Starting phenix.real_space_refine on Fri Aug 7 09:55:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gap_29903/08_2026/8gap_29903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gap_29903/08_2026/8gap_29903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8gap_29903/08_2026/8gap_29903.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gap_29903/08_2026/8gap_29903.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gap_29903/08_2026/8gap_29903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gap_29903/08_2026/8gap_29903.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gap_29903/08_2026/8gap_29903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gap_29903/08_2026/8gap_29903.map" } resolution = 3.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 173 5.49 5 S 74 5.16 5 C 12567 2.51 5 N 3479 2.21 5 O 4336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20630 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 8542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1012, 8542 Classifications: {'peptide': 1012} Link IDs: {'PTRANS': 22, 'TRANS': 989} Chain breaks: 3 Chain: "D" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1554 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "E" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1195 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 4, 'TRANS': 143} Chain: "F" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 952 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 3, 'TRANS': 113} Chain: "G" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1542 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 1, 'TRANS': 182} Chain: "C" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 300 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "B" Number of atoms: 3357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 3357 Classifications: {'RNAv2': 159} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 23, 'rna3p_pur': 62, 'rna3p_pyr': 59} Link IDs: {'rna2p': 37, 'rna3p': 121} Chain: "H" Number of atoms: 3187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 3187 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 8, 'TRANS': 375} Chain breaks: 2 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8923 SG CYS D 555 77.920 74.231 84.235 1.00345.25 S ATOM 8936 SG CYS D 557 76.660 71.913 86.938 1.00361.63 S ATOM 9056 SG CYS D 572 74.310 73.202 84.225 1.00370.03 S ATOM 9077 SG CYS D 575 75.523 75.571 86.923 1.00381.69 S Time building chain proxies: 3.97, per 1000 atoms: 0.19 Number of scatterers: 20630 At special positions: 0 Unit cell: (150.96, 189.04, 118.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 74 16.00 P 173 15.00 O 4336 8.00 N 3479 7.00 C 12567 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: 1.99 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 900 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 572 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 555 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 557 " pdb="ZN ZN D 900 " - pdb=" SG CYS D 575 " Number of angles added : 6 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3942 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 18 sheets defined 49.9% alpha, 20.4% beta 40 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 36 through 43 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 88 through 101 Processing helix chain 'A' and resid 127 through 133 Processing helix chain 'A' and resid 133 through 144 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.875A pdb=" N TYR A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 153 " --> pdb=" O LYS A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 178 Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.520A pdb=" N PHE A 230 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.602A pdb=" N SER A 250 " --> pdb=" O PHE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 289 Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 300 through 319 removed outlier: 3.593A pdb=" N HIS A 319 " --> pdb=" O VAL A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 331 Processing helix chain 'A' and resid 336 through 350 Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.678A pdb=" N ASN A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.913A pdb=" N TYR A 406 " --> pdb=" O LEU A 402 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'A' and resid 427 through 431 Processing helix chain 'A' and resid 444 through 475 removed outlier: 3.593A pdb=" N ILE A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP A 458 " --> pdb=" O LYS A 454 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ILE A 469 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Proline residue: A 470 - end of helix Processing helix chain 'A' and resid 493 through 511 removed outlier: 3.601A pdb=" N GLU A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 560 through 580 removed outlier: 5.267A pdb=" N ASP A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N MET A 578 " --> pdb=" O ASN A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 608 Processing helix chain 'A' and resid 622 through 626 removed outlier: 3.628A pdb=" N ILE A 626 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 638 Processing helix chain 'A' and resid 691 through 694 Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.766A pdb=" N LYS A 717 " --> pdb=" O GLN A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 777 through 794 removed outlier: 3.614A pdb=" N LEU A 789 " --> pdb=" O TYR A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 804 removed outlier: 3.995A pdb=" N LYS A 798 " --> pdb=" O THR A 794 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASN A 799 " --> pdb=" O GLN A 795 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU A 801 " --> pdb=" O LEU A 797 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLN A 802 " --> pdb=" O LYS A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 842 Processing helix chain 'A' and resid 845 through 847 No H-bonds generated for 'chain 'A' and resid 845 through 847' Processing helix chain 'A' and resid 895 through 901 removed outlier: 3.608A pdb=" N GLN A 901 " --> pdb=" O GLN A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 911 through 926 Processing helix chain 'A' and resid 927 through 932 removed outlier: 3.907A pdb=" N PHE A 932 " --> pdb=" O ILE A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 965 removed outlier: 3.784A pdb=" N MET A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) Proline residue: A 959 - end of helix Processing helix chain 'A' and resid 966 through 967 No H-bonds generated for 'chain 'A' and resid 966 through 967' Processing helix chain 'A' and resid 968 through 971 removed outlier: 3.604A pdb=" N LYS A 971 " --> pdb=" O ASP A 968 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 968 through 971' Processing helix chain 'A' and resid 972 through 980 removed outlier: 4.368A pdb=" N GLN A 978 " --> pdb=" O GLN A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1009 Processing helix chain 'A' and resid 1014 through 1038 Processing helix chain 'A' and resid 1045 through 1075 removed outlier: 3.939A pdb=" N LYS A1049 " --> pdb=" O GLY A1045 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A1050 " --> pdb=" O TYR A1046 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN A1070 " --> pdb=" O CYS A1066 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN A1075 " --> pdb=" O LEU A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1095 Processing helix chain 'A' and resid 1102 through 1109 removed outlier: 4.337A pdb=" N LYS A1106 " --> pdb=" O THR A1102 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1109 " --> pdb=" O PRO A1105 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 527 Processing helix chain 'D' and resid 603 through 615 Processing helix chain 'D' and resid 621 through 634 removed outlier: 4.479A pdb=" N GLN D 625 " --> pdb=" O GLN D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 645 Processing helix chain 'D' and resid 679 through 697 removed outlier: 4.115A pdb=" N GLU D 683 " --> pdb=" O ASN D 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 110 through 123 Processing helix chain 'E' and resid 153 through 175 removed outlier: 4.089A pdb=" N SER E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 22 Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'F' and resid 99 through 111 Processing helix chain 'F' and resid 111 through 119 removed outlier: 4.026A pdb=" N SER F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 9 through 29 removed outlier: 3.735A pdb=" N LYS G 13 " --> pdb=" O ASN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 41 Processing helix chain 'G' and resid 87 through 94 removed outlier: 4.013A pdb=" N LEU G 91 " --> pdb=" O ASP G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 157 removed outlier: 3.577A pdb=" N LYS G 157 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 161 Processing helix chain 'G' and resid 162 through 184 Processing helix chain 'H' and resid 83 through 107 removed outlier: 3.543A pdb=" N LEU H 93 " --> pdb=" O HIS H 89 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE H 95 " --> pdb=" O THR H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 130 Processing helix chain 'H' and resid 131 through 139 Processing helix chain 'H' and resid 140 through 148 removed outlier: 3.760A pdb=" N SER H 148 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 160 removed outlier: 3.727A pdb=" N LEU H 159 " --> pdb=" O ILE H 155 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 155 through 160' Processing helix chain 'H' and resid 164 through 168 Processing helix chain 'H' and resid 203 through 215 removed outlier: 3.945A pdb=" N HIS H 208 " --> pdb=" O LYS H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 247 removed outlier: 3.572A pdb=" N ALA H 240 " --> pdb=" O ASN H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 267 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 333 through 350 removed outlier: 4.426A pdb=" N SER H 342 " --> pdb=" O GLU H 338 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE H 343 " --> pdb=" O GLU H 339 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER H 347 " --> pdb=" O PHE H 343 " (cutoff:3.500A) Processing helix chain 'H' and resid 357 through 368 removed outlier: 4.229A pdb=" N ALA H 364 " --> pdb=" O GLN H 360 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N SER H 365 " --> pdb=" O SER H 361 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP H 366 " --> pdb=" O ARG H 362 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 374 Processing helix chain 'H' and resid 376 through 378 No H-bonds generated for 'chain 'H' and resid 376 through 378' Processing helix chain 'H' and resid 391 through 401 removed outlier: 3.596A pdb=" N VAL H 395 " --> pdb=" O LEU H 391 " (cutoff:3.500A) Processing helix chain 'H' and resid 468 through 480 Processing helix chain 'H' and resid 503 through 531 removed outlier: 3.797A pdb=" N PHE H 525 " --> pdb=" O PHE H 521 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN H 531 " --> pdb=" O MET H 527 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.668A pdb=" N VAL A 157 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR A 166 " --> pdb=" O VAL A 731 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ASN A 733 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N GLN A 168 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 35 removed outlier: 6.668A pdb=" N VAL A 157 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TYR A 166 " --> pdb=" O VAL A 731 " (cutoff:3.500A) removed outlier: 8.232A pdb=" N ASN A 733 " --> pdb=" O TYR A 166 " (cutoff:3.500A) removed outlier: 8.797A pdb=" N GLN A 168 " --> pdb=" O ASN A 733 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 476 through 479 Processing sheet with id=AA5, first strand: chain 'A' and resid 512 through 514 removed outlier: 6.631A pdb=" N GLY A 531 " --> pdb=" O SER A 759 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 808 through 813 removed outlier: 3.512A pdb=" N LEU A 617 " --> pdb=" O TYR A 817 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP A 618 " --> pdb=" O LYS A 849 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LYS A 849 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE A 850 " --> pdb=" O SER A 869 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 874 through 876 removed outlier: 3.668A pdb=" N CYS A 874 " --> pdb=" O ILE A 881 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 532 through 545 removed outlier: 5.686A pdb=" N LEU D 541 " --> pdb=" O GLN D 592 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLN D 592 " --> pdb=" O LEU D 541 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N SER D 543 " --> pdb=" O PHE D 590 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE D 590 " --> pdb=" O SER D 543 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG D 588 " --> pdb=" O GLN D 545 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 589 " --> pdb=" O VAL D 600 " (cutoff:3.500A) removed outlier: 13.472A pdb=" N THR D 597 " --> pdb=" O ILE D 668 " (cutoff:3.500A) removed outlier: 10.661A pdb=" N TYR D 670 " --> pdb=" O THR D 597 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N VAL D 672 " --> pdb=" O PRO D 599 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N MET D 601 " --> pdb=" O VAL D 672 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N LYS D 674 " --> pdb=" O MET D 601 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU D 654 " --> pdb=" O LEU D 673 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE D 675 " --> pdb=" O ILE D 652 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE D 652 " --> pdb=" O ILE D 675 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS D 533 " --> pdb=" O PHE D 657 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 551 through 554 removed outlier: 3.523A pdb=" N GLN D 582 " --> pdb=" O ARG D 554 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 562 through 564 removed outlier: 3.895A pdb=" N LEU D 563 " --> pdb=" O PHE D 571 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE D 571 " --> pdb=" O LEU D 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'E' and resid 31 through 33 removed outlier: 3.619A pdb=" N LYS E 72 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER E 90 " --> pdb=" O LYS E 72 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N MET E 86 " --> pdb=" O LEU E 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 31 through 33 removed outlier: 3.508A pdb=" N TYR E 146 " --> pdb=" O MET E 133 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS E 135 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU E 144 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL E 99 " --> pdb=" O LEU E 144 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N TYR E 146 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 11.156A pdb=" N GLN E 101 " --> pdb=" O TYR E 146 " (cutoff:3.500A) removed outlier: 14.310A pdb=" N SER E 148 " --> pdb=" O GLN E 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 87 through 91 removed outlier: 3.511A pdb=" N GLU F 87 " --> pdb=" O ARG F 74 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR F 89 " --> pdb=" O GLU F 72 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU F 72 " --> pdb=" O THR F 89 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N VAL F 83 " --> pdb=" O HIS F 53 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL F 55 " --> pdb=" O VAL F 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.875A pdb=" N LEU G 46 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR G 116 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE G 48 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 114 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER G 103 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE G 62 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR G 75 " --> pdb=" O ILE G 62 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA G 64 " --> pdb=" O GLN G 73 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS G 80 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 46 through 51 removed outlier: 6.875A pdb=" N LEU G 46 " --> pdb=" O TYR G 116 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N TYR G 116 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE G 48 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 114 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N SER G 103 " --> pdb=" O ASP G 134 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP G 134 " --> pdb=" O SER G 103 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL G 105 " --> pdb=" O CYS G 132 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS G 132 " --> pdb=" O VAL G 105 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE G 107 " --> pdb=" O MET G 130 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N MET G 130 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN G 109 " --> pdb=" O ASP G 128 " (cutoff:3.500A) removed outlier: 15.962A pdb=" N LYS G 80 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 12.893A pdb=" N LEU G 125 " --> pdb=" O LYS G 80 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ILE G 82 " --> pdb=" O LEU G 125 " (cutoff:3.500A) removed outlier: 9.315A pdb=" N ILE G 127 " --> pdb=" O ILE G 82 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ASN G 84 " --> pdb=" O ILE G 127 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N GLU G 129 " --> pdb=" O ASN G 84 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS G 80 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 153 through 154 removed outlier: 3.821A pdb=" N LYS H 230 " --> pdb=" O LYS H 221 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 272 through 276 Processing sheet with id=AB9, first strand: chain 'H' and resid 406 through 409 831 hydrogen bonds defined for protein. 2370 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 5.09 Time building geometry restraints manager: 2.63 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: 4908 1.33 - 1.45: 5271 1.45 - 1.58: 10738 1.58 - 1.70: 344 1.70 - 1.82: 110 Bond restraints: 21371 Sorted by residual: bond pdb=" C3' DT C 56 " pdb=" C2' DT C 56 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.08e+00 bond pdb=" C1' DT C 51 " pdb=" N1 DT C 51 " ideal model delta sigma weight residual 1.468 1.503 -0.035 1.40e-02 5.10e+03 6.38e+00 bond pdb=" C3' DT C 50 " pdb=" C2' DT C 50 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.68e+00 bond pdb=" O4' DT C 56 " pdb=" C1' DT C 56 " ideal model delta sigma weight residual 1.420 1.399 0.021 1.10e-02 8.26e+03 3.80e+00 bond pdb=" O4' DT C 50 " pdb=" C1' DT C 50 " ideal model delta sigma weight residual 1.420 1.400 0.020 1.10e-02 8.26e+03 3.23e+00 ... (remaining 21366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 28778 2.19 - 4.37: 689 4.37 - 6.56: 87 6.56 - 8.75: 10 8.75 - 10.93: 7 Bond angle restraints: 29571 Sorted by residual: angle pdb=" N ASN F 81 " pdb=" CA ASN F 81 " pdb=" CB ASN F 81 " ideal model delta sigma weight residual 114.17 108.32 5.85 1.14e+00 7.69e-01 2.64e+01 angle pdb=" C3' C B 109 " pdb=" O3' C B 109 " pdb=" P A B 110 " ideal model delta sigma weight residual 119.70 125.08 -5.38 1.20e+00 6.94e-01 2.01e+01 angle pdb=" N3 DT C 50 " pdb=" C4 DT C 50 " pdb=" O4 DT C 50 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT C 51 " pdb=" C4 DT C 51 " pdb=" O4 DT C 51 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT C 56 " pdb=" C4 DT C 56 " pdb=" O4 DT C 56 " ideal model delta sigma weight residual 119.90 122.29 -2.39 6.00e-01 2.78e+00 1.58e+01 ... (remaining 29566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.46: 11889 34.46 - 68.93: 660 68.93 - 103.39: 83 103.39 - 137.85: 0 137.85 - 172.32: 3 Dihedral angle restraints: 12635 sinusoidal: 6573 harmonic: 6062 Sorted by residual: dihedral pdb=" C4' A B 155 " pdb=" C3' A B 155 " pdb=" C2' A B 155 " pdb=" C1' A B 155 " ideal model delta sinusoidal sigma weight residual 36.35 -38.28 74.62 1 3.10e+00 1.04e-01 7.34e+02 dihedral pdb=" C4' U B 13 " pdb=" C3' U B 13 " pdb=" C2' U B 13 " pdb=" C1' U B 13 " ideal model delta sinusoidal sigma weight residual 36.34 -37.45 73.79 1 3.10e+00 1.04e-01 7.20e+02 dihedral pdb=" C4' U B 42 " pdb=" C3' U B 42 " pdb=" C2' U B 42 " pdb=" C1' U B 42 " ideal model delta sinusoidal sigma weight residual 36.34 -37.40 73.74 1 3.10e+00 1.04e-01 7.19e+02 ... (remaining 12632 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2876 0.072 - 0.143: 265 0.143 - 0.215: 29 0.215 - 0.287: 203 0.287 - 0.358: 9 Chirality restraints: 3382 Sorted by residual: chirality pdb=" P A B 110 " pdb=" OP1 A B 110 " pdb=" OP2 A B 110 " pdb=" O5' A B 110 " both_signs ideal model delta sigma weight residual True 2.17 -2.53 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" P U B 159 " pdb=" OP1 U B 159 " pdb=" OP2 U B 159 " pdb=" O5' U B 159 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C2' G B 128 " pdb=" C3' G B 128 " pdb=" O2' G B 128 " pdb=" C1' G B 128 " both_signs ideal model delta sigma weight residual False -2.79 -2.47 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 3379 not shown) Planarity restraints: 3145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN F 81 " -0.015 2.00e-02 2.50e+03 2.90e-02 8.43e+00 pdb=" C ASN F 81 " 0.050 2.00e-02 2.50e+03 pdb=" O ASN F 81 " -0.019 2.00e-02 2.50e+03 pdb=" N ILE F 82 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 52 " -0.024 2.00e-02 2.50e+03 1.42e-02 6.04e+00 pdb=" N9 DG C 52 " 0.016 2.00e-02 2.50e+03 pdb=" C8 DG C 52 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DG C 52 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DG C 52 " -0.015 2.00e-02 2.50e+03 pdb=" C6 DG C 52 " 0.000 2.00e-02 2.50e+03 pdb=" O6 DG C 52 " 0.000 2.00e-02 2.50e+03 pdb=" N1 DG C 52 " -0.012 2.00e-02 2.50e+03 pdb=" C2 DG C 52 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG C 52 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DG C 52 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DG C 52 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU H 124 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C LEU H 124 " 0.031 2.00e-02 2.50e+03 pdb=" O LEU H 124 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN H 125 " -0.010 2.00e-02 2.50e+03 ... (remaining 3142 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1765 2.74 - 3.28: 21341 3.28 - 3.82: 36791 3.82 - 4.36: 42311 4.36 - 4.90: 67804 Nonbonded interactions: 170012 Sorted by model distance: nonbonded pdb=" O2' A B 90 " pdb=" O4' A B 91 " model vdw 2.199 3.040 nonbonded pdb=" NZ LYS A 990 " pdb=" O4 U B 60 " model vdw 2.199 3.120 nonbonded pdb=" NH2 ARG A 446 " pdb=" O4 U B 139 " model vdw 2.206 3.120 nonbonded pdb=" OE1 GLN A1008 " pdb=" OH TYR A1025 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR G 112 " pdb=" OH TYR G 168 " model vdw 2.207 3.040 ... (remaining 170007 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 group one per residue 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: 1.450 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 24.180 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 : 0.003 0.035 21375 Z= 0.152 Angle : 0.722 10.932 29577 Z= 0.361 Chirality : 0.075 0.358 3382 Planarity : 0.003 0.042 3145 Dihedral : 19.262 172.316 8693 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.68 % Favored : 96.27 % Rotamer: Outliers : 0.21 % Allowed : 12.42 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.20), residues: 2010 helix: 2.07 (0.18), residues: 889 sheet: -0.02 (0.31), residues: 279 loop : -0.37 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 231 TYR 0.024 0.001 TYR H 513 PHE 0.012 0.001 PHE H 233 TRP 0.015 0.002 TRP G 110 HIS 0.018 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (21371) covalent geometry : angle 0.72195 / 0.36 (29571) hydrogen bonds : bond 0.15936 / 10.21 ( 908) hydrogen bonds : angle 5.89487 / 4.02 ( 2556) metal coordination : bond 0.00249 / 0.13 ( 4) metal coordination : angle 1.26687 / 0.60 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.9032 (mmm) cc_final: 0.8789 (tpp) REVERT: F 18 MET cc_start: 0.9440 (ptp) cc_final: 0.9194 (mpp) REVERT: F 88 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8435 (tp) REVERT: H 121 SER cc_start: 0.9465 (m) cc_final: 0.9245 (p) REVERT: H 463 MET cc_start: 0.7779 (tpp) cc_final: 0.7546 (tpt) outliers start: 4 outliers final: 1 residues processed: 79 average time/residue: 0.1348 time to fit residues: 17.1189 Evaluate side-chains 75 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain H residue 223 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 200 optimal weight: 7.9990 chunk 212 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN A 590 ASN A 926 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN H 125 GLN H 166 GLN ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.040100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.028153 restraints weight = 188449.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.029000 restraints weight = 116037.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.029552 restraints weight = 87006.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.029896 restraints weight = 72844.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.030092 restraints weight = 65411.323| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 21375 Z= 0.250 Angle : 1.172 28.190 29577 Z= 0.490 Chirality : 0.112 1.584 3382 Planarity : 0.004 0.042 3145 Dihedral : 17.846 164.268 4232 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 1.09 % Allowed : 12.06 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.20), residues: 2010 helix: 2.09 (0.18), residues: 899 sheet: -0.14 (0.30), residues: 273 loop : -0.38 (0.22), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 522 TYR 0.022 0.001 TYR H 513 PHE 0.011 0.001 PHE E 73 TRP 0.010 0.001 TRP A 604 HIS 0.011 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.25 (21371) covalent geometry : angle 1.17138 / 0.49 (29571) hydrogen bonds : bond 0.05553 / 3.64 ( 908) hydrogen bonds : angle 4.87686 / 3.32 ( 2556) metal coordination : bond 0.00811 / 0.41 ( 4) metal coordination : angle 3.02721 / 1.49 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 566 MET cc_start: 0.9080 (ppp) cc_final: 0.8818 (ppp) REVERT: F 9 MET cc_start: 0.8924 (tmm) cc_final: 0.8699 (tmm) REVERT: F 108 LEU cc_start: 0.9705 (OUTLIER) cc_final: 0.9455 (pp) REVERT: H 463 MET cc_start: 0.7798 (tpp) cc_final: 0.7476 (tpt) outliers start: 21 outliers final: 9 residues processed: 86 average time/residue: 0.1309 time to fit residues: 18.3375 Evaluate side-chains 75 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 166 GLN Chi-restraints excluded: chain H residue 223 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 79 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 27 optimal weight: 0.0970 chunk 205 optimal weight: 6.9990 chunk 184 optimal weight: 0.7980 chunk 208 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 ASN ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN H 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.041144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.028848 restraints weight = 186871.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.029806 restraints weight = 111615.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.030400 restraints weight = 81980.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.030772 restraints weight = 68211.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.030987 restraints weight = 61045.604| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 21375 Z= 0.139 Angle : 0.864 18.115 29577 Z= 0.374 Chirality : 0.080 1.287 3382 Planarity : 0.003 0.036 3145 Dihedral : 18.194 162.719 4230 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 0.78 % Allowed : 13.05 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.20), residues: 2010 helix: 2.15 (0.18), residues: 899 sheet: -0.01 (0.32), residues: 252 loop : -0.44 (0.22), residues: 859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 22 TYR 0.025 0.001 TYR F 10 PHE 0.011 0.001 PHE H 235 TRP 0.011 0.001 TRP H 336 HIS 0.009 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (21371) covalent geometry : angle 0.86298 / 0.37 (29571) hydrogen bonds : bond 0.04744 / 3.00 ( 908) hydrogen bonds : angle 4.47823 / 3.05 ( 2556) metal coordination : bond 0.00526 / 0.27 ( 4) metal coordination : angle 2.48565 / 1.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 MET cc_start: 0.9055 (ppp) cc_final: 0.8855 (ppp) REVERT: A 741 THR cc_start: 0.9585 (OUTLIER) cc_final: 0.9373 (p) REVERT: A 811 MET cc_start: 0.8782 (mtt) cc_final: 0.8503 (mpp) REVERT: E 34 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9270 (pp) REVERT: E 86 MET cc_start: 0.7892 (tpp) cc_final: 0.7185 (tpp) REVERT: F 9 MET cc_start: 0.9146 (tmm) cc_final: 0.8929 (tmm) REVERT: F 89 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8601 (p) REVERT: G 40 MET cc_start: 0.9036 (mmt) cc_final: 0.8832 (mmt) REVERT: H 267 PHE cc_start: 0.8974 (OUTLIER) cc_final: 0.8119 (m-80) outliers start: 15 outliers final: 5 residues processed: 87 average time/residue: 0.1299 time to fit residues: 19.2843 Evaluate side-chains 76 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain H residue 267 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 99 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 16 optimal weight: 3.9990 chunk 205 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 199 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 48 optimal weight: 0.6980 chunk 177 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 892 GLN A 897 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 GLN G 101 ASN ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN H 162 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.039215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.027120 restraints weight = 195181.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.028017 restraints weight = 117629.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.028596 restraints weight = 86805.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.028931 restraints weight = 71997.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.029131 restraints weight = 64747.129| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21375 Z= 0.242 Angle : 0.865 12.866 29577 Z= 0.385 Chirality : 0.071 1.336 3382 Planarity : 0.004 0.046 3145 Dihedral : 18.305 172.316 4226 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.03 % Favored : 95.87 % Rotamer: Outliers : 1.92 % Allowed : 13.57 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 2010 helix: 2.08 (0.18), residues: 904 sheet: -0.10 (0.30), residues: 281 loop : -0.48 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 74 TYR 0.017 0.002 TYR A 995 PHE 0.022 0.002 PHE E 112 TRP 0.009 0.002 TRP A 496 HIS 0.004 0.001 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.24 (21371) covalent geometry : angle 0.86434 / 0.38 (29571) hydrogen bonds : bond 0.05342 / 3.59 ( 908) hydrogen bonds : angle 4.56362 / 3.09 ( 2556) metal coordination : bond 0.00816 / 0.41 ( 4) metal coordination : angle 2.53199 / 1.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 64 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.9133 (tpp) cc_final: 0.8599 (tpp) REVERT: A 566 MET cc_start: 0.9060 (ppp) cc_final: 0.8748 (ppp) REVERT: D 546 MET cc_start: 0.8219 (ppp) cc_final: 0.8010 (ppp) REVERT: E 34 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9368 (pp) REVERT: E 86 MET cc_start: 0.8006 (tpp) cc_final: 0.7391 (tpp) REVERT: F 9 MET cc_start: 0.9215 (tmm) cc_final: 0.8997 (tmm) REVERT: F 37 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7503 (mp10) REVERT: G 40 MET cc_start: 0.9188 (mmt) cc_final: 0.8923 (mmt) REVERT: G 129 GLU cc_start: 0.8641 (tp30) cc_final: 0.8058 (tm-30) REVERT: H 267 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8291 (m-80) REVERT: H 463 MET cc_start: 0.8582 (tpp) cc_final: 0.7657 (tpt) outliers start: 37 outliers final: 23 residues processed: 99 average time/residue: 0.1202 time to fit residues: 20.5982 Evaluate side-chains 89 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 222 VAL Chi-restraints excluded: chain H residue 267 PHE Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 416 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 204 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 141 optimal weight: 20.0000 chunk 28 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.038810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.026927 restraints weight = 191459.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.027786 restraints weight = 115573.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.028356 restraints weight = 85582.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.028692 restraints weight = 70955.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.028888 restraints weight = 63628.715| |-----------------------------------------------------------------------------| r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21375 Z= 0.240 Angle : 0.821 11.590 29577 Z= 0.371 Chirality : 0.066 1.054 3382 Planarity : 0.004 0.042 3145 Dihedral : 18.356 175.794 4226 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.43 % Favored : 95.47 % Rotamer: Outliers : 2.34 % Allowed : 14.03 % Favored : 83.63 % 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: 0.94 (0.19), residues: 2010 helix: 1.96 (0.18), residues: 902 sheet: -0.23 (0.31), residues: 265 loop : -0.53 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 231 TYR 0.017 0.001 TYR H 513 PHE 0.014 0.001 PHE A 960 TRP 0.009 0.001 TRP A 496 HIS 0.006 0.001 HIS H 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.24 (21371) covalent geometry : angle 0.82043 / 0.37 (29571) hydrogen bonds : bond 0.04885 / 3.24 ( 908) hydrogen bonds : angle 4.53796 / 3.07 ( 2556) metal coordination : bond 0.00842 / 0.43 ( 4) metal coordination : angle 2.13496 / 1.01 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 67 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 MET cc_start: 0.9095 (ppp) cc_final: 0.8678 (ppp) REVERT: A 631 LEU cc_start: 0.9804 (tt) cc_final: 0.9585 (pp) REVERT: A 767 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8617 (tt0) REVERT: E 34 LEU cc_start: 0.9449 (OUTLIER) cc_final: 0.9200 (pp) REVERT: E 86 MET cc_start: 0.7997 (tpp) cc_final: 0.7345 (tpp) REVERT: F 9 MET cc_start: 0.9194 (tmm) cc_final: 0.8884 (tmm) REVERT: F 22 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7472 (tpm170) REVERT: F 37 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7611 (mp10) REVERT: G 40 MET cc_start: 0.9219 (mmt) cc_final: 0.8914 (mmt) REVERT: G 129 GLU cc_start: 0.8638 (tp30) cc_final: 0.8311 (tm-30) outliers start: 45 outliers final: 23 residues processed: 107 average time/residue: 0.1309 time to fit residues: 23.0629 Evaluate side-chains 90 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 63 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 954 VAL Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 169 LYS Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 235 PHE Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 501 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 170 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 180 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 0.2980 chunk 75 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 187 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 511 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.039746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.027878 restraints weight = 183699.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.028744 restraints weight = 113545.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.029295 restraints weight = 84701.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.029622 restraints weight = 70755.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.029862 restraints weight = 63721.211| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21375 Z= 0.127 Angle : 0.764 11.417 29577 Z= 0.340 Chirality : 0.064 1.004 3382 Planarity : 0.003 0.038 3145 Dihedral : 18.244 177.132 4226 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.12 % Rotamer: Outliers : 1.66 % Allowed : 15.38 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.20), residues: 2010 helix: 2.09 (0.18), residues: 902 sheet: -0.18 (0.31), residues: 263 loop : -0.46 (0.22), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 22 TYR 0.018 0.001 TYR H 513 PHE 0.015 0.001 PHE H 235 TRP 0.009 0.001 TRP H 336 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (21371) covalent geometry : angle 0.76356 / 0.34 (29571) hydrogen bonds : bond 0.04356 / 2.82 ( 908) hydrogen bonds : angle 4.31651 / 2.94 ( 2556) metal coordination : bond 0.00491 / 0.25 ( 4) metal coordination : angle 1.82231 / 0.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 68 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 MET cc_start: 0.9087 (ppp) cc_final: 0.8697 (ppp) REVERT: E 34 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9263 (pp) REVERT: E 86 MET cc_start: 0.7998 (tpp) cc_final: 0.7328 (tpp) REVERT: E 136 MET cc_start: 0.8670 (pmm) cc_final: 0.8470 (pmm) REVERT: F 9 MET cc_start: 0.9198 (tmm) cc_final: 0.8926 (tmm) REVERT: F 22 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7338 (tpm170) REVERT: F 79 ASN cc_start: 0.9286 (t0) cc_final: 0.8822 (p0) REVERT: F 91 PHE cc_start: 0.9345 (m-80) cc_final: 0.8854 (m-80) REVERT: G 40 MET cc_start: 0.9282 (mmt) cc_final: 0.8836 (mmt) REVERT: G 129 GLU cc_start: 0.8707 (tp30) cc_final: 0.8435 (tm-30) REVERT: H 223 LYS cc_start: 0.9135 (OUTLIER) cc_final: 0.8840 (pttp) REVERT: H 267 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: H 463 MET cc_start: 0.8538 (tpp) cc_final: 0.7783 (tpp) outliers start: 32 outliers final: 22 residues processed: 96 average time/residue: 0.1096 time to fit residues: 17.5167 Evaluate side-chains 90 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain D residue 511 GLN Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 140 TYR Chi-restraints excluded: chain H residue 169 LYS Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 235 PHE Chi-restraints excluded: chain H residue 267 PHE Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 492 ARG Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 501 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 142 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 208 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 167 optimal weight: 20.0000 chunk 207 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 chunk 185 optimal weight: 0.5980 chunk 84 optimal weight: 7.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 355 ASN A1048 ASN D 511 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.038798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.026956 restraints weight = 191707.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.027830 restraints weight = 115260.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.028361 restraints weight = 84986.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.028728 restraints weight = 71138.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.028932 restraints weight = 63338.866| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21375 Z= 0.229 Angle : 0.802 13.082 29577 Z= 0.361 Chirality : 0.063 0.995 3382 Planarity : 0.003 0.046 3145 Dihedral : 18.280 177.319 4226 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.18 % Favored : 95.67 % Rotamer: Outliers : 2.13 % Allowed : 15.18 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 2010 helix: 2.07 (0.18), residues: 901 sheet: -0.23 (0.30), residues: 273 loop : -0.50 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 22 TYR 0.016 0.001 TYR H 513 PHE 0.016 0.001 PHE H 235 TRP 0.008 0.001 TRP A1027 HIS 0.003 0.001 HIS H 208 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.23 (21371) covalent geometry : angle 0.80194 / 0.36 (29571) hydrogen bonds : bond 0.04742 / 3.14 ( 908) hydrogen bonds : angle 4.42358 / 2.99 ( 2556) metal coordination : bond 0.00689 / 0.35 ( 4) metal coordination : angle 1.92831 / 0.92 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 63 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8650 (tpp) cc_final: 0.7531 (tpp) REVERT: A 380 LEU cc_start: 0.9661 (mm) cc_final: 0.9417 (mm) REVERT: A 546 MET cc_start: 0.9366 (mtm) cc_final: 0.9070 (pmm) REVERT: A 566 MET cc_start: 0.9083 (ppp) cc_final: 0.8702 (ppp) REVERT: A 767 GLN cc_start: 0.8946 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: E 34 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9246 (pp) REVERT: E 86 MET cc_start: 0.8039 (tpp) cc_final: 0.7395 (tpp) REVERT: E 136 MET cc_start: 0.8662 (pmm) cc_final: 0.8368 (pmm) REVERT: F 9 MET cc_start: 0.9200 (tmm) cc_final: 0.8968 (tmm) REVERT: F 22 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7485 (tpm170) REVERT: F 37 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7683 (mp10) REVERT: F 79 ASN cc_start: 0.9331 (t0) cc_final: 0.8896 (p0) REVERT: F 91 PHE cc_start: 0.9370 (m-80) cc_final: 0.8893 (m-80) REVERT: G 40 MET cc_start: 0.9323 (mmt) cc_final: 0.8874 (mmt) REVERT: G 129 GLU cc_start: 0.8653 (tp30) cc_final: 0.8346 (tm-30) REVERT: H 267 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: H 463 MET cc_start: 0.8523 (tpp) cc_final: 0.7624 (tpp) outliers start: 41 outliers final: 29 residues processed: 100 average time/residue: 0.1328 time to fit residues: 21.9552 Evaluate side-chains 96 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 62 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain D residue 511 GLN Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 169 LYS Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 267 PHE Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 416 ASN Chi-restraints excluded: chain H residue 492 ARG Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 501 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 1 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 511 GLN D 545 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.039676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.027824 restraints weight = 185086.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028696 restraints weight = 113178.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.029256 restraints weight = 84182.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.029608 restraints weight = 70239.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.029805 restraints weight = 63078.928| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21375 Z= 0.126 Angle : 0.758 13.503 29577 Z= 0.338 Chirality : 0.062 0.928 3382 Planarity : 0.003 0.038 3145 Dihedral : 18.225 177.511 4226 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.83 % Favored : 96.02 % Rotamer: Outliers : 1.72 % Allowed : 15.54 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.20), residues: 2010 helix: 2.14 (0.18), residues: 901 sheet: -0.04 (0.32), residues: 243 loop : -0.50 (0.22), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 512 TYR 0.017 0.001 TYR H 513 PHE 0.020 0.001 PHE H 235 TRP 0.009 0.001 TRP H 336 HIS 0.005 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (21371) covalent geometry : angle 0.75748 / 0.34 (29571) hydrogen bonds : bond 0.04243 / 2.72 ( 908) hydrogen bonds : angle 4.23360 / 2.88 ( 2556) metal coordination : bond 0.00475 / 0.24 ( 4) metal coordination : angle 1.59629 / 0.81 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 64 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 LEU cc_start: 0.9692 (mm) cc_final: 0.9409 (mm) REVERT: A 546 MET cc_start: 0.9412 (mtm) cc_final: 0.9051 (pmm) REVERT: A 566 MET cc_start: 0.9071 (ppp) cc_final: 0.8693 (ppp) REVERT: D 586 MET cc_start: 0.9113 (tpp) cc_final: 0.8886 (tpp) REVERT: E 34 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9308 (pp) REVERT: E 86 MET cc_start: 0.8017 (tpp) cc_final: 0.7353 (tpp) REVERT: E 136 MET cc_start: 0.8625 (pmm) cc_final: 0.8296 (pmm) REVERT: F 9 MET cc_start: 0.9288 (tmm) cc_final: 0.9062 (tmm) REVERT: F 22 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7416 (tpm170) REVERT: F 79 ASN cc_start: 0.9323 (t0) cc_final: 0.8869 (p0) REVERT: F 91 PHE cc_start: 0.9432 (m-80) cc_final: 0.8847 (m-80) REVERT: G 40 MET cc_start: 0.9328 (mmt) cc_final: 0.8886 (mmt) REVERT: G 129 GLU cc_start: 0.8702 (tp30) cc_final: 0.8446 (tm-30) REVERT: H 223 LYS cc_start: 0.9168 (OUTLIER) cc_final: 0.8881 (pttp) REVERT: H 267 PHE cc_start: 0.9054 (OUTLIER) cc_final: 0.8306 (m-80) REVERT: H 463 MET cc_start: 0.8576 (tpp) cc_final: 0.7743 (tpp) outliers start: 33 outliers final: 27 residues processed: 93 average time/residue: 0.1287 time to fit residues: 19.8520 Evaluate side-chains 94 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 63 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain D residue 511 GLN Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 231 ARG Chi-restraints excluded: chain H residue 267 PHE Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 492 ARG Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 501 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 147 optimal weight: 6.9990 chunk 174 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 166 optimal weight: 9.9990 chunk 149 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 213 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 282 ASN H 325 GLN ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.037922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.026533 restraints weight = 197042.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.027397 restraints weight = 117217.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.027941 restraints weight = 86055.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.028245 restraints weight = 71215.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.028473 restraints weight = 64106.221| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 21375 Z= 0.363 Angle : 0.931 14.120 29577 Z= 0.426 Chirality : 0.064 0.968 3382 Planarity : 0.004 0.055 3145 Dihedral : 18.411 176.320 4226 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.88 % Favored : 94.98 % Rotamer: Outliers : 2.03 % Allowed : 15.54 % Favored : 82.43 % 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: 0.67 (0.19), residues: 2010 helix: 1.75 (0.17), residues: 898 sheet: -0.67 (0.28), residues: 311 loop : -0.53 (0.23), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 74 TYR 0.017 0.002 TYR H 129 PHE 0.025 0.002 PHE A 600 TRP 0.011 0.002 TRP A1027 HIS 0.005 0.002 HIS A 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00747 / 0.36 (21371) covalent geometry : angle 0.93025 / 0.43 (29571) hydrogen bonds : bond 0.05820 / 3.94 ( 908) hydrogen bonds : angle 4.69376 / 3.16 ( 2556) metal coordination : bond 0.00883 / 0.44 ( 4) metal coordination : angle 2.51309 / 1.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 64 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8779 (tpp) cc_final: 0.7825 (tpp) REVERT: A 380 LEU cc_start: 0.9684 (mm) cc_final: 0.9394 (mm) REVERT: A 411 MET cc_start: 0.9029 (tpp) cc_final: 0.8797 (tpp) REVERT: A 566 MET cc_start: 0.9120 (ppp) cc_final: 0.8837 (ppp) REVERT: A 767 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8592 (tt0) REVERT: E 34 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9260 (pp) REVERT: E 86 MET cc_start: 0.8108 (tpp) cc_final: 0.7482 (tpp) REVERT: E 136 MET cc_start: 0.8633 (pmm) cc_final: 0.8258 (pmm) REVERT: F 9 MET cc_start: 0.9280 (tmm) cc_final: 0.9033 (tmm) REVERT: F 18 MET cc_start: 0.9471 (ptp) cc_final: 0.9196 (mpp) REVERT: F 22 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7475 (tpm170) REVERT: F 37 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: F 91 PHE cc_start: 0.9347 (m-80) cc_final: 0.8832 (m-80) REVERT: G 40 MET cc_start: 0.9345 (mmt) cc_final: 0.8908 (mmt) REVERT: G 129 GLU cc_start: 0.8750 (tp30) cc_final: 0.8079 (tm-30) REVERT: G 134 ASP cc_start: 0.8272 (t0) cc_final: 0.7988 (t0) outliers start: 39 outliers final: 33 residues processed: 98 average time/residue: 0.1378 time to fit residues: 22.5031 Evaluate side-chains 100 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 767 GLN Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain D residue 511 GLN Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain G residue 130 MET Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 231 ARG Chi-restraints excluded: chain H residue 235 PHE Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 416 ASN Chi-restraints excluded: chain H residue 492 ARG Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 501 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 17 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 100 optimal weight: 0.0000 chunk 25 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 756 ASN D 511 GLN ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.039203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.027375 restraints weight = 187276.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.028281 restraints weight = 114253.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028853 restraints weight = 84715.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.029189 restraints weight = 70582.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.029377 restraints weight = 63426.715| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21375 Z= 0.134 Angle : 0.781 14.995 29577 Z= 0.348 Chirality : 0.061 0.861 3382 Planarity : 0.003 0.038 3145 Dihedral : 18.321 176.703 4226 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.03 % Favored : 95.82 % Rotamer: Outliers : 1.56 % Allowed : 15.96 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.19), residues: 2010 helix: 2.00 (0.18), residues: 902 sheet: -0.33 (0.30), residues: 259 loop : -0.50 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 22 TYR 0.016 0.001 TYR H 513 PHE 0.021 0.001 PHE H 235 TRP 0.009 0.001 TRP H 336 HIS 0.003 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (21371) covalent geometry : angle 0.78108 / 0.35 (29571) hydrogen bonds : bond 0.04428 / 2.88 ( 908) hydrogen bonds : angle 4.32160 / 2.93 ( 2556) metal coordination : bond 0.00520 / 0.26 ( 4) metal coordination : angle 1.64379 / 0.82 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4020 Ramachandran restraints generated. 2010 Oldfield, 0 Emsley, 2010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 65 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8757 (tpp) cc_final: 0.7695 (tpp) REVERT: A 380 LEU cc_start: 0.9694 (mm) cc_final: 0.9389 (mm) REVERT: A 411 MET cc_start: 0.8981 (tpp) cc_final: 0.8710 (tpp) REVERT: A 566 MET cc_start: 0.9080 (ppp) cc_final: 0.8775 (ppp) REVERT: A 1029 MET cc_start: 0.9348 (mtp) cc_final: 0.8962 (mtp) REVERT: E 34 LEU cc_start: 0.9549 (OUTLIER) cc_final: 0.9334 (pp) REVERT: E 86 MET cc_start: 0.8046 (tpp) cc_final: 0.7385 (tpp) REVERT: E 136 MET cc_start: 0.8589 (pmm) cc_final: 0.8210 (pmm) REVERT: F 9 MET cc_start: 0.9247 (tmm) cc_final: 0.9029 (tmm) REVERT: F 18 MET cc_start: 0.9505 (ptp) cc_final: 0.9223 (mpp) REVERT: F 22 ARG cc_start: 0.8754 (OUTLIER) cc_final: 0.7664 (tpm170) REVERT: F 91 PHE cc_start: 0.9400 (m-80) cc_final: 0.8681 (m-80) REVERT: G 40 MET cc_start: 0.9344 (mmt) cc_final: 0.8880 (mmt) REVERT: G 129 GLU cc_start: 0.8704 (tp30) cc_final: 0.8435 (tm-30) REVERT: H 223 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8926 (pttp) REVERT: H 463 MET cc_start: 0.8612 (tpp) cc_final: 0.7344 (tpt) outliers start: 30 outliers final: 25 residues processed: 91 average time/residue: 0.1335 time to fit residues: 20.5030 Evaluate side-chains 90 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 520 ILE Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain A residue 807 ILE Chi-restraints excluded: chain A residue 888 ILE Chi-restraints excluded: chain A residue 961 MET Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1100 ILE Chi-restraints excluded: chain D residue 597 THR Chi-restraints excluded: chain D residue 686 TYR Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain F residue 22 ARG Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 273 ILE Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 492 ARG Chi-restraints excluded: chain H residue 498 VAL Chi-restraints excluded: chain H residue 501 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 119 optimal weight: 9.9990 chunk 197 optimal weight: 0.3980 chunk 214 optimal weight: 9.9990 chunk 158 optimal weight: 3.9990 chunk 199 optimal weight: 20.0000 chunk 130 optimal weight: 0.0060 chunk 124 optimal weight: 6.9990 chunk 185 optimal weight: 0.0270 chunk 167 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 overall best weight: 2.0858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 511 GLN ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN ** H 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.039108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.027273 restraints weight = 189013.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.028180 restraints weight = 113703.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.028754 restraints weight = 84064.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.029136 restraints weight = 69707.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.029321 restraints weight = 62007.457| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21375 Z= 0.153 Angle : 0.774 14.906 29577 Z= 0.346 Chirality : 0.061 0.863 3382 Planarity : 0.003 0.041 3145 Dihedral : 18.288 177.343 4226 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.08 % Favored : 95.77 % Rotamer: Outliers : 1.61 % Allowed : 16.11 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.20), residues: 2010 helix: 2.04 (0.18), residues: 903 sheet: -0.26 (0.31), residues: 261 loop : -0.50 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 61 TYR 0.016 0.001 TYR H 513 PHE 0.016 0.001 PHE H 235 TRP 0.009 0.001 TRP H 336 HIS 0.003 0.001 HIS F 107 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (21371) covalent geometry : angle 0.77383 / 0.35 (29571) hydrogen bonds : bond 0.04395 / 2.85 ( 908) hydrogen bonds : angle 4.26859 / 2.89 ( 2556) metal coordination : bond 0.00493 / 0.25 ( 4) metal coordination : angle 1.61159 / 0.79 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3212.97 seconds wall clock time: 56 minutes 44.75 seconds (3404.75 seconds total)