104 (m-30) cc_final: 0.7773 (m-30) REVERT: A 196 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8415 (mt-10) REVERT: A 275 LYS cc_start: 0.6744 (OUTLIER) cc_final: 0.6448 (mtmm) REVERT: A 417 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8264 (tp) REVERT: A 464 LYS cc_start: 0.8125 (pttt) cc_final: 0.7884 (pttp) REVERT: A 639 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6331 (tm-30) REVERT: A 773 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: A 925 TYR cc_start: 0.8826 (m-80) cc_final: 0.7112 (m-80) REVERT: A 953 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8347 (ttpt) REVERT: A 1463 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7658 (ptm160) REVERT: A 1488 ARG cc_start: 0.7023 (mtt90) cc_final: 0.6722 (mtt-85) REVERT: A 1528 ARG cc_start: 0.8507 (mpp80) cc_final: 0.8267 (mpp80) REVERT: A 1563 LYS cc_start: 0.7872 (tppt) cc_final: 0.7585 (tppt) REVERT: A 1630 TRP cc_start: 0.8318 (t60) cc_final: 0.7720 (t60) REVERT: D 209 ASP cc_start: 0.6148 (m-30) cc_final: 0.5801 (p0) REVERT: D 263 ARG cc_start: 0.7538 (mtp85) cc_final: 0.7155 (mmm160) REVERT: D 267 LYS cc_start: 0.7055 (OUTLIER) cc_final: 0.6702 (pttm) REVERT: D 331 MET cc_start: 0.7222 (mtp) cc_final: 0.6965 (mtm) REVERT: D 342 ASN cc_start: 0.5572 (OUTLIER) cc_final: 0.5092 (t0) REVERT: D 346 LYS cc_start: 0.6008 (mtmt) cc_final: 0.5671 (mtpt) REVERT: D 392 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6989 (tt0) REVERT: D 548 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7278 (mm-30) outliers start: 93 outliers final: 36 residues processed: 299 average time/residue: 0.6358 time to fit residues: 211.7684 Evaluate side-chains 260 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 215 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1519 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 138 GLU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 570 LEU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain D residue 714 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 76 optimal weight: 0.6980 chunk 94 optimal weight: 0.2980 chunk 7 optimal weight: 0.9980 chunk 86 optimal weight: 0.4980 chunk 173 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN A1584 GLN D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 621 GLN D 699 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.168435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119242 restraints weight = 17506.395| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.86 r_work: 0.3260 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17000 Z= 0.132 Angle : 0.542 9.519 23191 Z= 0.279 Chirality : 0.041 0.436 2526 Planarity : 0.004 0.050 2755 Dihedral : 11.680 172.566 2756 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.48 % Allowed : 27.83 % Favored : 67.70 % 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: 1850 helix: 0.89 (0.19), residues: 691 sheet: -0.80 (0.29), residues: 275 loop : 0.19 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 168 TYR 0.018 0.001 TYR D 704 PHE 0.026 0.001 PHE D 477 TRP 0.021 0.001 TRP D 675 HIS 0.006 0.001 HIS D 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (16984) covalent geometry : angle 0.53282 / 0.28 (23170) hydrogen bonds : bond 0.03940 / 2.64 ( 651) hydrogen bonds : angle 4.98389 / 3.47 ( 1883) metal coordination : bond 0.00630 / 0.39 ( 16) metal coordination : angle 3.31225 / 1.63 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 245 time to evaluate : 0.682 Fit side-chains REVERT: A 36 MET cc_start: 0.8956 (mmm) cc_final: 0.8695 (mmp) REVERT: A 138 ASN cc_start: 0.8133 (m-40) cc_final: 0.7908 (m-40) REVERT: A 159 ASP cc_start: 0.8083 (m-30) cc_final: 0.7736 (m-30) REVERT: A 275 LYS cc_start: 0.6809 (OUTLIER) cc_final: 0.6578 (mtmm) REVERT: A 417 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8162 (tp) REVERT: A 464 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7864 (pttp) REVERT: A 617 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8369 (mmtt) REVERT: A 639 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6181 (tm-30) REVERT: A 656 GLU cc_start: 0.8297 (mp0) cc_final: 0.8097 (mp0) REVERT: A 753 ASP cc_start: 0.8235 (m-30) cc_final: 0.7752 (m-30) REVERT: A 925 TYR cc_start: 0.8653 (m-80) cc_final: 0.7282 (m-80) REVERT: A 953 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8419 (ttpt) REVERT: A 997 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8414 (mmt) REVERT: A 1463 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7616 (pmm-80) REVERT: A 1474 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6960 (pm20) REVERT: A 1488 ARG cc_start: 0.7050 (mtt90) cc_final: 0.6799 (mtt-85) REVERT: A 1508 THR cc_start: 0.8103 (m) cc_final: 0.7871 (m) REVERT: A 1514 LYS cc_start: 0.7460 (ptpp) cc_final: 0.7111 (mtmm) REVERT: A 1584 GLN cc_start: 0.5964 (OUTLIER) cc_final: 0.5730 (tm-30) REVERT: A 1593 LYS cc_start: 0.7665 (mtpp) cc_final: 0.7126 (mttt) REVERT: A 1630 TRP cc_start: 0.8393 (t60) cc_final: 0.7670 (t60) REVERT: D 23 GLU cc_start: 0.7033 (tp30) cc_final: 0.6639 (tp30) REVERT: D 151 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6578 (tt0) REVERT: D 164 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5108 (tp30) REVERT: D 209 ASP cc_start: 0.6120 (m-30) cc_final: 0.5840 (p0) REVERT: D 267 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6395 (pttm) REVERT: D 323 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7367 (ptp-170) REVERT: D 342 ASN cc_start: 0.5628 (OUTLIER) cc_final: 0.5162 (t0) REVERT: D 346 LYS cc_start: 0.6111 (mtmt) cc_final: 0.5840 (mtpt) REVERT: D 429 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.6955 (mttp) REVERT: D 548 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7099 (mm-30) REVERT: D 621 GLN cc_start: 0.6870 (OUTLIER) cc_final: 0.6013 (mp10) REVERT: D 671 SER cc_start: 0.7992 (t) cc_final: 0.7404 (m) outliers start: 74 outliers final: 22 residues processed: 302 average time/residue: 0.6520 time to fit residues: 218.9928 Evaluate side-chains 257 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 275 LYS Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain A residue 1584 GLN Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 429 LYS Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 621 GLN Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 702 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 47 optimal weight: 0.9980 chunk 173 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN A1584 GLN A1592 ASN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.165032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114987 restraints weight = 17471.158| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.86 r_work: 0.3220 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 17000 Z= 0.207 Angle : 0.585 12.150 23191 Z= 0.301 Chirality : 0.043 0.419 2526 Planarity : 0.004 0.052 2755 Dihedral : 11.551 169.880 2750 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.60 % Allowed : 28.07 % Favored : 67.33 % 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: 0.23 (0.19), residues: 1850 helix: 0.82 (0.19), residues: 697 sheet: -0.86 (0.29), residues: 275 loop : 0.12 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 168 TYR 0.033 0.002 TYR A1595 PHE 0.026 0.002 PHE D 477 TRP 0.024 0.002 TRP D 675 HIS 0.005 0.001 HIS D 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (16984) covalent geometry : angle 0.57301 / 0.30 (23170) hydrogen bonds : bond 0.04172 / 2.80 ( 651) hydrogen bonds : angle 5.03125 / 3.51 ( 1883) metal coordination : bond 0.00945 / 0.57 ( 16) metal coordination : angle 4.00370 / 2.03 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 230 time to evaluate : 0.746 Fit side-chains REVERT: A 138 ASN cc_start: 0.8386 (m-40) cc_final: 0.8058 (m-40) REVERT: A 159 ASP cc_start: 0.8029 (m-30) cc_final: 0.7676 (m-30) REVERT: A 417 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8252 (tp) REVERT: A 464 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7891 (pttp) REVERT: A 639 GLU cc_start: 0.6736 (mt-10) cc_final: 0.6296 (tm-30) REVERT: A 773 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7237 (mm-30) REVERT: A 925 TYR cc_start: 0.8743 (m-80) cc_final: 0.7188 (m-80) REVERT: A 953 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.8410 (ttpt) REVERT: A 997 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8270 (mmt) REVERT: A 1488 ARG cc_start: 0.7036 (mtt90) cc_final: 0.6754 (mtt-85) REVERT: A 1508 THR cc_start: 0.8165 (m) cc_final: 0.7913 (m) REVERT: A 1563 LYS cc_start: 0.7831 (tppt) cc_final: 0.7622 (tppt) REVERT: A 1593 LYS cc_start: 0.7743 (mtpp) cc_final: 0.7216 (mttt) REVERT: A 1630 TRP cc_start: 0.8462 (t60) cc_final: 0.7702 (t60) REVERT: D 23 GLU cc_start: 0.7000 (tp30) cc_final: 0.6681 (tp30) REVERT: D 164 GLU cc_start: 0.6339 (OUTLIER) cc_final: 0.5116 (tp30) REVERT: D 267 LYS cc_start: 0.6870 (OUTLIER) cc_final: 0.6459 (pttm) REVERT: D 323 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7506 (ptp-170) REVERT: D 392 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7087 (tt0) REVERT: D 429 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7567 (mmtm) REVERT: D 548 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7172 (mm-30) REVERT: D 621 GLN cc_start: 0.6947 (mm-40) cc_final: 0.6236 (mp10) REVERT: D 670 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.6577 (mttp) REVERT: D 671 SER cc_start: 0.8015 (t) cc_final: 0.7416 (m) outliers start: 76 outliers final: 33 residues processed: 286 average time/residue: 0.6325 time to fit residues: 201.2815 Evaluate side-chains 262 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 218 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1393 LYS Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 323 ARG Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain D residue 429 LYS Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 670 LYS Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 702 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 31 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 150 optimal weight: 5.9990 chunk 177 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 163 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN D 133 ASN D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN D 621 GLN D 699 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.161328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110752 restraints weight = 17502.307| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.84 r_work: 0.3138 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 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 : 0.007 0.059 17000 Z= 0.323 Angle : 0.667 12.960 23191 Z= 0.340 Chirality : 0.047 0.399 2526 Planarity : 0.005 0.061 2755 Dihedral : 11.684 164.068 2750 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 5.93 % Allowed : 26.92 % Favored : 67.15 % 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: 1850 helix: 0.52 (0.19), residues: 697 sheet: -1.17 (0.29), residues: 276 loop : 0.01 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 768 TYR 0.023 0.002 TYR D 607 PHE 0.032 0.002 PHE D 477 TRP 0.027 0.002 TRP D 675 HIS 0.005 0.001 HIS A 306 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.32 (16984) covalent geometry : angle 0.65095 / 0.34 (23170) hydrogen bonds : bond 0.04569 / 3.07 ( 651) hydrogen bonds : angle 5.26287 / 3.66 ( 1883) metal coordination : bond 0.01383 / 0.83 ( 16) metal coordination : angle 4.86285 / 2.66 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 236 time to evaluate : 0.558 Fit side-chains REVERT: A 138 ASN cc_start: 0.8348 (m-40) cc_final: 0.8013 (m-40) REVERT: A 275 LYS cc_start: 0.6883 (mppt) cc_final: 0.6566 (mtmm) REVERT: A 417 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8302 (tp) REVERT: A 464 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7873 (pttp) REVERT: A 625 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.5974 (mtt90) REVERT: A 639 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6344 (tm-30) REVERT: A 773 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7246 (mm-30) REVERT: A 925 TYR cc_start: 0.8865 (m-80) cc_final: 0.7222 (m-80) REVERT: A 926 PHE cc_start: 0.8765 (m-80) cc_final: 0.8435 (m-80) REVERT: A 953 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8353 (ttpt) REVERT: A 997 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8288 (mmt) REVERT: A 1474 GLU cc_start: 0.7373 (pt0) cc_final: 0.6935 (pm20) REVERT: A 1488 ARG cc_start: 0.6992 (mtt90) cc_final: 0.6692 (mtt-85) REVERT: A 1493 LYS cc_start: 0.7366 (mttp) cc_final: 0.7111 (mmtp) REVERT: A 1593 LYS cc_start: 0.7779 (mtpp) cc_final: 0.7291 (mttm) REVERT: A 1630 TRP cc_start: 0.8529 (t60) cc_final: 0.8020 (t60) REVERT: D 164 GLU cc_start: 0.6332 (OUTLIER) cc_final: 0.5142 (tp30) REVERT: D 172 ARG cc_start: 0.7155 (OUTLIER) cc_final: 0.6599 (tpm170) REVERT: D 263 ARG cc_start: 0.7578 (mtp85) cc_final: 0.7142 (mmm160) REVERT: D 267 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6460 (pttm) REVERT: D 392 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.7153 (tt0) REVERT: D 429 LYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7640 (mmtm) REVERT: D 460 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8182 (p) REVERT: D 671 SER cc_start: 0.7961 (t) cc_final: 0.7392 (m) outliers start: 98 outliers final: 44 residues processed: 311 average time/residue: 0.6184 time to fit residues: 214.2353 Evaluate side-chains 274 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 218 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 745 GLU Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1676 THR Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain D residue 429 LYS Chi-restraints excluded: chain D residue 460 THR Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 561 VAL Chi-restraints excluded: chain D residue 567 SER Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 702 THR Chi-restraints excluded: chain D residue 714 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 187 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 5 optimal weight: 0.0170 chunk 162 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 38 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS A 900 ASN A1492 GLN A1592 ASN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN D 621 GLN D 699 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.168087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.119120 restraints weight = 17419.867| |-----------------------------------------------------------------------------| r_work (start): 0.3390 rms_B_bonded: 1.84 r_work: 0.3279 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17000 Z= 0.130 Angle : 0.553 9.444 23191 Z= 0.286 Chirality : 0.042 0.433 2526 Planarity : 0.004 0.053 2755 Dihedral : 11.627 171.627 2750 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.51 % Allowed : 29.46 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1850 helix: 0.92 (0.19), residues: 692 sheet: -1.01 (0.29), residues: 275 loop : 0.19 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 168 TYR 0.023 0.002 TYR A1595 PHE 0.035 0.002 PHE D 477 TRP 0.028 0.001 TRP D 675 HIS 0.009 0.001 HIS D 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (16984) covalent geometry : angle 0.54387 / 0.29 (23170) hydrogen bonds : bond 0.03771 / 2.53 ( 651) hydrogen bonds : angle 4.93654 / 3.44 ( 1883) metal coordination : bond 0.00616 / 0.37 ( 16) metal coordination : angle 3.38939 / 1.67 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 230 time to evaluate : 0.631 Fit side-chains REVERT: A 125 GLU cc_start: 0.7915 (tp30) cc_final: 0.6705 (pp20) REVERT: A 138 ASN cc_start: 0.8101 (m-40) cc_final: 0.7768 (m-40) REVERT: A 159 ASP cc_start: 0.8087 (m-30) cc_final: 0.7713 (m-30) REVERT: A 275 LYS cc_start: 0.6913 (mppt) cc_final: 0.6602 (mtmm) REVERT: A 417 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8164 (tp) REVERT: A 464 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7827 (pttp) REVERT: A 609 ILE cc_start: 0.8733 (mt) cc_final: 0.8529 (mt) REVERT: A 617 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8464 (mmtt) REVERT: A 639 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6149 (tm-30) REVERT: A 656 GLU cc_start: 0.8240 (mp0) cc_final: 0.7984 (mp0) REVERT: A 925 TYR cc_start: 0.8705 (m-80) cc_final: 0.7157 (m-80) REVERT: A 953 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8385 (ttpt) REVERT: A 997 MET cc_start: 0.9187 (OUTLIER) cc_final: 0.8433 (mmt) REVERT: A 1022 PHE cc_start: 0.7877 (t80) cc_final: 0.7561 (t80) REVERT: A 1474 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: A 1488 ARG cc_start: 0.6960 (mtt90) cc_final: 0.6708 (mtt-85) REVERT: A 1493 LYS cc_start: 0.7335 (mttp) cc_final: 0.7064 (mmtp) REVERT: A 1508 THR cc_start: 0.8094 (m) cc_final: 0.7838 (m) REVERT: A 1563 LYS cc_start: 0.7768 (tppt) cc_final: 0.7533 (tppt) REVERT: A 1584 GLN cc_start: 0.6547 (tt0) cc_final: 0.5726 (tm-30) REVERT: A 1586 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6825 (t70) REVERT: A 1593 LYS cc_start: 0.7682 (mtpp) cc_final: 0.7194 (mttt) REVERT: A 1630 TRP cc_start: 0.8444 (t60) cc_final: 0.7932 (t60) REVERT: D 23 GLU cc_start: 0.7046 (tp30) cc_final: 0.6620 (tp30) REVERT: D 164 GLU cc_start: 0.6311 (OUTLIER) cc_final: 0.5068 (tp30) REVERT: D 267 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6442 (pttm) REVERT: D 392 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7064 (tt0) REVERT: D 408 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8369 (m-40) REVERT: D 429 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7562 (mmtm) outliers start: 58 outliers final: 21 residues processed: 270 average time/residue: 0.5874 time to fit residues: 177.1958 Evaluate side-chains 244 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 429 LYS Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 702 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 44 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 171 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN A1592 ASN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN D 621 GLN D 699 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118305 restraints weight = 17452.055| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.80 r_work: 0.3248 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17000 Z= 0.144 Angle : 0.562 10.797 23191 Z= 0.290 Chirality : 0.042 0.431 2526 Planarity : 0.004 0.054 2755 Dihedral : 11.548 172.615 2748 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.27 % Allowed : 30.01 % Favored : 66.73 % 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: 0.36 (0.20), residues: 1850 helix: 0.99 (0.19), residues: 693 sheet: -0.94 (0.29), residues: 273 loop : 0.19 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 168 TYR 0.023 0.002 TYR A1595 PHE 0.035 0.002 PHE D 477 TRP 0.031 0.001 TRP D 675 HIS 0.006 0.001 HIS D 642 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (16984) covalent geometry : angle 0.55194 / 0.29 (23170) hydrogen bonds : bond 0.03786 / 2.54 ( 651) hydrogen bonds : angle 4.88201 / 3.41 ( 1883) metal coordination : bond 0.00661 / 0.39 ( 16) metal coordination : angle 3.52453 / 1.71 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 217 time to evaluate : 0.592 Fit side-chains revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8137 (m-30) REVERT: A 138 ASN cc_start: 0.8105 (m-40) cc_final: 0.7739 (m-40) REVERT: A 159 ASP cc_start: 0.8039 (m-30) cc_final: 0.7683 (m-30) REVERT: A 275 LYS cc_start: 0.6856 (mppt) cc_final: 0.6550 (mtmm) REVERT: A 417 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8134 (tp) REVERT: A 464 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7867 (pttp) REVERT: A 609 ILE cc_start: 0.8725 (mt) cc_final: 0.8500 (mt) REVERT: A 639 GLU cc_start: 0.6619 (mt-10) cc_final: 0.6176 (tm-30) REVERT: A 753 ASP cc_start: 0.8203 (m-30) cc_final: 0.7715 (m-30) REVERT: A 925 TYR cc_start: 0.8693 (m-80) cc_final: 0.7088 (m-80) REVERT: A 953 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8256 (ttpt) REVERT: A 997 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8381 (mmt) REVERT: A 1474 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6881 (pm20) REVERT: A 1488 ARG cc_start: 0.6964 (mtt90) cc_final: 0.6633 (mtt-85) REVERT: A 1493 LYS cc_start: 0.7279 (mttp) cc_final: 0.7013 (mmtp) REVERT: A 1508 THR cc_start: 0.8040 (m) cc_final: 0.7789 (m) REVERT: A 1563 LYS cc_start: 0.7732 (tppt) cc_final: 0.7461 (tppt) REVERT: A 1584 GLN cc_start: 0.6478 (tt0) cc_final: 0.5798 (tm-30) REVERT: A 1630 TRP cc_start: 0.8423 (t60) cc_final: 0.7951 (t60) REVERT: D 23 GLU cc_start: 0.6981 (tp30) cc_final: 0.6641 (tp30) REVERT: D 164 GLU cc_start: 0.6168 (OUTLIER) cc_final: 0.4947 (tp30) REVERT: D 180 MET cc_start: 0.7853 (mtp) cc_final: 0.7567 (mtp) REVERT: D 267 LYS cc_start: 0.6715 (OUTLIER) cc_final: 0.6394 (pttm) REVERT: D 392 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6996 (tt0) REVERT: D 408 ASN cc_start: 0.8598 (OUTLIER) cc_final: 0.8374 (m-40) REVERT: D 429 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7512 (mmtm) outliers start: 54 outliers final: 27 residues processed: 259 average time/residue: 0.5961 time to fit residues: 172.9148 Evaluate side-chains 251 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1393 LYS Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 429 LYS Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 702 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 9 optimal weight: 0.1980 chunk 136 optimal weight: 8.9990 chunk 165 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 chunk 137 optimal weight: 0.0050 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN D 699 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.168714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.120368 restraints weight = 17345.315| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.73 r_work: 0.3261 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17000 Z= 0.131 Angle : 0.553 10.371 23191 Z= 0.284 Chirality : 0.041 0.438 2526 Planarity : 0.004 0.054 2755 Dihedral : 11.544 174.213 2746 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.78 % Allowed : 30.97 % Favored : 66.24 % 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: 0.42 (0.20), residues: 1850 helix: 1.06 (0.19), residues: 693 sheet: -0.92 (0.30), residues: 273 loop : 0.21 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 168 TYR 0.037 0.002 TYR A1595 PHE 0.035 0.001 PHE D 477 TRP 0.033 0.001 TRP D 675 HIS 0.005 0.001 HIS D 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (16984) covalent geometry : angle 0.54414 / 0.28 (23170) hydrogen bonds : bond 0.03710 / 2.49 ( 651) hydrogen bonds : angle 4.82192 / 3.36 ( 1883) metal coordination : bond 0.00600 / 0.35 ( 16) metal coordination : angle 3.36930 / 1.64 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.8123 (m-30) REVERT: A 138 ASN cc_start: 0.8135 (m-40) cc_final: 0.7870 (m-40) REVERT: A 159 ASP cc_start: 0.8057 (m-30) cc_final: 0.7719 (m-30) REVERT: A 236 ARG cc_start: 0.7988 (ptp-170) cc_final: 0.7698 (mtp85) REVERT: A 275 LYS cc_start: 0.6878 (mppt) cc_final: 0.6506 (mtmm) REVERT: A 417 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8131 (tp) REVERT: A 464 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7843 (pttp) REVERT: A 609 ILE cc_start: 0.8719 (mt) cc_final: 0.8495 (mt) REVERT: A 639 GLU cc_start: 0.6599 (mt-10) cc_final: 0.6180 (tm-30) REVERT: A 674 TYR cc_start: 0.8842 (p90) cc_final: 0.8506 (p90) REVERT: A 753 ASP cc_start: 0.8218 (m-30) cc_final: 0.7894 (m-30) REVERT: A 925 TYR cc_start: 0.8661 (m-80) cc_final: 0.7183 (m-80) REVERT: A 953 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8240 (ttpt) REVERT: A 997 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8405 (mmt) REVERT: A 1022 PHE cc_start: 0.7776 (t80) cc_final: 0.7540 (t80) REVERT: A 1474 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6871 (pm20) REVERT: A 1488 ARG cc_start: 0.7017 (mtt90) cc_final: 0.6690 (mtt-85) REVERT: A 1508 THR cc_start: 0.7975 (m) cc_final: 0.7718 (m) REVERT: A 1514 LYS cc_start: 0.7346 (ptpp) cc_final: 0.7093 (mtmm) REVERT: A 1563 LYS cc_start: 0.7742 (tppt) cc_final: 0.7491 (tppt) REVERT: A 1584 GLN cc_start: 0.6503 (tt0) cc_final: 0.5809 (tm-30) REVERT: A 1586 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.6783 (t70) REVERT: A 1630 TRP cc_start: 0.8430 (t60) cc_final: 0.7726 (t60) REVERT: D 23 GLU cc_start: 0.7117 (tp30) cc_final: 0.6659 (tp30) REVERT: D 26 ARG cc_start: 0.6566 (ppt90) cc_final: 0.6333 (ppt170) REVERT: D 267 LYS cc_start: 0.6770 (OUTLIER) cc_final: 0.6435 (pttm) REVERT: D 392 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6994 (tt0) REVERT: D 429 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7052 (mttp) REVERT: D 475 ASP cc_start: 0.6589 (m-30) cc_final: 0.6211 (m-30) REVERT: D 480 ASN cc_start: 0.6878 (m-40) cc_final: 0.6502 (m-40) REVERT: D 637 ASP cc_start: 0.7692 (t0) cc_final: 0.7451 (t0) REVERT: D 639 MET cc_start: 0.8391 (mpp) cc_final: 0.8146 (mpt) REVERT: D 640 ASP cc_start: 0.7935 (t0) cc_final: 0.7677 (t0) outliers start: 46 outliers final: 27 residues processed: 263 average time/residue: 0.5572 time to fit residues: 163.9257 Evaluate side-chains 255 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain D residue 429 LYS Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 702 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 130 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 180 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 1 optimal weight: 0.0370 overall best weight: 1.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 HIS A1492 GLN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN D 699 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.167025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.117994 restraints weight = 17362.230| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.78 r_work: 0.3250 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17000 Z= 0.168 Angle : 0.569 11.283 23191 Z= 0.292 Chirality : 0.042 0.431 2526 Planarity : 0.004 0.055 2755 Dihedral : 11.499 172.468 2746 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.54 % Allowed : 31.82 % Favored : 65.64 % 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: 1850 helix: 0.96 (0.19), residues: 694 sheet: -0.96 (0.30), residues: 273 loop : 0.16 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 274 TYR 0.019 0.002 TYR D 704 PHE 0.034 0.002 PHE D 477 TRP 0.037 0.001 TRP D 675 HIS 0.005 0.001 HIS D 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 (16984) covalent geometry : angle 0.55831 / 0.29 (23170) hydrogen bonds : bond 0.03816 / 2.57 ( 651) hydrogen bonds : angle 4.87026 / 3.39 ( 1883) metal coordination : bond 0.00750 / 0.44 ( 16) metal coordination : angle 3.61198 / 1.78 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3700 Ramachandran restraints generated. 1850 Oldfield, 0 Emsley, 1850 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 215 time to evaluate : 0.606 Fit side-chains REVERT: A 27 ASP cc_start: 0.8338 (OUTLIER) cc_final: 0.8116 (m-30) REVERT: A 125 GLU cc_start: 0.7834 (tp30) cc_final: 0.6581 (pp20) REVERT: A 138 ASN cc_start: 0.8108 (m-40) cc_final: 0.7737 (m-40) REVERT: A 159 ASP cc_start: 0.8058 (m-30) cc_final: 0.7724 (m-30) REVERT: A 274 ARG cc_start: 0.6386 (ttm110) cc_final: 0.6026 (ttm-80) REVERT: A 275 LYS cc_start: 0.6891 (mppt) cc_final: 0.6520 (mtmm) REVERT: A 417 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8176 (tp) REVERT: A 437 ASP cc_start: 0.7490 (t70) cc_final: 0.7214 (m-30) REVERT: A 464 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.7898 (pttp) REVERT: A 617 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8403 (mtpt) REVERT: A 639 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6204 (tm-30) REVERT: A 753 ASP cc_start: 0.8230 (m-30) cc_final: 0.7895 (m-30) REVERT: A 925 TYR cc_start: 0.8728 (m-80) cc_final: 0.7230 (m-80) REVERT: A 953 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8254 (ttpt) REVERT: A 997 MET cc_start: 0.9173 (OUTLIER) cc_final: 0.8380 (mmt) REVERT: A 1022 PHE cc_start: 0.7824 (t80) cc_final: 0.7587 (t80) REVERT: A 1474 GLU cc_start: 0.7280 (OUTLIER) cc_final: 0.6893 (pm20) REVERT: A 1488 ARG cc_start: 0.7043 (mtt90) cc_final: 0.6708 (mtt-85) REVERT: A 1508 THR cc_start: 0.8048 (m) cc_final: 0.7793 (m) REVERT: A 1563 LYS cc_start: 0.7763 (tppt) cc_final: 0.7505 (tppt) REVERT: A 1584 GLN cc_start: 0.6544 (tt0) cc_final: 0.5817 (tm-30) REVERT: A 1586 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.6814 (t70) REVERT: A 1593 LYS cc_start: 0.7570 (mtpp) cc_final: 0.7123 (mttm) REVERT: A 1630 TRP cc_start: 0.8482 (t60) cc_final: 0.7779 (t60) REVERT: D 23 GLU cc_start: 0.7095 (tp30) cc_final: 0.6649 (tp30) REVERT: D 267 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6467 (pttm) REVERT: D 392 GLU cc_start: 0.7225 (OUTLIER) cc_final: 0.6861 (tt0) REVERT: D 429 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7579 (mmtm) REVERT: D 637 ASP cc_start: 0.7823 (t0) cc_final: 0.7554 (t0) REVERT: D 639 MET cc_start: 0.8435 (mpp) cc_final: 0.8220 (mpt) outliers start: 42 outliers final: 30 residues processed: 248 average time/residue: 0.6171 time to fit residues: 170.9528 Evaluate side-chains 246 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 206 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 473 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 972 GLU Chi-restraints excluded: chain A residue 997 MET Chi-restraints excluded: chain A residue 1001 SER Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1393 LYS Chi-restraints excluded: chain A residue 1458 VAL Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 202 TYR Chi-restraints excluded: chain D residue 204 PHE Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain D residue 429 LYS Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 571 GLU Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 647 THR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 702 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 173 optimal weight: 1.9990 chunk 106 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 0.2980 chunk 192 optimal weight: 0.9980 chunk 9 optimal weight: 0.0020 chunk 172 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 HIS A1492 GLN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN D 699 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.169474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.121387 restraints weight = 17345.176| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.72 r_work: 0.3275 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17000 Z= 0.126 Angle : 0.546 10.157 23191 Z= 0.281 Chirality : 0.041 0.443 2526 Planarity : 0.004 0.054 2755 Dihedral : 11.490 174.687 2746 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.66 % Allowed : 32.12 % Favored : 65.21 % 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: 0.44 (0.20), residues: 1850 helix: 1.11 (0.19), residues: 689 sheet: -0.91 (0.30), residues: 273 loop : 0.19 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 274 TYR 0.029 0.002 TYR A1595 PHE 0.035 0.002 PHE D 477 TRP 0.038 0.001 TRP D 675 HIS 0.005 0.001 HIS D 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (16984) covalent geometry : angle 0.53712 / 0.28 (23170) hydrogen bonds : bond 0.03662 / 2.45 ( 651) hydrogen bonds : angle 4.79821 / 3.34 ( 1883) metal coordination : bond 0.00589 / 0.35 ( 16) metal coordination : angle 3.29007 / 1.61 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6466.65 seconds wall clock time: 111 minutes 17.69 seconds (6677.69 seconds total)