Starting phenix.real_space_refine on Sat Sep 12 15:01:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y83_33679/09_2026/7y83_33679.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y83_33679/09_2026/7y83_33679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y83_33679/09_2026/7y83_33679.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y83_33679/09_2026/7y83_33679.map" model { file = "/net/cci-nas-00/data/ceres_data/7y83_33679/09_2026/7y83_33679.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y83_33679/09_2026/7y83_33679.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7y83_33679/09_2026/7y83_33679.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y83_33679/09_2026/7y83_33679.cif" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.194 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 54 5.16 5 C 10165 2.51 5 N 2832 2.21 5 O 3185 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16300 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1221, 9841 Classifications: {'peptide': 1221} Link IDs: {'PTRANS': 57, 'TRANS': 1163} Chain breaks: 10 Chain: "B" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 757 Classifications: {'RNAv2': 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: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 499 Classifications: {'RNAv2': 23} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 13, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 18} Chain: "D" Number of atoms: 5198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 5198 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 18, 'TRANS': 621} Chain breaks: 7 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 5607 SG CYS A 750 57.794 37.629 86.522 1.00 61.47 S ATOM 5620 SG CYS A 752 60.495 38.229 84.299 1.00 70.59 S ATOM 5642 SG CYS A 755 58.314 41.212 85.509 1.00 55.64 S ATOM 3532 SG CYS A 491 51.998 54.037 109.845 1.00 58.61 S ATOM 3600 SG CYS A 501 50.556 53.661 113.214 1.00 52.17 S ATOM 3614 SG CYS A 503 53.912 55.703 112.412 1.00 34.79 S ATOM 3636 SG CYS A 506 50.622 57.124 111.245 1.00 19.20 S ATOM 7502 SG CYS A1018 48.595 37.915 50.331 1.00 73.90 S ATOM 7698 SG CYS A1406 48.536 36.234 53.762 1.00 67.74 S ATOM 7749 SG CYS A1414 51.772 36.647 51.673 1.00 66.74 S ATOM 7766 SG CYS A1417 50.371 39.562 53.406 1.00 69.54 S ATOM 668 SG CYS A 88 39.646 69.655 135.709 1.00 45.02 S ATOM 939 SG CYS A 121 37.304 71.424 138.127 1.00 67.64 S ATOM 985 SG CYS A 127 38.123 72.925 134.705 1.00 56.97 S ATOM 1009 SG CYS A 130 35.985 69.764 134.962 1.00 42.23 S Time building chain proxies: 3.31, per 1000 atoms: 0.20 Number of scatterers: 16300 At special positions: 0 Unit cell: (105.6, 102.3, 160.6, 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 54 16.00 P 59 15.00 Mg 1 11.99 O 3185 8.00 N 2832 7.00 C 10165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 586.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" ND1 HIS A 747 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 750 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 752 " 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 506 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 503 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 501 " pdb=" ZN A1803 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1414 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1417 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1018 " pdb="ZN ZN A1803 " - pdb=" SG CYS A1406 " pdb=" ZN A1805 " 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 130 " pdb="ZN ZN A1805 " - pdb=" SG CYS A 121 " Number of angles added : 21 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3442 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 25 sheets defined 43.1% alpha, 15.9% beta 15 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.972A 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 removed outlier: 3.643A pdb=" N ASP A 148 " --> pdb=" O ARG A 145 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 149 " --> pdb=" O ASN A 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 149' Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.740A pdb=" N ILE A 172 " --> pdb=" O ARG A 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 168 through 172' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 269 through 287 Processing helix chain 'A' and resid 291 through 303 removed outlier: 4.198A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 307 removed outlier: 3.823A pdb=" N GLY A 307 " --> pdb=" O ARG A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 307' Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 354 through 374 Processing helix chain 'A' and resid 471 through 488 Processing helix chain 'A' and resid 503 through 511 Processing helix chain 'A' and resid 569 through 580 Processing helix chain 'A' and resid 594 through 598 Processing helix chain 'A' and resid 617 through 625 Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 630 through 637 Processing helix chain 'A' and resid 654 through 657 Processing helix chain 'A' and resid 658 through 664 Processing helix chain 'A' and resid 686 through 693 removed outlier: 3.770A pdb=" N THR A 692 " --> pdb=" O ILE A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 739 Processing helix chain 'A' and resid 752 through 759 Processing helix chain 'A' and resid 776 through 780 removed outlier: 3.644A pdb=" N PHE A 780 " --> pdb=" O GLY A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 847 Processing helix chain 'A' and resid 855 through 859 removed outlier: 3.684A pdb=" N GLY A 859 " --> pdb=" O GLY A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.786A 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 removed outlier: 3.648A pdb=" N LYS A1398 " --> pdb=" O THR A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1414 through 1421 Processing helix chain 'A' and resid 1463 through 1468 removed outlier: 3.610A pdb=" N SER A1467 " --> pdb=" O ARG A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1493 removed outlier: 3.926A pdb=" N ILE A1489 " --> pdb=" O ASN A1485 " (cutoff:3.500A) 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 removed outlier: 3.619A pdb=" N VAL A1618 " --> pdb=" O GLN A1615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1615 through 1618' Processing helix chain 'A' and resid 1619 through 1629 Processing helix chain 'A' and resid 1662 through 1668 removed outlier: 3.962A pdb=" N ASP A1668 " --> pdb=" O LYS A1664 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1682 Processing helix chain 'D' and resid 16 through 33 removed outlier: 3.629A pdb=" N ASN D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 60 removed outlier: 3.589A pdb=" N LYS D 43 " --> pdb=" O VAL D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 81 Processing helix chain 'D' and resid 90 through 110 removed outlier: 3.507A pdb=" N LYS D 94 " --> pdb=" O PRO D 90 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 136 Processing helix chain 'D' and resid 141 through 155 Processing helix chain 'D' and resid 163 through 177 removed outlier: 3.695A pdb=" N ILE D 167 " --> pdb=" O TYR D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 183 through 190 Processing helix chain 'D' and resid 194 through 205 removed outlier: 3.616A pdb=" N ILE D 205 " --> pdb=" O ALA D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 224 removed outlier: 3.650A pdb=" N LYS D 224 " --> pdb=" O THR D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 246 removed outlier: 4.153A pdb=" N ASP D 234 " --> pdb=" O HIS D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 Processing helix chain 'D' and resid 270 through 277 removed outlier: 4.012A pdb=" N ARG D 275 " --> pdb=" O THR D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 280 No H-bonds generated for 'chain 'D' and resid 278 through 280' Processing helix chain 'D' and resid 281 through 296 removed outlier: 3.864A pdb=" N TYR D 285 " --> pdb=" O HIS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 320 removed outlier: 3.740A pdb=" N LEU D 320 " --> pdb=" O ILE D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 329 Processing helix chain 'D' and resid 342 through 357 Processing helix chain 'D' and resid 433 through 450 Processing helix chain 'D' and resid 451 through 453 No H-bonds generated for 'chain 'D' and resid 451 through 453' Processing helix chain 'D' and resid 454 through 469 Processing helix chain 'D' and resid 470 through 474 Processing helix chain 'D' and resid 489 through 495 Processing helix chain 'D' and resid 496 through 500 removed outlier: 3.632A pdb=" N SER D 500 " --> pdb=" O LEU D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 514 removed outlier: 3.998A 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 566 through 572 Processing helix chain 'D' and resid 592 through 595 Processing helix chain 'D' and resid 607 through 611 Processing helix chain 'D' and resid 644 through 652 removed outlier: 3.528A pdb=" N ILE D 652 " --> pdb=" O ALA D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 665 through 675 removed outlier: 3.675A pdb=" N THR D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 691 removed outlier: 3.704A pdb=" N TRP D 687 " --> pdb=" O LYS D 683 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 708 removed outlier: 3.884A pdb=" N ALA D 708 " --> pdb=" O TYR D 704 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 151 through 153 removed outlier: 6.701A pdb=" N SER A 56 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ARG A 19 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N TRP A 44 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A 21 " --> pdb=" O TRP A 44 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N TRP A 46 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLU A 22 " --> pdb=" O ARG A 193 " (cutoff:3.500A) removed outlier: 12.858A pdb=" N ARG A 193 " --> pdb=" O GLU A 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA3, first strand: chain 'A' and resid 81 through 82 Processing sheet with id=AA4, first strand: chain 'A' and resid 109 through 111 Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.927A pdb=" N ARG A 180 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 333 through 334 Processing sheet with id=AA7, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AA8, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.623A pdb=" N VAL A 419 " --> pdb=" O ILE A 607 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ILE A 607 " --> pdb=" O VAL A 419 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 431 through 432 removed outlier: 3.945A pdb=" N ASN A 459 " --> pdb=" O VAL A 432 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 469 through 470 Processing sheet with id=AB2, first strand: chain 'A' and resid 526 through 533 removed outlier: 9.989A pdb=" N GLU A 526 " --> pdb=" O ASP A 547 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N ASP A 547 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 10.802A pdb=" N ARG A 528 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 9.225A pdb=" N LEU A 545 " --> pdb=" O ARG A 528 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N ARG A 530 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N GLY A 543 " --> pdb=" O ARG A 530 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ALA A 532 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 610 through 612 Processing sheet with id=AB4, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.764A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 703 through 704 removed outlier: 5.764A pdb=" N PHE A 720 " --> pdb=" O LEU A 774 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 707 through 708 Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 920 through 921 Processing sheet with id=AB9, first strand: chain 'A' and resid 924 through 927 Processing sheet with id=AC1, first strand: chain 'A' and resid 991 through 992 removed outlier: 6.223A pdb=" N LEU A 996 " --> pdb=" O TYR A1436 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL A1517 " --> pdb=" O GLU A1437 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN A1516 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A1526 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1429 through 1431 removed outlier: 3.852A pdb=" N ASN A1516 " --> pdb=" O THR A 960 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A1526 " --> pdb=" O LEU A 950 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU A 950 " --> pdb=" O ASN A1526 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N SER A 951 " --> pdb=" O THR A1569 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N THR A1569 " --> pdb=" O SER A 951 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS A 953 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A1567 " --> pdb=" O LYS A 953 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ASN A 955 " --> pdb=" O ASP A1565 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 985 through 987 removed outlier: 6.345A pdb=" N LYS A 985 " --> pdb=" O THR A1508 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N GLU A1510 " --> pdb=" O LYS A 985 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N TYR A 987 " --> pdb=" O GLU A1510 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 425 through 427 removed outlier: 6.111A pdb=" N VAL D 484 " --> pdb=" O CYS D 517 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 406 through 407 Processing sheet with id=AC6, first strand: chain 'D' and resid 580 through 582 removed outlier: 6.213A pdb=" N LEU D 580 " --> pdb=" O ILE D 623 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 585 through 587 removed outlier: 4.184A pdb=" N HIS D 585 " --> pdb=" O LYS D 599 " (cutoff:3.500A) 652 hydrogen bonds defined for protein. 1827 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4595 1.33 - 1.45: 3256 1.45 - 1.57: 8737 1.57 - 1.69: 116 1.69 - 1.81: 74 Bond restraints: 16778 Sorted by residual: bond pdb=" CB PRO D 397 " pdb=" CG PRO D 397 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.64e+00 bond pdb=" CG1 ILE D 169 " pdb=" CD1 ILE D 169 " ideal model delta sigma weight residual 1.513 1.457 0.056 3.90e-02 6.57e+02 2.09e+00 bond pdb=" C THR A 556 " pdb=" N PHE A 557 " ideal model delta sigma weight residual 1.333 1.296 0.036 2.74e-02 1.33e+03 1.75e+00 bond pdb=" CB PRO A 694 " pdb=" CG PRO A 694 " ideal model delta sigma weight residual 1.492 1.557 -0.065 5.00e-02 4.00e+02 1.71e+00 bond pdb=" CG1 ILE D 712 " pdb=" CD1 ILE D 712 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.59e+00 ... (remaining 16773 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 22103 1.55 - 3.10: 554 3.10 - 4.64: 184 4.64 - 6.19: 45 6.19 - 7.74: 10 Bond angle restraints: 22896 Sorted by residual: angle pdb=" CA PRO D 397 " pdb=" N PRO D 397 " pdb=" CD PRO D 397 " ideal model delta sigma weight residual 112.00 106.54 5.46 1.40e+00 5.10e-01 1.52e+01 angle pdb=" CA TYR D 696 " pdb=" CB TYR D 696 " pdb=" CG TYR D 696 " ideal model delta sigma weight residual 113.90 120.14 -6.24 1.80e+00 3.09e-01 1.20e+01 angle pdb=" CG ARG A 208 " pdb=" CD ARG A 208 " pdb=" NE ARG A 208 " ideal model delta sigma weight residual 112.00 118.46 -6.46 2.20e+00 2.07e-01 8.61e+00 angle pdb=" CA ARG A 51 " pdb=" CB ARG A 51 " pdb=" CG ARG A 51 " ideal model delta sigma weight residual 114.10 119.83 -5.73 2.00e+00 2.50e-01 8.21e+00 angle pdb=" CA GLU D 241 " pdb=" CB GLU D 241 " pdb=" CG GLU D 241 " ideal model delta sigma weight residual 114.10 119.70 -5.60 2.00e+00 2.50e-01 7.83e+00 ... (remaining 22891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 8001 17.82 - 35.64: 1259 35.64 - 53.46: 452 53.46 - 71.28: 166 71.28 - 89.10: 38 Dihedral angle restraints: 9916 sinusoidal: 4566 harmonic: 5350 Sorted by residual: dihedral pdb=" C4' U B 28 " pdb=" C3' U B 28 " pdb=" C2' U B 28 " pdb=" C1' U B 28 " ideal model delta sinusoidal sigma weight residual 36.34 -37.14 73.48 1 3.10e+00 1.04e-01 7.15e+02 dihedral pdb=" C4' G B 32 " pdb=" C3' G B 32 " pdb=" C2' G B 32 " pdb=" C1' G B 32 " ideal model delta sinusoidal sigma weight residual 36.34 -36.85 73.19 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' G C 21 " pdb=" C3' G C 21 " pdb=" C2' G C 21 " pdb=" C1' G C 21 " ideal model delta sinusoidal sigma weight residual 36.34 -36.74 73.09 1 3.10e+00 1.04e-01 7.08e+02 ... (remaining 9913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2113 0.064 - 0.128: 265 0.128 - 0.192: 23 0.192 - 0.255: 65 0.255 - 0.319: 40 Chirality restraints: 2506 Sorted by residual: chirality pdb=" C3' G B 47 " pdb=" C4' G B 47 " pdb=" O3' G B 47 " pdb=" C2' G B 47 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" C3' U B 41 " pdb=" C4' U B 41 " pdb=" O3' U B 41 " pdb=" C2' U B 41 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C2' C B 45 " pdb=" C3' C B 45 " pdb=" O2' C B 45 " pdb=" C1' C B 45 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 2503 not shown) Planarity restraints: 2709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 687 " -0.031 2.00e-02 2.50e+03 2.55e-02 1.62e+01 pdb=" CG TRP D 687 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 TRP D 687 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP D 687 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 687 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 687 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 687 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 687 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 687 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 687 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 396 " 0.052 5.00e-02 4.00e+02 7.59e-02 9.22e+00 pdb=" N PRO D 397 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO D 397 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 397 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G B 47 " -0.031 2.00e-02 2.50e+03 1.48e-02 6.57e+00 pdb=" N9 G B 47 " 0.040 2.00e-02 2.50e+03 pdb=" C8 G B 47 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G B 47 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G B 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 47 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G B 47 " -0.009 2.00e-02 2.50e+03 pdb=" N1 G B 47 " -0.002 2.00e-02 2.50e+03 pdb=" C2 G B 47 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 47 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 47 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G B 47 " 0.001 2.00e-02 2.50e+03 ... (remaining 2706 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 190 2.52 - 3.11: 11976 3.11 - 3.71: 28543 3.71 - 4.30: 40777 4.30 - 4.90: 66897 Nonbonded interactions: 148383 Sorted by model distance: nonbonded pdb=" OD1 ASP A 137 " pdb="MG MG A1804 " model vdw 1.923 2.170 nonbonded pdb=" OP2 U B 26 " pdb="MG MG A1804 " model vdw 1.930 2.170 nonbonded pdb=" OG1 THR A 941 " pdb=" OE1 GLU A 943 " model vdw 2.101 3.040 nonbonded pdb=" O ALA D 588 " pdb=" OG SER D 596 " model vdw 2.129 3.040 nonbonded pdb=" OG SER A1001 " pdb=" OP1 G B 47 " model vdw 2.137 3.040 ... (remaining 148378 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 19.710 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 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 0.081 16794 Z= 0.159 Angle : 0.691 11.509 22917 Z= 0.328 Chirality : 0.065 0.319 2506 Planarity : 0.005 0.085 2709 Dihedral : 20.658 89.097 6474 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.52 % Allowed : 32.09 % Favored : 62.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.20), residues: 1823 helix: 0.99 (0.20), residues: 680 sheet: -1.41 (0.30), residues: 258 loop : -0.12 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 208 TYR 0.017 0.001 TYR D 696 PHE 0.028 0.002 PHE D 477 TRP 0.068 0.002 TRP D 687 HIS 0.004 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (16778) covalent geometry : angle 0.67546 / 0.33 (22896) hydrogen bonds : bond 0.13416 / 8.74 ( 668) hydrogen bonds : angle 6.59021 / 4.73 ( 1905) metal coordination : bond 0.01076 / 0.77 ( 16) metal coordination : angle 4.83521 / 2.80 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 185 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 752 CYS cc_start: 0.7263 (m) cc_final: 0.6911 (m) REVERT: A 773 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7466 (mt-10) REVERT: D 216 MET cc_start: 0.7532 (tpt) cc_final: 0.7101 (tpt) REVERT: D 687 TRP cc_start: 0.8000 (t60) cc_final: 0.7384 (t60) outliers start: 90 outliers final: 87 residues processed: 268 average time/residue: 0.4554 time to fit residues: 138.9154 Evaluate side-chains 266 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 178 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 103 SER Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 451 VAL 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 547 ASP Chi-restraints excluded: chain A residue 573 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 GLU Chi-restraints excluded: chain A residue 635 LEU Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 680 SER Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 762 HIS Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 839 THR Chi-restraints excluded: chain A residue 840 THR Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 866 ILE Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 986 ASN Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 1029 SER Chi-restraints excluded: chain A residue 1424 ASP Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain A residue 1686 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 104 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 287 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 401 VAL Chi-restraints excluded: chain D residue 474 CYS Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 618 LYS Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 667 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 306 HIS A 586 ASN A 664 ASN ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1526 ASN ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.182016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.147858 restraints weight = 18321.112| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 1.72 r_work: 0.3616 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16794 Z= 0.220 Angle : 0.953 20.165 22917 Z= 0.408 Chirality : 0.094 1.384 2506 Planarity : 0.005 0.053 2709 Dihedral : 15.295 163.195 2863 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 7.12 % Allowed : 29.02 % Favored : 63.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.20), residues: 1823 helix: 1.12 (0.20), residues: 692 sheet: -1.46 (0.32), residues: 251 loop : -0.17 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 208 TYR 0.018 0.002 TYR D 607 PHE 0.020 0.002 PHE D 703 TRP 0.040 0.002 TRP D 687 HIS 0.005 0.001 HIS D 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.22 (16778) covalent geometry : angle 0.94226 / 0.41 (22896) hydrogen bonds : bond 0.04317 / 2.84 ( 668) hydrogen bonds : angle 5.36082 / 3.89 ( 1905) metal coordination : bond 0.01070 / 0.73 ( 16) metal coordination : angle 4.71478 / 2.76 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 212 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 8 ILE cc_start: 0.7911 (OUTLIER) cc_final: 0.7024 (pt) REVERT: A 123 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7692 (tmtt) REVERT: A 145 ARG cc_start: 0.7517 (mtm-85) cc_final: 0.7268 (mtm-85) REVERT: A 217 LYS cc_start: 0.6549 (OUTLIER) cc_final: 0.6194 (tptm) REVERT: A 464 LYS cc_start: 0.6910 (OUTLIER) cc_final: 0.6388 (mmtt) REVERT: A 506 CYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7753 (m) REVERT: A 547 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8103 (p0) REVERT: A 633 GLU cc_start: 0.7254 (mp0) cc_final: 0.6983 (mt-10) REVERT: A 752 CYS cc_start: 0.7410 (m) cc_final: 0.6819 (m) REVERT: A 823 ARG cc_start: 0.8383 (ptp-170) cc_final: 0.7786 (ptp-170) REVERT: A 852 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8614 (mt) REVERT: A 1004 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.7187 (ttp-170) REVERT: A 1400 ASP cc_start: 0.5562 (t70) cc_final: 0.5245 (t70) REVERT: A 1463 ARG cc_start: 0.7577 (mmt90) cc_final: 0.7284 (mmt90) REVERT: A 1479 LYS cc_start: 0.6541 (OUTLIER) cc_final: 0.6250 (tttt) REVERT: A 1504 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: A 1616 TRP cc_start: 0.6965 (m100) cc_final: 0.6734 (m100) REVERT: D 109 ASN cc_start: 0.7573 (m-40) cc_final: 0.7367 (m-40) REVERT: D 290 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7936 (mt) REVERT: D 687 TRP cc_start: 0.8287 (t60) cc_final: 0.7648 (t60) outliers start: 116 outliers final: 55 residues processed: 304 average time/residue: 0.5000 time to fit residues: 171.9883 Evaluate side-chains 254 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 188 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1007 LEU Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1647 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 268 GLU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 667 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 83 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 164 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 94 optimal weight: 30.0000 chunk 75 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.184573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.150281 restraints weight = 18346.541| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 1.74 r_work: 0.3648 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16794 Z= 0.182 Angle : 0.814 18.318 22917 Z= 0.356 Chirality : 0.075 1.274 2506 Planarity : 0.004 0.052 2709 Dihedral : 14.507 175.732 2779 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 7.36 % Allowed : 29.39 % Favored : 63.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1823 helix: 1.21 (0.20), residues: 687 sheet: -1.33 (0.32), residues: 251 loop : -0.22 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 208 TYR 0.017 0.002 TYR D 607 PHE 0.014 0.001 PHE A 15 TRP 0.027 0.002 TRP D 687 HIS 0.004 0.001 HIS D 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (16778) covalent geometry : angle 0.80485 / 0.36 (22896) hydrogen bonds : bond 0.04178 / 2.83 ( 668) hydrogen bonds : angle 5.05770 / 3.66 ( 1905) metal coordination : bond 0.00864 / 0.59 ( 16) metal coordination : angle 4.02927 / 2.42 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 219 time to evaluate : 0.577 Fit side-chains REVERT: A 8 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.5915 (tp) REVERT: A 123 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7673 (tmtt) REVERT: A 145 ARG cc_start: 0.7600 (mtm-85) cc_final: 0.7298 (mtm-85) REVERT: A 217 LYS cc_start: 0.6579 (OUTLIER) cc_final: 0.6265 (tptm) REVERT: A 352 ASP cc_start: 0.7541 (OUTLIER) cc_final: 0.7091 (p0) REVERT: A 458 PHE cc_start: 0.9189 (m-80) cc_final: 0.8965 (m-80) REVERT: A 464 LYS cc_start: 0.6868 (OUTLIER) cc_final: 0.6427 (mmtt) REVERT: A 506 CYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7770 (m) REVERT: A 547 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.8020 (p0) REVERT: A 633 GLU cc_start: 0.7261 (mp0) cc_final: 0.7013 (mt-10) REVERT: A 731 PHE cc_start: 0.8951 (m-80) cc_final: 0.8740 (m-80) REVERT: A 781 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: A 823 ARG cc_start: 0.8387 (ptp-170) cc_final: 0.7726 (ptp-170) REVERT: A 835 LYS cc_start: 0.7134 (OUTLIER) cc_final: 0.6895 (mmtt) REVERT: A 852 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8525 (mt) REVERT: A 1004 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7154 (ttp-170) REVERT: A 1400 ASP cc_start: 0.5484 (t70) cc_final: 0.5095 (t70) REVERT: A 1463 ARG cc_start: 0.7497 (mmt90) cc_final: 0.6893 (mmt90) REVERT: A 1479 LYS cc_start: 0.6454 (OUTLIER) cc_final: 0.6215 (tttt) REVERT: A 1504 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7595 (pm20) REVERT: A 1616 TRP cc_start: 0.6963 (m100) cc_final: 0.6740 (m100) REVERT: D 40 ASP cc_start: 0.7093 (m-30) cc_final: 0.6379 (p0) REVERT: D 125 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7551 (tptm) REVERT: D 143 ILE cc_start: 0.7519 (mm) cc_final: 0.7083 (tp) REVERT: D 172 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7764 (tpt-90) REVERT: D 357 GLN cc_start: 0.8550 (mt0) cc_final: 0.8267 (mm110) REVERT: D 490 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8476 (t70) REVERT: D 687 TRP cc_start: 0.8275 (t60) cc_final: 0.7746 (t60) outliers start: 120 outliers final: 50 residues processed: 309 average time/residue: 0.5383 time to fit residues: 186.9138 Evaluate side-chains 264 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 198 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 217 LYS Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 506 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 SER Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 667 ASN Chi-restraints excluded: chain D residue 714 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 86 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 65 optimal weight: 4.9990 chunk 149 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 99 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 HIS ** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 991 ASN ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 493 HIS D 699 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.180874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.146002 restraints weight = 18277.524| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.75 r_work: 0.3595 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16794 Z= 0.252 Angle : 0.866 18.463 22917 Z= 0.379 Chirality : 0.079 1.379 2506 Planarity : 0.005 0.059 2709 Dihedral : 14.587 168.505 2762 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 7.24 % Allowed : 30.25 % Favored : 62.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.19), residues: 1823 helix: 1.08 (0.20), residues: 686 sheet: -1.63 (0.31), residues: 258 loop : -0.26 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 476 TYR 0.019 0.002 TYR D 607 PHE 0.020 0.002 PHE D 184 TRP 0.021 0.002 TRP A 612 HIS 0.006 0.001 HIS D 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (16778) covalent geometry : angle 0.85573 / 0.38 (22896) hydrogen bonds : bond 0.04329 / 2.92 ( 668) hydrogen bonds : angle 5.16472 / 3.75 ( 1905) metal coordination : bond 0.00967 / 0.61 ( 16) metal coordination : angle 4.43166 / 2.59 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 197 time to evaluate : 0.607 Fit side-chains REVERT: A 8 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7113 (pt) REVERT: A 123 LYS cc_start: 0.8180 (OUTLIER) cc_final: 0.7684 (tmtt) REVERT: A 145 ARG cc_start: 0.7603 (mtm-85) cc_final: 0.7295 (mtm-85) REVERT: A 157 ASP cc_start: 0.8095 (m-30) cc_final: 0.7610 (m-30) REVERT: A 450 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7563 (mt) REVERT: A 464 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6423 (mmtt) REVERT: A 547 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7946 (p0) REVERT: A 633 GLU cc_start: 0.7261 (mp0) cc_final: 0.7028 (mt-10) REVERT: A 723 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8468 (mtpp) REVERT: A 781 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: A 823 ARG cc_start: 0.8407 (ptp-170) cc_final: 0.7755 (ptp-170) REVERT: A 835 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6829 (mmtt) REVERT: A 852 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8536 (mt) REVERT: A 961 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6520 (pt) REVERT: A 991 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7763 (p0) REVERT: A 1004 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7198 (ttp-170) REVERT: A 1400 ASP cc_start: 0.5459 (t70) cc_final: 0.5103 (t70) REVERT: A 1463 ARG cc_start: 0.7593 (mmt90) cc_final: 0.7213 (mmt90) REVERT: A 1479 LYS cc_start: 0.6519 (OUTLIER) cc_final: 0.6173 (tttt) REVERT: A 1504 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7598 (pm20) REVERT: A 1616 TRP cc_start: 0.6910 (m100) cc_final: 0.6673 (m100) REVERT: D 40 ASP cc_start: 0.7126 (m-30) cc_final: 0.6428 (p0) REVERT: D 172 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7740 (tpt-90) REVERT: D 181 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6811 (tp30) REVERT: D 275 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7705 (mmm160) REVERT: D 490 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8552 (t70) REVERT: D 578 ARG cc_start: 0.7424 (ptt180) cc_final: 0.5916 (tpp-160) REVERT: D 687 TRP cc_start: 0.8313 (t60) cc_final: 0.7813 (t60) outliers start: 118 outliers final: 64 residues processed: 288 average time/residue: 0.5307 time to fit residues: 172.0769 Evaluate side-chains 265 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 183 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 991 ASN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 611 LEU Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 666 SER Chi-restraints excluded: chain D residue 667 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 137 optimal weight: 2.9990 chunk 11 optimal weight: 40.0000 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 156 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 991 ASN ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 ASN D 699 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.186086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152223 restraints weight = 18170.358| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.73 r_work: 0.3671 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16794 Z= 0.154 Angle : 0.769 16.316 22917 Z= 0.340 Chirality : 0.070 1.363 2506 Planarity : 0.004 0.063 2709 Dihedral : 14.491 173.963 2762 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 6.69 % Allowed : 30.12 % Favored : 63.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.20), residues: 1823 helix: 1.27 (0.20), residues: 687 sheet: -1.49 (0.31), residues: 254 loop : -0.22 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 208 TYR 0.015 0.001 TYR D 607 PHE 0.016 0.001 PHE D 184 TRP 0.018 0.001 TRP A 612 HIS 0.005 0.001 HIS D 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (16778) covalent geometry : angle 0.76087 / 0.34 (22896) hydrogen bonds : bond 0.03898 / 2.64 ( 668) hydrogen bonds : angle 4.95737 / 3.59 ( 1905) metal coordination : bond 0.00844 / 0.61 ( 16) metal coordination : angle 3.85335 / 2.30 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 210 time to evaluate : 0.562 Fit side-chains REVERT: A 8 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.5901 (tp) REVERT: A 123 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7650 (tmtt) REVERT: A 145 ARG cc_start: 0.7653 (mtm-85) cc_final: 0.7317 (mtm-85) REVERT: A 458 PHE cc_start: 0.9115 (m-80) cc_final: 0.8874 (m-80) REVERT: A 464 LYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6339 (mmtt) REVERT: A 731 PHE cc_start: 0.8948 (m-80) cc_final: 0.8730 (m-80) REVERT: A 752 CYS cc_start: 0.7406 (m) cc_final: 0.6765 (m) REVERT: A 781 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: A 823 ARG cc_start: 0.8366 (ptp-170) cc_final: 0.7708 (ptp-170) REVERT: A 835 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6789 (mmtt) REVERT: A 852 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8467 (mt) REVERT: A 961 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.6539 (pt) REVERT: A 991 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7567 (p0) REVERT: A 1004 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.6984 (ttp-170) REVERT: A 1400 ASP cc_start: 0.5568 (t70) cc_final: 0.5196 (t70) REVERT: A 1463 ARG cc_start: 0.7494 (mmt90) cc_final: 0.7028 (mmt90) REVERT: A 1479 LYS cc_start: 0.6510 (OUTLIER) cc_final: 0.6159 (tttt) REVERT: A 1504 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: D 40 ASP cc_start: 0.6960 (m-30) cc_final: 0.6331 (p0) REVERT: D 125 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.7566 (tptm) REVERT: D 357 GLN cc_start: 0.8558 (mt0) cc_final: 0.8281 (mm110) REVERT: D 687 TRP cc_start: 0.8364 (t60) cc_final: 0.7888 (t60) outliers start: 109 outliers final: 53 residues processed: 292 average time/residue: 0.4996 time to fit residues: 165.9027 Evaluate side-chains 254 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 189 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 LYS Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 991 ASN Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 624 LEU Chi-restraints excluded: chain D residue 627 CYS Chi-restraints excluded: chain D residue 652 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 12 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 169 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 991 ASN ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.184272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.150221 restraints weight = 18158.452| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.72 r_work: 0.3648 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3514 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16794 Z= 0.187 Angle : 0.794 15.858 22917 Z= 0.349 Chirality : 0.072 1.297 2506 Planarity : 0.004 0.070 2709 Dihedral : 14.515 175.187 2758 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 6.32 % Allowed : 30.67 % Favored : 63.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.20), residues: 1823 helix: 1.25 (0.20), residues: 686 sheet: -1.48 (0.32), residues: 249 loop : -0.26 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 208 TYR 0.018 0.002 TYR A1663 PHE 0.020 0.002 PHE D 184 TRP 0.019 0.001 TRP A 612 HIS 0.004 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 (16778) covalent geometry : angle 0.78457 / 0.35 (22896) hydrogen bonds : bond 0.03989 / 2.70 ( 668) hydrogen bonds : angle 4.96146 / 3.60 ( 1905) metal coordination : bond 0.00857 / 0.59 ( 16) metal coordination : angle 4.01607 / 2.38 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 190 time to evaluate : 0.575 Fit side-chains REVERT: A 8 ILE cc_start: 0.7867 (OUTLIER) cc_final: 0.6928 (pt) REVERT: A 123 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7656 (tmtt) REVERT: A 145 ARG cc_start: 0.7602 (mtm-85) cc_final: 0.7239 (mtm-85) REVERT: A 157 ASP cc_start: 0.8116 (m-30) cc_final: 0.7643 (m-30) REVERT: A 458 PHE cc_start: 0.9113 (m-80) cc_final: 0.8802 (m-80) REVERT: A 731 PHE cc_start: 0.8935 (m-80) cc_final: 0.8687 (m-80) REVERT: A 781 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: A 823 ARG cc_start: 0.8368 (ptp-170) cc_final: 0.7707 (ptp-170) REVERT: A 835 LYS cc_start: 0.7123 (OUTLIER) cc_final: 0.6893 (mmtt) REVERT: A 961 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.6640 (pt) REVERT: A 991 ASN cc_start: 0.8085 (OUTLIER) cc_final: 0.7698 (p0) REVERT: A 1004 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.6990 (ttp-170) REVERT: A 1400 ASP cc_start: 0.5523 (t70) cc_final: 0.5126 (t70) REVERT: A 1463 ARG cc_start: 0.7531 (mmt90) cc_final: 0.7067 (mmt90) REVERT: A 1479 LYS cc_start: 0.6562 (OUTLIER) cc_final: 0.6158 (tttt) REVERT: A 1504 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7579 (pm20) REVERT: D 109 ASN cc_start: 0.7577 (m-40) cc_final: 0.7359 (m-40) REVERT: D 125 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.7556 (tptm) REVERT: D 357 GLN cc_start: 0.8558 (mt0) cc_final: 0.8282 (mm110) REVERT: D 490 ASP cc_start: 0.8766 (OUTLIER) cc_final: 0.8473 (t70) REVERT: D 578 ARG cc_start: 0.7416 (ptt180) cc_final: 0.5853 (tpp-160) REVERT: D 687 TRP cc_start: 0.8327 (t60) cc_final: 0.7922 (t60) REVERT: D 710 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7561 (ptp-170) outliers start: 103 outliers final: 63 residues processed: 271 average time/residue: 0.5092 time to fit residues: 156.3291 Evaluate side-chains 256 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 181 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 361 MET Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 808 TYR Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 991 ASN Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1394 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 710 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 182 optimal weight: 0.3980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 167 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 711 ASN A 991 ASN ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1689 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.188801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.155574 restraints weight = 18130.050| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 1.71 r_work: 0.3706 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16794 Z= 0.137 Angle : 0.743 14.738 22917 Z= 0.329 Chirality : 0.066 1.229 2506 Planarity : 0.004 0.072 2709 Dihedral : 14.344 177.857 2754 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.97 % Allowed : 32.09 % Favored : 62.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1823 helix: 1.42 (0.20), residues: 687 sheet: -1.40 (0.31), residues: 253 loop : -0.22 (0.21), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 208 TYR 0.016 0.001 TYR D 704 PHE 0.016 0.001 PHE D 184 TRP 0.017 0.001 TRP A 612 HIS 0.004 0.001 HIS D 457 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (16778) covalent geometry : angle 0.73561 / 0.33 (22896) hydrogen bonds : bond 0.03704 / 2.51 ( 668) hydrogen bonds : angle 4.79493 / 3.47 ( 1905) metal coordination : bond 0.00753 / 0.56 ( 16) metal coordination : angle 3.45870 / 2.14 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 215 time to evaluate : 0.546 Fit side-chains REVERT: A 8 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.5821 (tp) REVERT: A 123 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7649 (tmtt) REVERT: A 352 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.7156 (p0) REVERT: A 458 PHE cc_start: 0.9082 (m-80) cc_final: 0.8846 (m-80) REVERT: A 464 LYS cc_start: 0.6845 (mmtt) cc_final: 0.6515 (mmtt) REVERT: A 731 PHE cc_start: 0.8908 (m-80) cc_final: 0.8668 (m-80) REVERT: A 752 CYS cc_start: 0.7242 (m) cc_final: 0.6597 (m) REVERT: A 781 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: A 823 ARG cc_start: 0.8330 (ptp-170) cc_final: 0.7672 (ptp-170) REVERT: A 835 LYS cc_start: 0.7010 (OUTLIER) cc_final: 0.6793 (mmtt) REVERT: A 950 LEU cc_start: 0.8366 (pt) cc_final: 0.8039 (pp) REVERT: A 961 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6567 (pt) REVERT: A 1004 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.6880 (ttp-170) REVERT: A 1400 ASP cc_start: 0.5593 (t70) cc_final: 0.5161 (t70) REVERT: A 1463 ARG cc_start: 0.7456 (mmt90) cc_final: 0.7032 (mmt90) REVERT: A 1479 LYS cc_start: 0.6429 (OUTLIER) cc_final: 0.6125 (tttp) REVERT: A 1496 GLU cc_start: 0.6784 (mm-30) cc_final: 0.6323 (mt-10) REVERT: A 1504 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7583 (pm20) REVERT: A 1565 ASP cc_start: 0.7725 (p0) cc_final: 0.7465 (p0) REVERT: A 1665 LYS cc_start: 0.7601 (tptp) cc_final: 0.7268 (tttt) REVERT: D 80 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7105 (tp) REVERT: D 125 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7532 (tptm) REVERT: D 149 LEU cc_start: 0.6470 (mm) cc_final: 0.6045 (mm) REVERT: D 327 ARG cc_start: 0.8220 (mtt-85) cc_final: 0.7908 (mtp85) REVERT: D 357 GLN cc_start: 0.8550 (mt0) cc_final: 0.8256 (mm110) REVERT: D 490 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8476 (t70) REVERT: D 687 TRP cc_start: 0.8422 (t60) cc_final: 0.8017 (t60) outliers start: 81 outliers final: 50 residues processed: 277 average time/residue: 0.4745 time to fit residues: 149.6603 Evaluate side-chains 258 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 196 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 494 ARG Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 652 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 110 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 64 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN A 711 ASN A1689 ASN D 699 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.179672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144634 restraints weight = 18267.987| |-----------------------------------------------------------------------------| r_work (start): 0.3708 rms_B_bonded: 1.76 r_work: 0.3584 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 16794 Z= 0.286 Angle : 0.892 17.034 22917 Z= 0.393 Chirality : 0.078 1.334 2506 Planarity : 0.005 0.067 2709 Dihedral : 14.510 173.685 2747 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.89 % Allowed : 31.72 % Favored : 62.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.19), residues: 1823 helix: 0.99 (0.19), residues: 686 sheet: -1.56 (0.32), residues: 253 loop : -0.32 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 476 TYR 0.021 0.002 TYR A1436 PHE 0.026 0.002 PHE D 184 TRP 0.022 0.002 TRP A 612 HIS 0.005 0.001 HIS A 727 Details of bonding type rmsd/Z covalent geometry : bond 0.00667 / 0.29 (16778) covalent geometry : angle 0.88075 / 0.39 (22896) hydrogen bonds : bond 0.04366 / 2.93 ( 668) hydrogen bonds : angle 5.11811 / 3.73 ( 1905) metal coordination : bond 0.01036 / 0.65 ( 16) metal coordination : angle 4.68444 / 2.70 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 194 time to evaluate : 0.443 Fit side-chains REVERT: A 8 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7255 (pt) REVERT: A 11 GLU cc_start: 0.7751 (tp30) cc_final: 0.7503 (tp30) REVERT: A 123 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7681 (tmtt) REVERT: A 157 ASP cc_start: 0.8168 (m-30) cc_final: 0.7668 (m-30) REVERT: A 731 PHE cc_start: 0.8963 (m-80) cc_final: 0.8688 (m-80) REVERT: A 781 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: A 823 ARG cc_start: 0.8425 (ptp-170) cc_final: 0.7775 (ptp-170) REVERT: A 835 LYS cc_start: 0.7146 (OUTLIER) cc_final: 0.6866 (mmtt) REVERT: A 1004 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.7212 (ttp-170) REVERT: A 1400 ASP cc_start: 0.5579 (t70) cc_final: 0.5148 (t70) REVERT: A 1463 ARG cc_start: 0.7578 (mmt90) cc_final: 0.7112 (mmt90) REVERT: A 1479 LYS cc_start: 0.6595 (OUTLIER) cc_final: 0.6261 (tttt) REVERT: A 1504 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: A 1665 LYS cc_start: 0.7602 (tptp) cc_final: 0.7218 (tttt) REVERT: D 125 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7487 (tptm) REVERT: D 357 GLN cc_start: 0.8582 (mt0) cc_final: 0.8319 (mm110) REVERT: D 490 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8508 (t70) REVERT: D 535 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6650 (pm20) REVERT: D 687 TRP cc_start: 0.8375 (t60) cc_final: 0.8020 (t60) outliers start: 96 outliers final: 62 residues processed: 271 average time/residue: 0.5165 time to fit residues: 158.1525 Evaluate side-chains 256 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 184 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 16 GLU Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 704 LYS Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 SER Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 962 THR Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1479 LYS Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1527 LEU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1649 ASN Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 344 GLU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 418 VAL Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 666 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 49 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 chunk 51 optimal weight: 0.0670 chunk 128 optimal weight: 10.0000 chunk 142 optimal weight: 0.0470 chunk 170 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 chunk 169 optimal weight: 0.6980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN A 711 ASN ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1568 HIS D 109 ASN D 612 ASN D 699 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.189216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.155828 restraints weight = 18068.729| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 1.72 r_work: 0.3713 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 16794 Z= 0.136 Angle : 0.752 14.490 22917 Z= 0.337 Chirality : 0.067 1.237 2506 Planarity : 0.004 0.055 2709 Dihedral : 14.298 178.620 2747 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.66 % Allowed : 33.44 % Favored : 61.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.20), residues: 1823 helix: 1.33 (0.20), residues: 686 sheet: -1.21 (0.32), residues: 244 loop : -0.30 (0.21), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 168 TYR 0.018 0.001 TYR A1663 PHE 0.019 0.001 PHE D 703 TRP 0.017 0.001 TRP A 612 HIS 0.006 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (16778) covalent geometry : angle 0.74539 / 0.34 (22896) hydrogen bonds : bond 0.03708 / 2.50 ( 668) hydrogen bonds : angle 4.85235 / 3.52 ( 1905) metal coordination : bond 0.00842 / 0.65 ( 16) metal coordination : angle 3.38735 / 2.13 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 202 time to evaluate : 0.473 Fit side-chains REVERT: A 8 ILE cc_start: 0.7728 (OUTLIER) cc_final: 0.5918 (tp) REVERT: A 157 ASP cc_start: 0.8215 (m-30) cc_final: 0.7728 (m-30) REVERT: A 464 LYS cc_start: 0.6922 (mmtt) cc_final: 0.6604 (mmtt) REVERT: A 655 ARG cc_start: 0.7623 (ttp80) cc_final: 0.7392 (ttp-170) REVERT: A 731 PHE cc_start: 0.8910 (m-80) cc_final: 0.8707 (m-80) REVERT: A 752 CYS cc_start: 0.7201 (m) cc_final: 0.6572 (m) REVERT: A 781 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: A 782 LYS cc_start: 0.7885 (mmmt) cc_final: 0.7682 (tptm) REVERT: A 823 ARG cc_start: 0.8322 (ptp-170) cc_final: 0.7675 (ptp-170) REVERT: A 835 LYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6858 (mmtt) REVERT: A 950 LEU cc_start: 0.8391 (pt) cc_final: 0.8082 (pp) REVERT: A 961 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6604 (pt) REVERT: A 1004 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.6998 (ttp-170) REVERT: A 1400 ASP cc_start: 0.5613 (t70) cc_final: 0.5228 (t70) REVERT: A 1463 ARG cc_start: 0.7511 (mmt90) cc_final: 0.7107 (mmt90) REVERT: A 1496 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6331 (mt-10) REVERT: A 1565 ASP cc_start: 0.7796 (p0) cc_final: 0.7580 (p0) REVERT: A 1665 LYS cc_start: 0.7550 (tptp) cc_final: 0.7127 (tttt) REVERT: D 80 ILE cc_start: 0.7374 (OUTLIER) cc_final: 0.7013 (tp) REVERT: D 109 ASN cc_start: 0.7552 (m-40) cc_final: 0.7338 (m-40) REVERT: D 125 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7530 (tptm) REVERT: D 180 MET cc_start: 0.7431 (mmm) cc_final: 0.7192 (mmp) REVERT: D 216 MET cc_start: 0.7320 (tpt) cc_final: 0.6948 (tpt) REVERT: D 327 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.7909 (mtp85) REVERT: D 357 GLN cc_start: 0.8564 (mt0) cc_final: 0.8278 (mm110) REVERT: D 490 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8436 (t70) REVERT: D 535 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6833 (pm20) REVERT: D 578 ARG cc_start: 0.7366 (ptt180) cc_final: 0.6010 (tpp-160) REVERT: D 647 THR cc_start: 0.7678 (m) cc_final: 0.7323 (m) REVERT: D 687 TRP cc_start: 0.8425 (t60) cc_final: 0.8010 (t60) outliers start: 76 outliers final: 46 residues processed: 256 average time/residue: 0.5042 time to fit residues: 146.1533 Evaluate side-chains 248 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 193 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 835 LYS Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 666 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 129 optimal weight: 0.8980 chunk 181 optimal weight: 2.9990 chunk 180 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 163 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 711 ASN D 699 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.185075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.150744 restraints weight = 18115.430| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 1.73 r_work: 0.3653 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16794 Z= 0.188 Angle : 0.798 14.368 22917 Z= 0.354 Chirality : 0.070 1.247 2506 Planarity : 0.004 0.061 2709 Dihedral : 14.314 176.888 2740 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.23 % Allowed : 33.93 % Favored : 61.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.20), residues: 1823 helix: 1.23 (0.20), residues: 687 sheet: -1.39 (0.31), residues: 254 loop : -0.25 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 168 TYR 0.028 0.002 TYR A1663 PHE 0.028 0.002 PHE D 703 TRP 0.019 0.002 TRP A 612 HIS 0.005 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (16778) covalent geometry : angle 0.78860 / 0.35 (22896) hydrogen bonds : bond 0.03898 / 2.63 ( 668) hydrogen bonds : angle 4.90809 / 3.57 ( 1905) metal coordination : bond 0.00868 / 0.61 ( 16) metal coordination : angle 4.04034 / 2.40 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3646 Ramachandran restraints generated. 1823 Oldfield, 0 Emsley, 1823 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 191 time to evaluate : 0.581 Fit side-chains REVERT: A 8 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.6927 (pt) REVERT: A 157 ASP cc_start: 0.8265 (m-30) cc_final: 0.7777 (m-30) REVERT: A 464 LYS cc_start: 0.7006 (mmtt) cc_final: 0.6651 (mmtt) REVERT: A 731 PHE cc_start: 0.8929 (m-80) cc_final: 0.8650 (m-80) REVERT: A 752 CYS cc_start: 0.7381 (m) cc_final: 0.6756 (m) REVERT: A 781 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7733 (pm20) REVERT: A 823 ARG cc_start: 0.8364 (ptp-170) cc_final: 0.7702 (ptp-170) REVERT: A 950 LEU cc_start: 0.8445 (pt) cc_final: 0.8128 (pp) REVERT: A 961 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6638 (pt) REVERT: A 1004 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7034 (ttp-170) REVERT: A 1400 ASP cc_start: 0.5566 (t70) cc_final: 0.5157 (t70) REVERT: A 1463 ARG cc_start: 0.7470 (mmt90) cc_final: 0.6719 (mmt90) REVERT: A 1496 GLU cc_start: 0.6801 (mm-30) cc_final: 0.6326 (mt-10) REVERT: A 1504 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: A 1565 ASP cc_start: 0.7790 (p0) cc_final: 0.7536 (p0) REVERT: A 1665 LYS cc_start: 0.7648 (tptp) cc_final: 0.7150 (tttt) REVERT: D 80 ILE cc_start: 0.7450 (OUTLIER) cc_final: 0.7095 (tp) REVERT: D 125 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7519 (tptm) REVERT: D 180 MET cc_start: 0.7494 (mmm) cc_final: 0.7255 (mmp) REVERT: D 357 GLN cc_start: 0.8553 (mt0) cc_final: 0.8311 (mm110) REVERT: D 490 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8456 (t70) REVERT: D 535 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.6796 (pm20) REVERT: D 578 ARG cc_start: 0.7376 (ptt180) cc_final: 0.6016 (tpp-160) REVERT: D 687 TRP cc_start: 0.8406 (t60) cc_final: 0.8009 (t60) outliers start: 69 outliers final: 47 residues processed: 244 average time/residue: 0.4704 time to fit residues: 130.5002 Evaluate side-chains 240 residues out of total 1630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 33 HIS Chi-restraints excluded: chain A residue 34 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 513 THR Chi-restraints excluded: chain A residue 547 ASP Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 751 THR Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 781 GLU Chi-restraints excluded: chain A residue 826 ILE Chi-restraints excluded: chain A residue 830 PHE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 987 TYR Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1004 ARG Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1467 SER Chi-restraints excluded: chain A residue 1504 GLU Chi-restraints excluded: chain A residue 1596 GLN Chi-restraints excluded: chain A residue 1662 THR Chi-restraints excluded: chain D residue 80 ILE Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 125 LYS Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 219 CYS Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 343 HIS Chi-restraints excluded: chain D residue 391 LEU Chi-restraints excluded: chain D residue 396 VAL Chi-restraints excluded: chain D residue 490 ASP Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 537 VAL Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 549 THR Chi-restraints excluded: chain D residue 614 VAL Chi-restraints excluded: chain D residue 652 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 57 optimal weight: 0.0070 chunk 182 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 711 ASN ** A1547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 699 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.188941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.155264 restraints weight = 18068.349| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 1.73 r_work: 0.3700 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16794 Z= 0.142 Angle : 0.757 13.757 22917 Z= 0.337 Chirality : 0.066 1.204 2506 Planarity : 0.004 0.057 2709 Dihedral : 14.226 178.741 2740 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.62 % Allowed : 34.54 % Favored : 61.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.20), residues: 1823 helix: 1.37 (0.20), residues: 688 sheet: -1.39 (0.31), residues: 253 loop : -0.26 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 168 TYR 0.029 0.001 TYR A1663 PHE 0.017 0.001 PHE A1466 TRP 0.017 0.001 TRP A 612 HIS 0.006 0.001 HIS A 924 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (16778) covalent geometry : angle 0.74971 / 0.34 (22896) hydrogen bonds : bond 0.03680 / 2.49 ( 668) hydrogen bonds : angle 4.78892 / 3.47 ( 1905) metal coordination : bond 0.00809 / 0.60 ( 16) metal coordination : angle 3.49948 / 2.15 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5456.99 seconds wall clock time: 94 minutes 4.76 seconds (5644.76 seconds total)