Starting phenix.real_space_refine on Sun Jun 15 04:06:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y85_33681/06_2025/7y85_33681.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y85_33681/06_2025/7y85_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_33681/06_2025/7y85_33681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y85_33681/06_2025/7y85_33681.map" model { file = "/net/cci-nas-00/data/ceres_data/7y85_33681/06_2025/7y85_33681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y85_33681/06_2025/7y85_33681.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.80, per 1000 atoms: 0.59 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: 4.11 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 5.84 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: 7.37 Time building geometry restraints manager: 4.85 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: 9592 34.70 - 69.41: 627 69.41 - 104.11: 46 104.11 - 138.81: 1 138.81 - 173.52: 1 Dihedral angle restraints: 10267 sinusoidal: 4846 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 10264 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 46.700 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:10.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 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 : 19.991 173.518 6779 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (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 TRP 0.036 0.001 TRP D 675 HIS 0.004 0.001 HIS A 924 PHE 0.015 0.002 PHE D 204 TYR 0.022 0.002 TYR A 925 ARG 0.012 0.000 ARG D 252 Details of bonding type rmsd hydrogen bonds : bond 0.23553 ( 651) hydrogen bonds : angle 8.32052 ( 1883) metal coordination : bond 0.00908 ( 16) metal coordination : angle 3.55484 ( 21) covalent geometry : bond 0.00394 (16984) covalent geometry : angle 0.56668 (23170) *********************** 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 : 1.584 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: 1.0816 time to fit residues: 326.3130 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 : 1.783 ------------------------------------------------------------------------------- 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 162 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 81 optimal weight: 10.0000 chunk 49 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 151 optimal weight: 10.0000 chunk 58 optimal weight: 0.0970 chunk 91 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 427 GLN D 432 GLN 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 = 0.3885 r_free = 0.3885 target = 0.168694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120439 restraints weight = 17406.150| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.72 r_work: 0.3256 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17000 Z= 0.149 Angle : 0.567 9.483 23191 Z= 0.297 Chirality : 0.042 0.423 2526 Planarity : 0.004 0.047 2755 Dihedral : 16.143 173.696 3043 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.20 % Allowed : 25.77 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.19), residues: 1850 helix: 0.70 (0.19), residues: 691 sheet: -0.62 (0.28), residues: 275 loop : 0.06 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 675 HIS 0.006 0.001 HIS D 457 PHE 0.016 0.001 PHE D 204 TYR 0.021 0.002 TYR D 704 ARG 0.008 0.000 ARG D 252 Details of bonding type rmsd hydrogen bonds : bond 0.04931 ( 651) hydrogen bonds : angle 5.48835 ( 1883) metal coordination : bond 0.00700 ( 16) metal coordination : angle 3.25516 ( 21) covalent geometry : bond 0.00332 (16984) covalent geometry : angle 0.55829 (23170) *********************** 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 342 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 256 time to evaluate : 1.850 Fit side-chains REVERT: A 125 GLU cc_start: 0.7858 (tp30) cc_final: 0.6579 (pp20) REVERT: A 159 ASP cc_start: 0.8045 (m-30) cc_final: 0.7709 (m-30) REVERT: A 275 LYS cc_start: 0.6647 (OUTLIER) cc_final: 0.6395 (mtpt) REVERT: A 617 LYS cc_start: 0.8679 (mmtt) cc_final: 0.8462 (mmmt) REVERT: A 623 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.7986 (tppt) REVERT: A 656 GLU cc_start: 0.8261 (mp0) cc_final: 0.8031 (mp0) REVERT: A 703 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8286 (pttm) REVERT: A 802 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.6944 (mppt) REVERT: A 985 LYS cc_start: 0.7049 (mtmm) cc_final: 0.6610 (mttp) REVERT: A 1022 PHE cc_start: 0.7885 (t80) cc_final: 0.7550 (t80) REVERT: A 1395 LEU cc_start: 0.6977 (OUTLIER) cc_final: 0.6675 (mp) REVERT: A 1474 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6840 (pm20) REVERT: A 1488 ARG cc_start: 0.7137 (mtt90) cc_final: 0.6842 (mtt-85) REVERT: A 1563 LYS cc_start: 0.7752 (tppt) cc_final: 0.7504 (tppt) REVERT: A 1584 GLN cc_start: 0.5526 (tm-30) cc_final: 0.5311 (tm-30) REVERT: A 1630 TRP cc_start: 0.8131 (t60) cc_final: 0.7830 (t60) REVERT: D 181 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.6038 (mp0) REVERT: D 204 PHE cc_start: 0.6104 (OUTLIER) cc_final: 0.3926 (p90) REVERT: D 209 ASP cc_start: 0.6093 (m-30) cc_final: 0.5754 (p0) REVERT: D 260 ARG cc_start: 0.6896 (mtm-85) cc_final: 0.6674 (mtm-85) REVERT: D 267 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6720 (pttm) REVERT: D 342 ASN cc_start: 0.5549 (OUTLIER) cc_final: 0.5189 (t0) REVERT: D 513 ASN cc_start: 0.7892 (m-40) cc_final: 0.7673 (m-40) REVERT: D 548 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7262 (mm-30) REVERT: D 671 SER cc_start: 0.7861 (t) cc_final: 0.7308 (m) outliers start: 86 outliers final: 19 residues processed: 323 average time/residue: 1.3240 time to fit residues: 476.9424 Evaluate side-chains 246 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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 623 LYS 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 342 ASN 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 714 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 127 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 chunk 150 optimal weight: 0.9990 chunk 148 optimal weight: 0.2980 chunk 146 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 287 ASN ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3893 r_free = 0.3893 target = 0.168522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119293 restraints weight = 17426.244| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.86 r_work: 0.3275 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.1509 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 : 0.545 10.586 23191 Z= 0.283 Chirality : 0.042 0.426 2526 Planarity : 0.004 0.049 2755 Dihedral : 15.828 173.913 2972 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.60 % Allowed : 27.10 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1850 helix: 0.84 (0.19), residues: 697 sheet: -0.66 (0.29), residues: 275 loop : 0.12 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 675 HIS 0.006 0.001 HIS D 457 PHE 0.021 0.001 PHE D 477 TYR 0.019 0.001 TYR D 704 ARG 0.006 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 651) hydrogen bonds : angle 5.08734 ( 1883) metal coordination : bond 0.00707 ( 16) metal coordination : angle 3.41033 ( 21) covalent geometry : bond 0.00325 (16984) covalent geometry : angle 0.53558 (23170) *********************** 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 315 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 239 time to evaluate : 2.083 Fit side-chains REVERT: A 125 GLU cc_start: 0.7852 (tp30) cc_final: 0.6678 (pp20) REVERT: A 159 ASP cc_start: 0.8045 (m-30) cc_final: 0.7696 (m-30) REVERT: A 238 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7716 (mm-30) REVERT: A 275 LYS cc_start: 0.6757 (OUTLIER) cc_final: 0.6514 (mtmm) REVERT: A 417 ILE cc_start: 0.8730 (OUTLIER) cc_final: 0.8216 (tp) REVERT: A 617 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8468 (mmmt) REVERT: A 623 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8033 (tppt) REVERT: A 639 GLU cc_start: 0.6589 (mt-10) cc_final: 0.6137 (tm-30) REVERT: A 656 GLU cc_start: 0.8288 (mp0) cc_final: 0.8060 (mp0) REVERT: A 703 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8452 (pttm) REVERT: A 773 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7200 (mm-30) REVERT: A 802 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7146 (mppt) REVERT: A 816 LYS cc_start: 0.8335 (tttp) cc_final: 0.8029 (ttpp) REVERT: A 925 TYR cc_start: 0.8703 (m-80) cc_final: 0.7263 (m-80) REVERT: A 953 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8451 (ttpt) REVERT: A 985 LYS cc_start: 0.7174 (mtmm) cc_final: 0.6718 (mttp) REVERT: A 1395 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6744 (mp) REVERT: A 1463 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7557 (pmm-80) REVERT: A 1474 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.6787 (pm20) REVERT: A 1488 ARG cc_start: 0.7188 (mtt90) cc_final: 0.6853 (mtt-85) REVERT: A 1508 THR cc_start: 0.8077 (m) cc_final: 0.7835 (m) REVERT: A 1514 LYS cc_start: 0.7538 (ptpp) cc_final: 0.7122 (mtmm) REVERT: A 1563 LYS cc_start: 0.7861 (tppt) cc_final: 0.7575 (tppt) REVERT: A 1584 GLN cc_start: 0.5633 (tm-30) cc_final: 0.5409 (tm-30) REVERT: A 1630 TRP cc_start: 0.8281 (t60) cc_final: 0.7854 (t60) REVERT: D 122 PHE cc_start: 0.6365 (OUTLIER) cc_final: 0.5821 (t80) REVERT: D 181 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6059 (mp0) REVERT: D 183 HIS cc_start: 0.7050 (m170) cc_final: 0.6844 (m-70) REVERT: D 209 ASP cc_start: 0.6213 (m-30) cc_final: 0.5840 (p0) REVERT: D 260 ARG cc_start: 0.6925 (mtm-85) cc_final: 0.6674 (mtm-85) REVERT: D 267 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6528 (pttm) REVERT: D 392 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7041 (tt0) REVERT: D 548 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7116 (mm-30) REVERT: D 621 GLN cc_start: 0.6800 (OUTLIER) cc_final: 0.5989 (mp10) REVERT: D 670 LYS cc_start: 0.6803 (OUTLIER) cc_final: 0.6536 (mttp) outliers start: 76 outliers final: 28 residues processed: 297 average time/residue: 1.5148 time to fit residues: 504.5193 Evaluate side-chains 267 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 2.468 ------------------------------------------------------------------------------- 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 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 623 LYS Chi-restraints excluded: chain A residue 637 MET Chi-restraints excluded: chain A residue 703 LYS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 796 THR Chi-restraints excluded: chain A residue 802 LYS Chi-restraints excluded: chain A residue 953 LYS Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1393 LYS Chi-restraints excluded: chain A residue 1395 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 1519 SER Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 122 PHE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 181 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 392 GLU Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 552 ASN 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 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 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 178 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 HIS ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN A1592 ASN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 395 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 = 0.3863 r_free = 0.3863 target = 0.165534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.115642 restraints weight = 17451.391| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.85 r_work: 0.3221 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17000 Z= 0.200 Angle : 0.573 11.620 23191 Z= 0.295 Chirality : 0.043 0.419 2526 Planarity : 0.004 0.051 2755 Dihedral : 15.787 170.368 2966 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.08 % Allowed : 27.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1850 helix: 0.82 (0.19), residues: 697 sheet: -0.72 (0.29), residues: 271 loop : 0.09 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 675 HIS 0.006 0.001 HIS D 457 PHE 0.023 0.002 PHE D 477 TYR 0.031 0.002 TYR A1595 ARG 0.006 0.001 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 651) hydrogen bonds : angle 5.05937 ( 1883) metal coordination : bond 0.00949 ( 16) metal coordination : angle 3.83638 ( 21) covalent geometry : bond 0.00457 (16984) covalent geometry : angle 0.56199 (23170) *********************** 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 318 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 234 time to evaluate : 3.729 Fit side-chains REVERT: A 125 GLU cc_start: 0.7886 (tp30) cc_final: 0.6648 (pp20) REVERT: A 159 ASP cc_start: 0.8127 (m-30) cc_final: 0.7804 (m-30) REVERT: A 166 ASP cc_start: 0.6767 (OUTLIER) cc_final: 0.6287 (t0) REVERT: A 275 LYS cc_start: 0.6810 (OUTLIER) cc_final: 0.6549 (mtpt) REVERT: A 417 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8236 (tp) REVERT: A 464 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7924 (pttp) REVERT: A 617 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8419 (mmmt) REVERT: A 623 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8046 (tppt) REVERT: A 639 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6330 (tm-30) REVERT: A 656 GLU cc_start: 0.8286 (mp0) cc_final: 0.8035 (mp0) REVERT: A 773 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7236 (mm-30) REVERT: A 925 TYR cc_start: 0.8739 (m-80) cc_final: 0.7149 (m-80) REVERT: A 953 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8405 (ttpt) REVERT: A 1395 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6780 (mp) REVERT: A 1463 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7692 (pmm-80) REVERT: A 1474 GLU cc_start: 0.7320 (OUTLIER) cc_final: 0.6955 (pm20) REVERT: A 1488 ARG cc_start: 0.7065 (mtt90) cc_final: 0.6791 (mtt-85) REVERT: A 1508 THR cc_start: 0.8182 (m) cc_final: 0.7952 (m) REVERT: A 1563 LYS cc_start: 0.7909 (tppt) cc_final: 0.7592 (tppt) REVERT: A 1584 GLN cc_start: 0.5638 (tm-30) cc_final: 0.5370 (tm-30) REVERT: A 1593 LYS cc_start: 0.7556 (mtpp) cc_final: 0.7025 (mttt) REVERT: A 1630 TRP cc_start: 0.8365 (t60) cc_final: 0.7733 (t60) REVERT: D 23 GLU cc_start: 0.7362 (tp30) cc_final: 0.6938 (tp30) REVERT: D 164 GLU cc_start: 0.6348 (OUTLIER) cc_final: 0.5111 (tp30) REVERT: D 181 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.6249 (mp0) REVERT: D 209 ASP cc_start: 0.6184 (m-30) cc_final: 0.5892 (p0) REVERT: D 267 LYS cc_start: 0.6808 (OUTLIER) cc_final: 0.6403 (pttm) REVERT: D 331 MET cc_start: 0.7257 (mtp) cc_final: 0.6984 (mtm) REVERT: D 392 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6993 (tt0) REVERT: D 429 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7488 (mmtm) REVERT: D 548 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7123 (mm-30) REVERT: D 621 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.6128 (tp40) REVERT: D 671 SER cc_start: 0.7961 (t) cc_final: 0.7413 (m) outliers start: 84 outliers final: 35 residues processed: 297 average time/residue: 1.3529 time to fit residues: 448.4975 Evaluate side-chains 271 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 220 time to evaluate : 1.640 ------------------------------------------------------------------------------- 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 95 ASP Chi-restraints excluded: chain A residue 166 ASP 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 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 623 LYS 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 953 LYS 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 1395 LEU Chi-restraints excluded: chain A residue 1422 THR Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1463 ARG Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 181 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 552 ASN 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 111 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN ** A1483 HIS ** 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 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 = 0.3851 r_free = 0.3851 target = 0.164452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.114170 restraints weight = 17624.094| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.87 r_work: 0.3194 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1628 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= 0.220 Angle : 0.588 11.833 23191 Z= 0.302 Chirality : 0.044 0.418 2526 Planarity : 0.004 0.051 2755 Dihedral : 15.795 168.273 2963 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 5.44 % Allowed : 26.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 1850 helix: 0.76 (0.19), residues: 698 sheet: -0.85 (0.29), residues: 266 loop : 0.06 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 675 HIS 0.005 0.001 HIS D 457 PHE 0.027 0.002 PHE D 477 TYR 0.021 0.002 TYR D 704 ARG 0.006 0.001 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.04216 ( 651) hydrogen bonds : angle 5.05005 ( 1883) metal coordination : bond 0.01006 ( 16) metal coordination : angle 4.01079 ( 21) covalent geometry : bond 0.00505 (16984) covalent geometry : angle 0.57615 (23170) *********************** 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 324 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 234 time to evaluate : 3.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.7849 (tp30) cc_final: 0.6575 (pp20) REVERT: A 159 ASP cc_start: 0.8042 (m-30) cc_final: 0.7684 (m-30) REVERT: A 166 ASP cc_start: 0.6836 (OUTLIER) cc_final: 0.6329 (t0) REVERT: A 417 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8253 (tp) REVERT: A 464 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7894 (pttp) REVERT: A 617 LYS cc_start: 0.8707 (mmtt) cc_final: 0.7986 (mmtt) REVERT: A 623 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8028 (tppt) REVERT: A 639 GLU cc_start: 0.6750 (mt-10) cc_final: 0.6300 (tm-30) REVERT: A 656 GLU cc_start: 0.8292 (mp0) cc_final: 0.8019 (mp0) REVERT: A 773 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7268 (mm-30) REVERT: A 925 TYR cc_start: 0.8734 (m-80) cc_final: 0.7218 (m-80) REVERT: A 953 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8389 (ttpt) REVERT: A 997 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8251 (mmt) REVERT: A 1474 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6980 (pm20) REVERT: A 1488 ARG cc_start: 0.6990 (mtt90) cc_final: 0.6716 (mtt-85) REVERT: A 1493 LYS cc_start: 0.7410 (mttp) cc_final: 0.7148 (mmtp) REVERT: A 1508 THR cc_start: 0.8212 (m) cc_final: 0.7973 (m) REVERT: A 1584 GLN cc_start: 0.5674 (tm-30) cc_final: 0.5423 (tm-30) REVERT: A 1630 TRP cc_start: 0.8455 (t60) cc_final: 0.7687 (t60) REVERT: D 23 GLU cc_start: 0.7420 (tp30) cc_final: 0.7114 (tp30) REVERT: D 122 PHE cc_start: 0.6345 (OUTLIER) cc_final: 0.6059 (t80) REVERT: D 151 GLU cc_start: 0.6866 (mt-10) cc_final: 0.6614 (tt0) REVERT: D 164 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.5108 (tp30) REVERT: D 181 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6317 (mp0) REVERT: D 241 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7232 (mt-10) REVERT: D 267 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.6477 (pttm) REVERT: D 392 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.7021 (tt0) REVERT: D 429 LYS cc_start: 0.7746 (OUTLIER) cc_final: 0.7508 (mmtm) REVERT: D 548 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7108 (mm-30) REVERT: D 621 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6156 (tp40) outliers start: 90 outliers final: 37 residues processed: 300 average time/residue: 1.7220 time to fit residues: 579.2119 Evaluate side-chains 270 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 217 time to evaluate : 3.509 ------------------------------------------------------------------------------- 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 95 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 166 ASP 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 623 LYS Chi-restraints excluded: chain A residue 680 SER 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 1454 LEU Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain D residue 78 VAL Chi-restraints excluded: chain D residue 122 PHE 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 181 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 241 GLU 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 511 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 561 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 134 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 46 optimal weight: 0.0270 chunk 48 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 190 optimal weight: 0.6980 chunk 143 optimal weight: 2.9990 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A1483 HIS ** 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 395 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 = 0.3895 r_free = 0.3895 target = 0.168680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.119707 restraints weight = 17583.164| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.85 r_work: 0.3284 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1853 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= 0.129 Angle : 0.538 9.782 23191 Z= 0.278 Chirality : 0.041 0.438 2526 Planarity : 0.004 0.052 2755 Dihedral : 15.716 173.041 2963 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.36 % Allowed : 28.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 1850 helix: 0.95 (0.19), residues: 699 sheet: -0.78 (0.30), residues: 269 loop : 0.14 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 675 HIS 0.005 0.001 HIS D 457 PHE 0.031 0.001 PHE D 477 TYR 0.033 0.001 TYR A1595 ARG 0.007 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 651) hydrogen bonds : angle 4.85972 ( 1883) metal coordination : bond 0.00586 ( 16) metal coordination : angle 3.28390 ( 21) covalent geometry : bond 0.00290 (16984) covalent geometry : angle 0.52901 (23170) *********************** 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 308 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 236 time to evaluate : 1.649 Fit side-chains revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8381 (OUTLIER) cc_final: 0.8162 (m-30) REVERT: A 125 GLU cc_start: 0.7824 (tp30) cc_final: 0.6620 (pp20) REVERT: A 159 ASP cc_start: 0.8009 (m-30) cc_final: 0.7669 (m-30) REVERT: A 166 ASP cc_start: 0.6597 (OUTLIER) cc_final: 0.6039 (t0) REVERT: A 275 LYS cc_start: 0.6898 (mtpt) cc_final: 0.6595 (mtmm) REVERT: A 417 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8157 (tp) REVERT: A 464 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7850 (pttp) REVERT: A 526 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: A 617 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8385 (mmmt) REVERT: A 623 LYS cc_start: 0.8445 (OUTLIER) cc_final: 0.7852 (tmtp) REVERT: A 639 GLU cc_start: 0.6576 (mt-10) cc_final: 0.6151 (tm-30) REVERT: A 656 GLU cc_start: 0.8251 (mp0) cc_final: 0.7982 (mp0) REVERT: A 674 TYR cc_start: 0.8894 (p90) cc_final: 0.8632 (p90) REVERT: A 773 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7099 (mm-30) REVERT: A 925 TYR cc_start: 0.8648 (m-80) cc_final: 0.7202 (m-80) REVERT: A 953 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8353 (ttpt) REVERT: A 997 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8315 (mmt) REVERT: A 1022 PHE cc_start: 0.7840 (t80) cc_final: 0.7479 (t80) REVERT: A 1395 LEU cc_start: 0.7011 (mp) cc_final: 0.6717 (mp) REVERT: A 1474 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6840 (pm20) REVERT: A 1488 ARG cc_start: 0.6986 (mtt90) cc_final: 0.6655 (mtt-85) REVERT: A 1493 LYS cc_start: 0.7360 (mttp) cc_final: 0.7082 (mmtp) REVERT: A 1508 THR cc_start: 0.8037 (m) cc_final: 0.7792 (m) REVERT: A 1514 LYS cc_start: 0.7350 (ptpp) cc_final: 0.7045 (mtmm) REVERT: A 1563 LYS cc_start: 0.7647 (tppt) cc_final: 0.7394 (tppt) REVERT: A 1593 LYS cc_start: 0.7563 (mtpp) cc_final: 0.7002 (mttt) REVERT: A 1630 TRP cc_start: 0.8384 (t60) cc_final: 0.7862 (t60) REVERT: D 23 GLU cc_start: 0.7495 (tp30) cc_final: 0.6982 (tp30) REVERT: D 164 GLU cc_start: 0.6178 (OUTLIER) cc_final: 0.4915 (tp30) REVERT: D 181 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.6110 (mp0) REVERT: D 204 PHE cc_start: 0.5989 (OUTLIER) cc_final: 0.3908 (p90) REVERT: D 267 LYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6388 (pttm) REVERT: D 429 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.6919 (mttp) REVERT: D 548 GLU cc_start: 0.7385 (mm-30) cc_final: 0.7083 (mm-30) REVERT: D 621 GLN cc_start: 0.6807 (OUTLIER) cc_final: 0.6104 (tp40) REVERT: D 670 LYS cc_start: 0.6665 (mttt) cc_final: 0.6323 (mptt) outliers start: 72 outliers final: 26 residues processed: 291 average time/residue: 1.2940 time to fit residues: 418.5228 Evaluate side-chains 258 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 1.867 ------------------------------------------------------------------------------- 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 166 ASP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 324 ASP 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 526 GLU Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 680 SER 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 1007 LEU Chi-restraints excluded: chain A residue 1454 LEU Chi-restraints excluded: chain A residue 1474 GLU Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain D residue 26 ARG Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 181 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 429 LYS Chi-restraints excluded: chain D residue 511 LEU Chi-restraints excluded: chain D residue 552 ASN Chi-restraints excluded: chain D residue 567 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 154 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 172 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 94 optimal weight: 0.0170 chunk 83 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 overall best weight: 2.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN A1592 ASN ** A1635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN 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 = 0.3848 r_free = 0.3848 target = 0.164217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.114067 restraints weight = 17513.016| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.87 r_work: 0.3196 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 17000 Z= 0.241 Angle : 0.605 12.733 23191 Z= 0.309 Chirality : 0.044 0.414 2526 Planarity : 0.004 0.053 2755 Dihedral : 15.738 168.424 2959 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.72 % Allowed : 28.19 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 1850 helix: 0.76 (0.19), residues: 703 sheet: -0.95 (0.29), residues: 274 loop : 0.07 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 675 HIS 0.005 0.001 HIS D 457 PHE 0.032 0.002 PHE D 477 TYR 0.022 0.002 TYR D 704 ARG 0.012 0.001 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 651) hydrogen bonds : angle 5.01839 ( 1883) metal coordination : bond 0.01058 ( 16) metal coordination : angle 4.19357 ( 21) covalent geometry : bond 0.00557 (16984) covalent geometry : angle 0.59187 (23170) *********************** 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 307 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 229 time to evaluate : 1.808 Fit side-chains REVERT: A 27 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: A 36 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8474 (tpp) REVERT: A 125 GLU cc_start: 0.7846 (tp30) cc_final: 0.6549 (pp20) REVERT: A 159 ASP cc_start: 0.8042 (m-30) cc_final: 0.7688 (m-30) REVERT: A 166 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6194 (t0) REVERT: A 275 LYS cc_start: 0.6890 (mtpt) cc_final: 0.6582 (mtmm) REVERT: A 417 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8252 (tp) REVERT: A 464 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7886 (pttp) REVERT: A 617 LYS cc_start: 0.8693 (mmtt) cc_final: 0.7972 (mmtt) REVERT: A 623 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7954 (tppt) REVERT: A 625 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.5885 (mtt90) REVERT: A 639 GLU cc_start: 0.6750 (mt-10) cc_final: 0.6297 (tm-30) REVERT: A 676 ILE cc_start: 0.8812 (mm) cc_final: 0.8602 (mm) REVERT: A 737 ARG cc_start: 0.8701 (mtm180) cc_final: 0.8489 (mtm180) REVERT: A 773 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7214 (mm-30) REVERT: A 925 TYR cc_start: 0.8763 (m-80) cc_final: 0.7177 (m-80) REVERT: A 953 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8261 (ttpt) REVERT: A 997 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.8308 (mmt) REVERT: A 1488 ARG cc_start: 0.6959 (mtt90) cc_final: 0.6595 (mtt-85) REVERT: A 1493 LYS cc_start: 0.7320 (mttp) cc_final: 0.7070 (mmtp) REVERT: A 1508 THR cc_start: 0.8161 (m) cc_final: 0.7898 (m) REVERT: A 1563 LYS cc_start: 0.7762 (tppt) cc_final: 0.7467 (tppt) REVERT: A 1586 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.6867 (t70) REVERT: A 1593 LYS cc_start: 0.7674 (mtpp) cc_final: 0.7135 (mttt) REVERT: A 1630 TRP cc_start: 0.8473 (t60) cc_final: 0.7760 (t60) REVERT: D 23 GLU cc_start: 0.7500 (tp30) cc_final: 0.6980 (tp30) REVERT: D 164 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.4958 (tp30) REVERT: D 181 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6273 (mp0) REVERT: D 267 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6460 (pttm) REVERT: D 323 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7356 (ptp-170) REVERT: D 392 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7051 (tt0) REVERT: D 429 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7514 (mmtm) REVERT: D 548 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7147 (mm-30) outliers start: 78 outliers final: 32 residues processed: 289 average time/residue: 1.5979 time to fit residues: 514.5044 Evaluate side-chains 272 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 1.636 ------------------------------------------------------------------------------- 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 36 MET Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 324 ASP 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 522 SER Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 625 ARG Chi-restraints excluded: chain A residue 680 SER 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 1454 LEU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain A residue 1679 LYS 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 181 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 567 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 43 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 178 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 132 optimal weight: 9.9990 chunk 143 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 120 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN A1584 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.167935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.118957 restraints weight = 17417.288| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.83 r_work: 0.3273 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1935 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= 0.143 Angle : 0.551 10.109 23191 Z= 0.284 Chirality : 0.042 0.436 2526 Planarity : 0.004 0.054 2755 Dihedral : 15.691 172.606 2959 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.93 % Allowed : 29.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.19), residues: 1850 helix: 0.99 (0.19), residues: 694 sheet: -0.89 (0.29), residues: 275 loop : 0.13 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 675 HIS 0.005 0.001 HIS D 457 PHE 0.036 0.002 PHE D 477 TYR 0.032 0.001 TYR A1595 ARG 0.013 0.001 ARG A 577 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 651) hydrogen bonds : angle 4.85242 ( 1883) metal coordination : bond 0.00631 ( 16) metal coordination : angle 3.33149 ( 21) covalent geometry : bond 0.00325 (16984) covalent geometry : angle 0.54203 (23170) *********************** 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 295 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 230 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8294 (mmm) REVERT: A 125 GLU cc_start: 0.7892 (tp30) cc_final: 0.6675 (pp20) REVERT: A 159 ASP cc_start: 0.8032 (m-30) cc_final: 0.7680 (m-30) REVERT: A 166 ASP cc_start: 0.6555 (OUTLIER) cc_final: 0.6009 (t0) REVERT: A 275 LYS cc_start: 0.6944 (mppt) cc_final: 0.6629 (mtmm) REVERT: A 417 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8193 (tp) REVERT: A 464 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7860 (pttp) REVERT: A 526 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: A 617 LYS cc_start: 0.8630 (mmtt) cc_final: 0.8237 (mmmt) REVERT: A 623 LYS cc_start: 0.8459 (OUTLIER) cc_final: 0.7880 (tmtp) REVERT: A 639 GLU cc_start: 0.6625 (mt-10) cc_final: 0.6189 (tm-30) REVERT: A 676 ILE cc_start: 0.8736 (mm) cc_final: 0.8533 (mm) REVERT: A 773 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7128 (mm-30) REVERT: A 925 TYR cc_start: 0.8698 (m-80) cc_final: 0.7114 (m-80) REVERT: A 953 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8339 (ttpt) REVERT: A 997 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8286 (mmt) REVERT: A 1022 PHE cc_start: 0.7872 (t80) cc_final: 0.7527 (t80) REVERT: A 1488 ARG cc_start: 0.7012 (mtt90) cc_final: 0.6686 (mtt-85) REVERT: A 1493 LYS cc_start: 0.7341 (mttp) cc_final: 0.7069 (mmtp) REVERT: A 1508 THR cc_start: 0.8073 (m) cc_final: 0.7819 (m) REVERT: A 1514 LYS cc_start: 0.7391 (ptpp) cc_final: 0.7108 (mtmm) REVERT: A 1563 LYS cc_start: 0.7750 (tppt) cc_final: 0.7485 (tppt) REVERT: A 1584 GLN cc_start: 0.6624 (tt0) cc_final: 0.5796 (tm-30) REVERT: A 1586 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.6923 (t70) REVERT: A 1630 TRP cc_start: 0.8423 (t60) cc_final: 0.7718 (t60) REVERT: D 23 GLU cc_start: 0.7497 (tp30) cc_final: 0.6948 (tp30) REVERT: D 122 PHE cc_start: 0.6212 (OUTLIER) cc_final: 0.5525 (t80) REVERT: D 164 GLU cc_start: 0.6213 (OUTLIER) cc_final: 0.4945 (tp30) REVERT: D 181 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6141 (mp0) REVERT: D 241 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6907 (mt-10) REVERT: D 267 LYS cc_start: 0.6712 (OUTLIER) cc_final: 0.6347 (pttm) REVERT: D 392 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: D 429 LYS cc_start: 0.7650 (OUTLIER) cc_final: 0.7427 (mmtm) outliers start: 65 outliers final: 33 residues processed: 279 average time/residue: 1.5623 time to fit residues: 487.9277 Evaluate side-chains 267 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 217 time to evaluate : 1.751 ------------------------------------------------------------------------------- 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 36 MET Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE 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 522 SER Chi-restraints excluded: chain A residue 526 GLU Chi-restraints excluded: chain A residue 623 LYS Chi-restraints excluded: chain A residue 680 SER 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 1454 LEU Chi-restraints excluded: chain A residue 1586 ASP Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 122 PHE Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 181 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 241 GLU 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 511 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 567 SER 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 54 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 23 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 HIS ** 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 699 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.169045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.120585 restraints weight = 17324.193| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.78 r_work: 0.3268 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2054 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 : 0.546 10.557 23191 Z= 0.281 Chirality : 0.041 0.439 2526 Planarity : 0.004 0.054 2755 Dihedral : 15.605 174.111 2957 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.27 % Allowed : 30.85 % Favored : 65.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 1850 helix: 1.16 (0.19), residues: 687 sheet: -0.87 (0.29), residues: 275 loop : 0.22 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 675 HIS 0.005 0.001 HIS D 457 PHE 0.035 0.002 PHE D 477 TYR 0.033 0.001 TYR A1595 ARG 0.008 0.000 ARG A 168 Details of bonding type rmsd hydrogen bonds : bond 0.03682 ( 651) hydrogen bonds : angle 4.77884 ( 1883) metal coordination : bond 0.00608 ( 16) metal coordination : angle 3.38131 ( 21) covalent geometry : bond 0.00297 (16984) covalent geometry : angle 0.53669 (23170) *********************** 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 285 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 4.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.8788 (tpt) cc_final: 0.8462 (tpp) REVERT: A 125 GLU cc_start: 0.7821 (tp30) cc_final: 0.6576 (pp20) REVERT: A 159 ASP cc_start: 0.8069 (m-30) cc_final: 0.7726 (m-30) REVERT: A 166 ASP cc_start: 0.6480 (OUTLIER) cc_final: 0.5941 (t0) REVERT: A 238 GLU cc_start: 0.7529 (mm-30) cc_final: 0.7128 (mp0) REVERT: A 275 LYS cc_start: 0.6838 (mppt) cc_final: 0.6459 (mtmm) REVERT: A 417 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8210 (tp) REVERT: A 464 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7837 (pttp) REVERT: A 617 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8254 (mmmt) REVERT: A 639 GLU cc_start: 0.6591 (mt-10) cc_final: 0.6166 (tm-30) REVERT: A 674 TYR cc_start: 0.8873 (p90) cc_final: 0.8514 (p90) REVERT: A 773 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7098 (mm-30) REVERT: A 925 TYR cc_start: 0.8663 (m-80) cc_final: 0.7163 (m-80) REVERT: A 997 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8197 (mmt) REVERT: A 1488 ARG cc_start: 0.6878 (mtt90) cc_final: 0.6550 (mtt-85) REVERT: A 1493 LYS cc_start: 0.7263 (mttp) cc_final: 0.7000 (mmtp) REVERT: A 1508 THR cc_start: 0.7967 (m) cc_final: 0.7716 (m) REVERT: A 1514 LYS cc_start: 0.7225 (ptpp) cc_final: 0.7007 (mtmm) REVERT: A 1563 LYS cc_start: 0.7682 (tppt) cc_final: 0.7377 (tppt) REVERT: A 1584 GLN cc_start: 0.6560 (tt0) cc_final: 0.5751 (tm-30) REVERT: A 1595 TYR cc_start: 0.7412 (t80) cc_final: 0.7162 (t80) REVERT: A 1630 TRP cc_start: 0.8395 (t60) cc_final: 0.7897 (t60) REVERT: D 23 GLU cc_start: 0.7481 (tp30) cc_final: 0.6908 (tp30) REVERT: D 122 PHE cc_start: 0.6138 (OUTLIER) cc_final: 0.5774 (t80) REVERT: D 151 GLU cc_start: 0.6729 (mt-10) cc_final: 0.6388 (tt0) REVERT: D 181 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: D 267 LYS cc_start: 0.6664 (OUTLIER) cc_final: 0.6347 (pttm) REVERT: D 392 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6821 (tt0) REVERT: D 429 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.6837 (mttp) REVERT: D 687 TRP cc_start: 0.7353 (t60) cc_final: 0.7113 (t60) outliers start: 54 outliers final: 31 residues processed: 273 average time/residue: 1.9577 time to fit residues: 601.7552 Evaluate side-chains 257 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 216 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 95 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 166 ASP 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 419 VAL 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 680 SER 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 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 1458 VAL Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain D residue 122 PHE Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 132 PHE Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 181 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 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 567 SER 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 702 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 156 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 157 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1483 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN A1596 GLN A1635 ASN 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 = 0.3874 r_free = 0.3874 target = 0.167671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.117760 restraints weight = 17384.744| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.81 r_work: 0.3241 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2022 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= 0.163 Angle : 0.566 11.331 23191 Z= 0.291 Chirality : 0.042 0.436 2526 Planarity : 0.004 0.055 2755 Dihedral : 15.629 172.376 2957 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.02 % Allowed : 31.16 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 1850 helix: 1.03 (0.19), residues: 695 sheet: -0.86 (0.30), residues: 273 loop : 0.13 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 675 HIS 0.005 0.001 HIS D 457 PHE 0.038 0.002 PHE D 477 TYR 0.030 0.002 TYR A1595 ARG 0.009 0.000 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.03817 ( 651) hydrogen bonds : angle 4.84967 ( 1883) metal coordination : bond 0.00739 ( 16) metal coordination : angle 3.59560 ( 21) covalent geometry : bond 0.00374 (16984) covalent geometry : angle 0.55599 (23170) ********************** 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 269 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8437 (tpp) REVERT: A 125 GLU cc_start: 0.7820 (tp30) cc_final: 0.6576 (pp20) REVERT: A 159 ASP cc_start: 0.8018 (m-30) cc_final: 0.7678 (m-30) REVERT: A 166 ASP cc_start: 0.6465 (OUTLIER) cc_final: 0.5927 (t0) REVERT: A 238 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7143 (mp0) REVERT: A 275 LYS cc_start: 0.6798 (mppt) cc_final: 0.6441 (mtmm) REVERT: A 417 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8206 (tp) REVERT: A 464 LYS cc_start: 0.8098 (OUTLIER) cc_final: 0.7820 (pttp) REVERT: A 617 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8013 (mmtt) REVERT: A 639 GLU cc_start: 0.6624 (mt-10) cc_final: 0.6166 (tm-30) REVERT: A 676 ILE cc_start: 0.8732 (mm) cc_final: 0.8509 (mm) REVERT: A 773 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7147 (mm-30) REVERT: A 925 TYR cc_start: 0.8699 (m-80) cc_final: 0.7043 (m-80) REVERT: A 997 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8181 (mmt) REVERT: A 1022 PHE cc_start: 0.7778 (t80) cc_final: 0.7485 (t80) REVERT: A 1488 ARG cc_start: 0.6986 (mtt90) cc_final: 0.6661 (mtt-85) REVERT: A 1493 LYS cc_start: 0.7269 (mttp) cc_final: 0.7006 (mmtp) REVERT: A 1508 THR cc_start: 0.7985 (m) cc_final: 0.7731 (m) REVERT: A 1514 LYS cc_start: 0.7293 (ptpp) cc_final: 0.7053 (mtmm) REVERT: A 1563 LYS cc_start: 0.7756 (tppt) cc_final: 0.7424 (tppt) REVERT: A 1584 GLN cc_start: 0.6582 (tt0) cc_final: 0.5860 (tm-30) REVERT: A 1586 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.6807 (t70) REVERT: A 1595 TYR cc_start: 0.7280 (t80) cc_final: 0.7011 (t80) REVERT: A 1596 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.6649 (mt0) REVERT: A 1630 TRP cc_start: 0.8408 (t60) cc_final: 0.7933 (t60) REVERT: D 23 GLU cc_start: 0.7543 (tp30) cc_final: 0.6949 (tp30) REVERT: D 122 PHE cc_start: 0.6179 (OUTLIER) cc_final: 0.5751 (t80) REVERT: D 267 LYS cc_start: 0.6631 (OUTLIER) cc_final: 0.6306 (pttm) REVERT: D 347 LYS cc_start: 0.7026 (mttp) cc_final: 0.6788 (mttp) REVERT: D 392 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6808 (tt0) REVERT: D 429 LYS cc_start: 0.7600 (OUTLIER) cc_final: 0.6829 (mttp) REVERT: D 687 TRP cc_start: 0.7338 (t60) cc_final: 0.7134 (t60) outliers start: 50 outliers final: 31 residues processed: 256 average time/residue: 1.3194 time to fit residues: 374.8992 Evaluate side-chains 252 residues out of total 1653 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 166 ASP 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 419 VAL 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 680 SER 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 858 VAL Chi-restraints excluded: chain A residue 951 SER 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 1586 ASP Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1648 LEU Chi-restraints excluded: chain D residue 122 PHE Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 132 PHE 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 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 511 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 567 SER 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 702 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 193 random chunks: chunk 133 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1010 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1492 GLN A1596 GLN D 183 HIS ** D 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.167574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118387 restraints weight = 17426.622| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.79 r_work: 0.3235 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.205 17000 Z= 0.236 Angle : 0.980 61.563 23191 Z= 0.498 Chirality : 0.044 0.606 2526 Planarity : 0.005 0.175 2755 Dihedral : 15.618 172.377 2954 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.72 % Allowed : 31.58 % Favored : 65.70 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 1850 helix: 0.96 (0.19), residues: 694 sheet: -0.86 (0.30), residues: 273 loop : 0.15 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP D 675 HIS 0.012 0.001 HIS D 642 PHE 0.034 0.002 PHE D 477 TYR 0.019 0.002 TYR D 704 ARG 0.024 0.001 ARG D 710 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 651) hydrogen bonds : angle 4.87847 ( 1883) metal coordination : bond 0.00725 ( 16) metal coordination : angle 3.59429 ( 21) covalent geometry : bond 0.00475 (16984) covalent geometry : angle 0.97421 (23170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15259.79 seconds wall clock time: 269 minutes 7.39 seconds (16147.39 seconds total)