Starting phenix.real_space_refine on Wed May 21 04:56:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gap_29903/05_2025/8gap_29903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gap_29903/05_2025/8gap_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gap_29903/05_2025/8gap_29903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gap_29903/05_2025/8gap_29903.map" model { file = "/net/cci-nas-00/data/ceres_data/8gap_29903/05_2025/8gap_29903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gap_29903/05_2025/8gap_29903.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'RNA': 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: 10.96, per 1000 atoms: 0.53 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: 4.50 Conformation dependent library (CDL) restraints added in 2.1 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: 6.78 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: 8.61 Time building geometry restraints manager: 5.43 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=" O5' C B 116 " pdb=" C5' C B 116 " ideal model delta sigma weight residual 1.420 1.441 -0.021 1.50e-02 4.44e+03 1.99e+00 bond pdb=" O5' U B 117 " pdb=" C5' U B 117 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.80e+00 bond pdb=" SD MET A 411 " pdb=" CE MET A 411 " ideal model delta sigma weight residual 1.791 1.760 0.031 2.50e-02 1.60e+03 1.53e+00 bond pdb=" O5' A B 115 " pdb=" C5' A B 115 " ideal model delta sigma weight residual 1.420 1.438 -0.018 1.50e-02 4.44e+03 1.50e+00 bond pdb=" CB ASN F 81 " pdb=" CG ASN F 81 " ideal model delta sigma weight residual 1.516 1.546 -0.030 2.50e-02 1.60e+03 1.44e+00 ... (remaining 21366 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 29241 2.19 - 4.37: 281 4.37 - 6.56: 32 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=" CB MET A 411 " pdb=" CG MET A 411 " pdb=" SD MET A 411 " ideal model delta sigma weight residual 112.70 123.63 -10.93 3.00e+00 1.11e-01 1.33e+01 angle pdb=" CA ASN F 81 " pdb=" CB ASN F 81 " pdb=" CG ASN F 81 " ideal model delta sigma weight residual 112.60 116.21 -3.61 1.00e+00 1.00e+00 1.30e+01 angle pdb=" CA MET F 9 " pdb=" CB MET F 9 " pdb=" CG MET F 9 " ideal model delta sigma weight residual 114.10 121.21 -7.11 2.00e+00 2.50e-01 1.26e+01 angle pdb=" C LYS A 466 " pdb=" N ILE A 467 " pdb=" CA ILE A 467 " ideal model delta sigma weight residual 123.16 119.50 3.66 1.06e+00 8.90e-01 1.19e+01 ... (remaining 29566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 12401 35.99 - 71.98: 612 71.98 - 107.97: 77 107.97 - 143.96: 3 143.96 - 179.95: 8 Dihedral angle restraints: 13101 sinusoidal: 7039 harmonic: 6062 Sorted by residual: dihedral pdb=" O4' C B 120 " pdb=" C1' C B 120 " pdb=" N1 C B 120 " pdb=" C2 C B 120 " ideal model delta sinusoidal sigma weight residual 200.00 41.87 158.13 1 1.50e+01 4.44e-03 8.23e+01 dihedral pdb=" O4' C B 132 " pdb=" C1' C B 132 " pdb=" N1 C B 132 " pdb=" C2 C B 132 " ideal model delta sinusoidal sigma weight residual 200.00 52.48 147.52 1 1.50e+01 4.44e-03 7.87e+01 dihedral pdb=" O4' U B 57 " pdb=" C1' U B 57 " pdb=" N1 U B 57 " pdb=" C2 U B 57 " ideal model delta sinusoidal sigma weight residual -128.00 51.95 -179.95 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 13098 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2494 0.037 - 0.074: 634 0.074 - 0.111: 199 0.111 - 0.147: 48 0.147 - 0.184: 7 Chirality restraints: 3382 Sorted by residual: chirality pdb=" C3' A B 115 " pdb=" C4' A B 115 " pdb=" O3' A B 115 " pdb=" C2' A B 115 " both_signs ideal model delta sigma weight residual False -2.48 -2.66 0.18 2.00e-01 2.50e+01 8.48e-01 chirality pdb=" CB ILE H 328 " pdb=" CA ILE H 328 " pdb=" CG1 ILE H 328 " pdb=" CG2 ILE H 328 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.02e-01 chirality pdb=" C3' C B 109 " pdb=" C4' C B 109 " pdb=" O3' C B 109 " pdb=" C2' C B 109 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.18 2.00e-01 2.50e+01 7.66e-01 ... (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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 52.250 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 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 : 0.002 0.034 21375 Z= 0.120 Angle : 0.579 10.932 29577 Z= 0.315 Chirality : 0.039 0.184 3382 Planarity : 0.003 0.042 3145 Dihedral : 19.623 179.952 9159 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.015 0.002 TRP G 110 HIS 0.018 0.001 HIS F 107 PHE 0.012 0.001 PHE H 233 TYR 0.024 0.001 TYR H 513 ARG 0.005 0.000 ARG H 231 Details of bonding type rmsd hydrogen bonds : bond 0.15936 ( 908) hydrogen bonds : angle 5.89487 ( 2556) metal coordination : bond 0.00249 ( 4) metal coordination : angle 1.26687 ( 6) covalent geometry : bond 0.00233 (21371) covalent geometry : angle 0.57856 (29571) *********************** 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 : 1.980 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: 0.9246 (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: 0.3452 time to fit residues: 43.5232 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 : 2.101 ------------------------------------------------------------------------------- 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 182 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 65 optimal weight: 0.0770 chunk 102 optimal weight: 0.9980 chunk 126 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 overall best weight: 3.0144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 GLN ** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 444 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN A 926 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.039911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.028013 restraints weight = 187163.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.028869 restraints weight = 115124.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.029413 restraints weight = 86099.734| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21375 Z= 0.183 Angle : 0.565 9.770 29577 Z= 0.300 Chirality : 0.039 0.172 3382 Planarity : 0.003 0.038 3145 Dihedral : 20.540 179.496 4698 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.63 % Favored : 96.32 % Rotamer: Outliers : 0.99 % Allowed : 11.95 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 2010 helix: 2.12 (0.18), residues: 898 sheet: -0.14 (0.30), residues: 268 loop : -0.36 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 604 HIS 0.010 0.001 HIS F 107 PHE 0.012 0.001 PHE A 960 TYR 0.020 0.001 TYR H 513 ARG 0.007 0.001 ARG H 522 Details of bonding type rmsd hydrogen bonds : bond 0.05050 ( 908) hydrogen bonds : angle 4.68681 ( 2556) metal coordination : bond 0.00695 ( 4) metal coordination : angle 2.69629 ( 6) covalent geometry : bond 0.00370 (21371) covalent geometry : angle 0.56371 (29571) *********************** 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 89 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 70 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.8820 (pmm) cc_final: 0.8536 (pmm) REVERT: A 566 MET cc_start: 0.9071 (ppp) cc_final: 0.8817 (ppp) REVERT: A 687 MET cc_start: 0.6996 (mpp) cc_final: 0.6711 (mpp) REVERT: E 34 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9262 (pp) REVERT: E 86 MET cc_start: 0.7789 (tpp) cc_final: 0.7284 (tpp) REVERT: F 9 MET cc_start: 0.9048 (tmm) cc_final: 0.8773 (tmm) REVERT: F 108 LEU cc_start: 0.9725 (mm) cc_final: 0.9453 (pp) REVERT: H 463 MET cc_start: 0.8172 (tpp) cc_final: 0.7906 (tpp) outliers start: 19 outliers final: 8 residues processed: 87 average time/residue: 0.3018 time to fit residues: 43.8373 Evaluate side-chains 73 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 2.227 ------------------------------------------------------------------------------- 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 E residue 34 LEU Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain H residue 101 ASN 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 214 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 chunk 7 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** 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 = 0.3234 r_free = 0.3234 target = 0.039493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.027663 restraints weight = 188178.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.028510 restraints weight = 115638.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.029017 restraints weight = 86493.479| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21375 Z= 0.178 Angle : 0.549 8.427 29577 Z= 0.290 Chirality : 0.039 0.194 3382 Planarity : 0.003 0.042 3145 Dihedral : 20.619 179.341 4696 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.98 % Favored : 95.92 % Rotamer: Outliers : 1.87 % Allowed : 12.63 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.20), residues: 2010 helix: 2.13 (0.18), residues: 904 sheet: -0.16 (0.31), residues: 260 loop : -0.43 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 604 HIS 0.007 0.001 HIS F 107 PHE 0.015 0.001 PHE E 147 TYR 0.025 0.001 TYR F 10 ARG 0.007 0.001 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 908) hydrogen bonds : angle 4.49665 ( 2556) metal coordination : bond 0.00680 ( 4) metal coordination : angle 1.99097 ( 6) covalent geometry : bond 0.00364 (21371) covalent geometry : angle 0.54825 (29571) *********************** 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 105 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 69 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.8800 (pmm) cc_final: 0.8429 (pmm) REVERT: A 566 MET cc_start: 0.9101 (ppp) cc_final: 0.8837 (ppp) REVERT: A 687 MET cc_start: 0.6813 (mpp) cc_final: 0.6524 (mpp) REVERT: A 741 THR cc_start: 0.9620 (OUTLIER) cc_final: 0.9396 (p) REVERT: E 34 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9337 (pp) REVERT: E 86 MET cc_start: 0.7922 (tpp) cc_final: 0.7377 (tpp) REVERT: F 9 MET cc_start: 0.9195 (tmm) cc_final: 0.8865 (tmm) REVERT: F 37 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7530 (mp10) REVERT: F 89 THR cc_start: 0.9281 (OUTLIER) cc_final: 0.8346 (p) REVERT: G 129 GLU cc_start: 0.8693 (tp30) cc_final: 0.8291 (tm-30) REVERT: G 134 ASP cc_start: 0.8323 (t0) cc_final: 0.7952 (t70) REVERT: H 267 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8300 (m-80) outliers start: 36 outliers final: 14 residues processed: 102 average time/residue: 0.2746 time to fit residues: 47.8893 Evaluate side-chains 85 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 2.157 ------------------------------------------------------------------------------- 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 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 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 89 THR Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain H residue 101 ASN Chi-restraints excluded: chain H residue 157 VAL Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 235 PHE Chi-restraints excluded: chain H residue 267 PHE Chi-restraints excluded: chain H residue 416 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 13 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 171 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 24 optimal weight: 0.0570 chunk 129 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 ASN F 80 GLN F 121 GLN ** G 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 236 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.040547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.028542 restraints weight = 185063.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.029434 restraints weight = 112546.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.030010 restraints weight = 83627.144| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21375 Z= 0.100 Angle : 0.510 9.341 29577 Z= 0.266 Chirality : 0.038 0.167 3382 Planarity : 0.003 0.034 3145 Dihedral : 20.436 179.656 4692 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.28 % Favored : 96.62 % Rotamer: Outliers : 1.56 % Allowed : 13.46 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.20), residues: 2010 helix: 2.21 (0.18), residues: 903 sheet: 0.03 (0.32), residues: 247 loop : -0.40 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 336 HIS 0.006 0.001 HIS F 107 PHE 0.017 0.001 PHE F 91 TYR 0.019 0.001 TYR H 513 ARG 0.006 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 908) hydrogen bonds : angle 4.21979 ( 2556) metal coordination : bond 0.00414 ( 4) metal coordination : angle 1.72356 ( 6) covalent geometry : bond 0.00203 (21371) covalent geometry : angle 0.50969 (29571) *********************** 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 104 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8668 (tpp) cc_final: 0.7640 (tpp) REVERT: A 546 MET cc_start: 0.8781 (pmm) cc_final: 0.8344 (pmm) REVERT: A 566 MET cc_start: 0.9068 (ppp) cc_final: 0.8732 (ppp) REVERT: A 741 THR cc_start: 0.9592 (OUTLIER) cc_final: 0.9389 (p) REVERT: E 34 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9314 (pp) REVERT: E 86 MET cc_start: 0.7959 (tpp) cc_final: 0.7451 (tpp) REVERT: F 9 MET cc_start: 0.9147 (tmm) cc_final: 0.8889 (tmm) REVERT: F 22 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7451 (tpm170) REVERT: F 43 ILE cc_start: 0.9695 (pt) cc_final: 0.9360 (mm) REVERT: F 120 ASP cc_start: 0.8999 (p0) cc_final: 0.8239 (p0) REVERT: G 129 GLU cc_start: 0.8706 (tp30) cc_final: 0.8443 (tm-30) REVERT: H 267 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8190 (m-80) REVERT: H 463 MET cc_start: 0.8490 (tpp) cc_final: 0.7770 (tpp) outliers start: 30 outliers final: 12 residues processed: 100 average time/residue: 0.2831 time to fit residues: 47.2187 Evaluate side-chains 84 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 68 time to evaluate : 1.977 ------------------------------------------------------------------------------- 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 741 THR 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 D residue 591 VAL 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 H residue 101 ASN Chi-restraints excluded: chain H residue 131 CYS Chi-restraints excluded: chain H residue 223 LYS Chi-restraints excluded: chain H residue 267 PHE Chi-restraints excluded: chain H residue 273 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 120 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 99 optimal weight: 0.5980 chunk 132 optimal weight: 10.0000 chunk 180 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 892 GLN ** E 41 GLN ** 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 325 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.039574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.027658 restraints weight = 189526.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.028548 restraints weight = 113992.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.029112 restraints weight = 84027.645| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21375 Z= 0.161 Angle : 0.537 9.993 29577 Z= 0.280 Chirality : 0.039 0.196 3382 Planarity : 0.003 0.039 3145 Dihedral : 20.478 179.618 4692 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.27 % Rotamer: Outliers : 1.72 % Allowed : 13.46 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.20), residues: 2010 helix: 2.21 (0.18), residues: 903 sheet: 0.05 (0.32), residues: 258 loop : -0.43 (0.22), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 336 HIS 0.005 0.001 HIS F 107 PHE 0.014 0.001 PHE H 235 TYR 0.016 0.001 TYR H 513 ARG 0.006 0.001 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.04220 ( 908) hydrogen bonds : angle 4.21949 ( 2556) metal coordination : bond 0.00554 ( 4) metal coordination : angle 1.62248 ( 6) covalent geometry : bond 0.00331 (21371) covalent geometry : angle 0.53617 (29571) *********************** 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 101 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 68 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8522 (tpp) cc_final: 0.7422 (tpp) REVERT: A 411 MET cc_start: 0.9113 (tpp) cc_final: 0.8817 (tpp) REVERT: A 546 MET cc_start: 0.8866 (pmm) cc_final: 0.8379 (pmm) REVERT: A 566 MET cc_start: 0.9062 (ppp) cc_final: 0.8687 (ppp) REVERT: E 34 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9363 (pp) REVERT: E 86 MET cc_start: 0.8028 (tpp) cc_final: 0.7538 (tpp) REVERT: F 9 MET cc_start: 0.9250 (tmm) cc_final: 0.9019 (tmm) REVERT: F 22 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7569 (tpm170) REVERT: F 37 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7605 (mp10) REVERT: F 120 ASP cc_start: 0.9000 (p0) cc_final: 0.8786 (p0) REVERT: G 72 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9066 (tp) REVERT: G 129 GLU cc_start: 0.8708 (tp30) cc_final: 0.8411 (tm-30) REVERT: G 134 ASP cc_start: 0.8408 (t0) cc_final: 0.8077 (t0) REVERT: H 220 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9045 (mm) REVERT: H 223 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8958 (pttp) REVERT: H 267 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8245 (m-80) outliers start: 33 outliers final: 21 residues processed: 98 average time/residue: 0.2763 time to fit residues: 45.6708 Evaluate side-chains 92 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 1.987 ------------------------------------------------------------------------------- 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 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 D residue 591 VAL 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 F residue 71 VAL Chi-restraints excluded: chain G residue 72 LEU 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 169 LYS Chi-restraints excluded: chain H residue 220 LEU 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 498 VAL 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 41 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 192 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 130 optimal weight: 10.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.040282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.028282 restraints weight = 185063.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.029182 restraints weight = 110908.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.029791 restraints weight = 82037.264| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21375 Z= 0.102 Angle : 0.512 10.851 29577 Z= 0.265 Chirality : 0.038 0.197 3382 Planarity : 0.003 0.041 3145 Dihedral : 20.364 179.925 4692 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.43 % Favored : 96.47 % Rotamer: Outliers : 1.40 % Allowed : 14.29 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 2010 helix: 2.25 (0.18), residues: 902 sheet: 0.17 (0.33), residues: 248 loop : -0.45 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 336 HIS 0.004 0.000 HIS F 107 PHE 0.012 0.001 PHE H 235 TYR 0.017 0.001 TYR H 513 ARG 0.005 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 908) hydrogen bonds : angle 4.06158 ( 2556) metal coordination : bond 0.00369 ( 4) metal coordination : angle 1.40698 ( 6) covalent geometry : bond 0.00209 (21371) covalent geometry : angle 0.51146 (29571) *********************** 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 96 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8277 (tpp) cc_final: 0.7363 (tpp) REVERT: A 411 MET cc_start: 0.9197 (tpp) cc_final: 0.8808 (tpp) REVERT: A 566 MET cc_start: 0.9049 (ppp) cc_final: 0.8682 (ppp) REVERT: E 34 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9392 (pp) REVERT: E 86 MET cc_start: 0.8018 (tpp) cc_final: 0.7567 (tpp) REVERT: F 9 MET cc_start: 0.9289 (tmm) cc_final: 0.9058 (tmm) REVERT: F 22 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7536 (tpm170) REVERT: F 43 ILE cc_start: 0.9689 (pt) cc_final: 0.9336 (mm) REVERT: F 120 ASP cc_start: 0.9033 (p0) cc_final: 0.8737 (p0) REVERT: G 134 ASP cc_start: 0.8371 (t0) cc_final: 0.8052 (t0) REVERT: H 223 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8834 (pttp) REVERT: H 267 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8265 (m-80) REVERT: H 463 MET cc_start: 0.8484 (tpp) cc_final: 0.7643 (tpp) outliers start: 27 outliers final: 15 residues processed: 93 average time/residue: 0.2776 time to fit residues: 43.3611 Evaluate side-chains 86 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 67 time to evaluate : 1.975 ------------------------------------------------------------------------------- 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 520 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 D residue 591 VAL 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 131 CYS 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 501 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 175 optimal weight: 10.0000 chunk 104 optimal weight: 0.6980 chunk 177 optimal weight: 10.0000 chunk 163 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 141 optimal weight: 20.0000 chunk 171 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 overall best weight: 6.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 482 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 897 GLN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 282 ASN ** H 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 488 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 = 0.3180 r_free = 0.3180 target = 0.037739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.026034 restraints weight = 195863.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.026883 restraints weight = 117954.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.027420 restraints weight = 87277.270| |-----------------------------------------------------------------------------| r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 21375 Z= 0.342 Angle : 0.730 12.144 29577 Z= 0.379 Chirality : 0.043 0.256 3382 Planarity : 0.005 0.059 3145 Dihedral : 20.850 177.004 4692 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.78 % Favored : 95.12 % Rotamer: Outliers : 2.44 % Allowed : 14.35 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.19), residues: 2010 helix: 1.66 (0.17), residues: 899 sheet: -0.46 (0.29), residues: 288 loop : -0.55 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 604 HIS 0.006 0.002 HIS H 208 PHE 0.022 0.002 PHE A 600 TYR 0.023 0.002 TYR H 129 ARG 0.006 0.001 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.06001 ( 908) hydrogen bonds : angle 4.70354 ( 2556) metal coordination : bond 0.00983 ( 4) metal coordination : angle 2.65104 ( 6) covalent geometry : bond 0.00695 (21371) covalent geometry : angle 0.72941 (29571) *********************** 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 111 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 64 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 MET cc_start: 0.8561 (mmm) cc_final: 0.8337 (mmm) REVERT: A 411 MET cc_start: 0.9260 (tpp) cc_final: 0.8970 (tpp) REVERT: A 546 MET cc_start: 0.9043 (pmm) cc_final: 0.8757 (pmm) REVERT: A 566 MET cc_start: 0.9137 (ppp) cc_final: 0.8801 (ppp) REVERT: A 767 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8447 (tt0) REVERT: E 34 LEU cc_start: 0.9462 (OUTLIER) cc_final: 0.9226 (pp) REVERT: E 86 MET cc_start: 0.8054 (tpp) cc_final: 0.7597 (tpp) REVERT: F 9 MET cc_start: 0.9256 (tmm) cc_final: 0.9039 (tmm) REVERT: F 22 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7915 (tpm170) REVERT: F 37 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7750 (mp10) REVERT: G 129 GLU cc_start: 0.8714 (tp30) cc_final: 0.7987 (tm-30) REVERT: G 134 ASP cc_start: 0.8471 (t0) cc_final: 0.8168 (t0) outliers start: 47 outliers final: 32 residues processed: 104 average time/residue: 0.3174 time to fit residues: 53.7573 Evaluate side-chains 99 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 63 time to evaluate : 2.586 ------------------------------------------------------------------------------- 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 520 ILE Chi-restraints excluded: chain A residue 575 LEU 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 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 F residue 50 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 91 PHE Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain G residue 90 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 140 TYR 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 231 ARG Chi-restraints excluded: chain H residue 235 PHE 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 27 optimal weight: 0.2980 chunk 108 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 185 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 128 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 213 optimal weight: 9.9990 chunk 156 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 756 ASN D 511 GLN F 93 GLN H 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.039436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.027635 restraints weight = 187922.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.028518 restraints weight = 113871.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.029031 restraints weight = 84347.311| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21375 Z= 0.113 Angle : 0.551 12.894 29577 Z= 0.285 Chirality : 0.040 0.232 3382 Planarity : 0.003 0.045 3145 Dihedral : 20.529 179.495 4692 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.63 % Favored : 96.27 % Rotamer: Outliers : 1.35 % Allowed : 15.59 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 2010 helix: 2.04 (0.18), residues: 903 sheet: 0.14 (0.33), residues: 234 loop : -0.46 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 336 HIS 0.003 0.001 HIS F 107 PHE 0.012 0.001 PHE E 147 TYR 0.017 0.001 TYR H 513 ARG 0.007 0.001 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 908) hydrogen bonds : angle 4.20693 ( 2556) metal coordination : bond 0.00389 ( 4) metal coordination : angle 1.47133 ( 6) covalent geometry : bond 0.00234 (21371) covalent geometry : angle 0.55054 (29571) *********************** 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 98 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.9222 (tpp) cc_final: 0.8863 (tpp) REVERT: A 566 MET cc_start: 0.9064 (ppp) cc_final: 0.8751 (ppp) REVERT: A 631 LEU cc_start: 0.9817 (tt) cc_final: 0.9593 (pp) REVERT: D 546 MET cc_start: 0.8323 (ppp) cc_final: 0.8120 (ppp) REVERT: D 586 MET cc_start: 0.9114 (tpp) cc_final: 0.8839 (tpp) REVERT: D 601 MET cc_start: 0.9381 (mmp) cc_final: 0.9026 (mmt) REVERT: E 34 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9230 (pp) REVERT: E 86 MET cc_start: 0.8102 (tpp) cc_final: 0.7671 (tpp) REVERT: F 22 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.7560 (tpm170) REVERT: F 37 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: F 43 ILE cc_start: 0.9690 (pt) cc_final: 0.9387 (mm) REVERT: G 21 CYS cc_start: 0.9738 (t) cc_final: 0.9509 (p) REVERT: G 129 GLU cc_start: 0.8702 (tp30) cc_final: 0.8448 (tm-30) REVERT: G 134 ASP cc_start: 0.8316 (t0) cc_final: 0.8031 (t0) REVERT: H 125 GLN cc_start: 0.8910 (tt0) cc_final: 0.7592 (tp-100) REVERT: H 463 MET cc_start: 0.8588 (tpp) cc_final: 0.7749 (tpp) outliers start: 26 outliers final: 21 residues processed: 93 average time/residue: 0.2995 time to fit residues: 45.7489 Evaluate side-chains 93 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 1.983 ------------------------------------------------------------------------------- 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 520 ILE Chi-restraints excluded: chain A residue 741 THR 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 50 LEU Chi-restraints excluded: chain F residue 71 VAL Chi-restraints excluded: chain F residue 91 PHE 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 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 146 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 105 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 195 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 511 GLN ** H 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.039195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.027358 restraints weight = 188932.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.028214 restraints weight = 113266.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.028776 restraints weight = 84316.824| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21375 Z= 0.142 Angle : 0.568 13.729 29577 Z= 0.291 Chirality : 0.039 0.269 3382 Planarity : 0.003 0.045 3145 Dihedral : 20.473 179.169 4692 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.83 % Favored : 96.02 % Rotamer: Outliers : 1.46 % Allowed : 15.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.20), residues: 2010 helix: 2.05 (0.18), residues: 904 sheet: 0.12 (0.33), residues: 235 loop : -0.44 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 336 HIS 0.004 0.001 HIS F 107 PHE 0.016 0.001 PHE H 235 TYR 0.014 0.001 TYR H 513 ARG 0.005 0.001 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.04177 ( 908) hydrogen bonds : angle 4.19320 ( 2556) metal coordination : bond 0.00485 ( 4) metal coordination : angle 1.47632 ( 6) covalent geometry : bond 0.00294 (21371) covalent geometry : angle 0.56794 (29571) *********************** 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 96 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 68 time to evaluate : 2.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8652 (tpp) cc_final: 0.7449 (tpp) REVERT: A 411 MET cc_start: 0.9205 (tpp) cc_final: 0.8815 (tpp) REVERT: A 546 MET cc_start: 0.8963 (pmm) cc_final: 0.8666 (pmm) REVERT: A 566 MET cc_start: 0.9047 (ppp) cc_final: 0.8740 (ppp) REVERT: A 1029 MET cc_start: 0.9289 (mtp) cc_final: 0.8948 (mtp) REVERT: D 546 MET cc_start: 0.8411 (ppp) cc_final: 0.8107 (ppp) REVERT: D 601 MET cc_start: 0.9362 (mmp) cc_final: 0.9014 (mmt) REVERT: E 34 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9199 (pp) REVERT: E 86 MET cc_start: 0.8139 (tpp) cc_final: 0.7713 (tpp) REVERT: F 22 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7552 (tpm170) REVERT: F 41 LEU cc_start: 0.9193 (tp) cc_final: 0.8880 (mt) REVERT: F 43 ILE cc_start: 0.9700 (pt) cc_final: 0.9421 (mm) REVERT: G 129 GLU cc_start: 0.8697 (tp30) cc_final: 0.8452 (tm-30) REVERT: G 134 ASP cc_start: 0.8370 (t0) cc_final: 0.7999 (t70) REVERT: H 125 GLN cc_start: 0.8851 (tt0) cc_final: 0.7524 (tp-100) REVERT: H 463 MET cc_start: 0.8573 (tpp) cc_final: 0.7504 (tpp) outliers start: 28 outliers final: 23 residues processed: 91 average time/residue: 0.2989 time to fit residues: 45.2450 Evaluate side-chains 92 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 2.098 ------------------------------------------------------------------------------- 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 520 ILE 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 30 ILE 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 F residue 91 PHE 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 169 LYS Chi-restraints excluded: chain H residue 223 LYS 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 31 optimal weight: 0.0020 chunk 177 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 74 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 159 optimal weight: 0.5980 chunk 140 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 25 optimal weight: 6.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 511 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.040197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.028384 restraints weight = 184919.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.029281 restraints weight = 112005.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.029860 restraints weight = 82673.867| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 21375 Z= 0.102 Angle : 0.562 15.004 29577 Z= 0.285 Chirality : 0.039 0.285 3382 Planarity : 0.003 0.047 3145 Dihedral : 20.291 179.225 4692 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 1.25 % Allowed : 16.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.20), residues: 2010 helix: 2.09 (0.18), residues: 904 sheet: 0.30 (0.33), residues: 234 loop : -0.47 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 336 HIS 0.004 0.001 HIS F 107 PHE 0.012 0.001 PHE H 235 TYR 0.016 0.001 TYR H 513 ARG 0.005 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.03878 ( 908) hydrogen bonds : angle 4.02298 ( 2556) metal coordination : bond 0.00274 ( 4) metal coordination : angle 1.34629 ( 6) covalent geometry : bond 0.00209 (21371) covalent geometry : angle 0.56162 (29571) ********************** 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: 24 poor density : 71 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 MET cc_start: 0.8591 (tpp) cc_final: 0.7321 (tpp) REVERT: A 411 MET cc_start: 0.9154 (tpp) cc_final: 0.8742 (tpp) REVERT: A 566 MET cc_start: 0.9044 (ppp) cc_final: 0.8769 (ppp) REVERT: A 1029 MET cc_start: 0.9285 (mtp) cc_final: 0.8929 (mtp) REVERT: D 546 MET cc_start: 0.8369 (ppp) cc_final: 0.8129 (ppp) REVERT: E 34 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9372 (pp) REVERT: E 86 MET cc_start: 0.8068 (tpp) cc_final: 0.7638 (tpp) REVERT: F 18 MET cc_start: 0.9455 (pmm) cc_final: 0.9180 (pmm) REVERT: F 22 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.7507 (tpm170) REVERT: F 41 LEU cc_start: 0.9106 (tp) cc_final: 0.8887 (mt) REVERT: F 43 ILE cc_start: 0.9707 (pt) cc_final: 0.9426 (mm) REVERT: G 21 CYS cc_start: 0.9737 (t) cc_final: 0.9509 (p) REVERT: G 134 ASP cc_start: 0.8339 (t0) cc_final: 0.7999 (t70) REVERT: H 267 PHE cc_start: 0.9123 (OUTLIER) cc_final: 0.8379 (m-80) REVERT: H 463 MET cc_start: 0.8553 (tpp) cc_final: 0.7494 (tpp) outliers start: 24 outliers final: 20 residues processed: 91 average time/residue: 0.2987 time to fit residues: 45.0412 Evaluate side-chains 92 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 1.937 ------------------------------------------------------------------------------- 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 520 ILE Chi-restraints excluded: chain A residue 741 THR 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 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 267 PHE 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 114 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 202 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 212 optimal weight: 10.0000 chunk 183 optimal weight: 0.6980 chunk 149 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 123 optimal weight: 8.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 243 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.040141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.028334 restraints weight = 186195.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.029247 restraints weight = 112302.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.029806 restraints weight = 82525.456| |-----------------------------------------------------------------------------| r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.175 21375 Z= 0.160 Angle : 0.721 59.169 29577 Z= 0.404 Chirality : 0.039 0.276 3382 Planarity : 0.003 0.047 3145 Dihedral : 20.288 179.231 4692 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer: Outliers : 1.30 % Allowed : 16.11 % Favored : 82.59 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 2010 helix: 2.07 (0.18), residues: 904 sheet: 0.31 (0.33), residues: 234 loop : -0.50 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 336 HIS 0.004 0.001 HIS F 107 PHE 0.011 0.001 PHE H 235 TYR 0.017 0.001 TYR H 513 ARG 0.005 0.000 ARG F 22 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 908) hydrogen bonds : angle 4.02698 ( 2556) metal coordination : bond 0.00305 ( 4) metal coordination : angle 1.34635 ( 6) covalent geometry : bond 0.00349 (21371) covalent geometry : angle 0.72058 (29571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5520.89 seconds wall clock time: 98 minutes 28.31 seconds (5908.31 seconds total)