Starting phenix.real_space_refine on Fri Aug 7 20:38:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b1t_15804/08_2026/8b1t_15804.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b1t_15804/08_2026/8b1t_15804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b1t_15804/08_2026/8b1t_15804.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b1t_15804/08_2026/8b1t_15804.map" model { file = "/net/cci-nas-00/data/ceres_data/8b1t_15804/08_2026/8b1t_15804.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b1t_15804/08_2026/8b1t_15804.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8b1t_15804/08_2026/8b1t_15804.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b1t_15804/08_2026/8b1t_15804.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 P 53 5.49 5 Mg 1 5.21 5 S 104 5.16 5 C 15000 2.51 5 N 4224 2.21 5 O 4604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23986 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 9145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1141, 9145 Classifications: {'peptide': 1141} Link IDs: {'PTRANS': 50, 'TRANS': 1090} Chain breaks: 1 Chain: "C" Number of atoms: 8738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8738 Classifications: {'peptide': 1080} Link IDs: {'PCIS': 1, 'PTRANS': 64, 'TRANS': 1014} Chain breaks: 1 Chain: "D" Number of atoms: 4644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4644 Classifications: {'peptide': 601} Link IDs: {'PTRANS': 25, 'TRANS': 575} Chain breaks: 1 Chain: "X" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1035 Classifications: {'DNA': 51} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 50} Chain breaks: 1 Chain: "A" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 392 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.51, per 1000 atoms: 0.23 Number of scatterers: 23986 At special positions: 0 Unit cell: (154.76, 152.64, 116.6, 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) S 104 16.00 P 53 15.00 Mg 1 11.99 O 4604 8.00 N 4224 7.00 C 15000 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: 2.07 Conformation dependent library (CDL) restraints added in 1.0 seconds 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5412 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 18 sheets defined 56.3% alpha, 10.4% beta 18 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.732A pdb=" N ILE B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ALA B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA B 35 " --> pdb=" O PHE B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 55 through 57 No H-bonds generated for 'chain 'B' and resid 55 through 57' Processing helix chain 'B' and resid 65 through 90 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 106 through 121 Processing helix chain 'B' and resid 122 through 124 No H-bonds generated for 'chain 'B' and resid 122 through 124' Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 140 through 145 Processing helix chain 'B' and resid 156 through 172 Processing helix chain 'B' and resid 176 through 187 removed outlier: 3.612A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.519A pdb=" N ASP B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 239 Processing helix chain 'B' and resid 241 through 250 removed outlier: 4.151A pdb=" N ALA B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.851A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 307 through 317 Processing helix chain 'B' and resid 323 through 347 removed outlier: 3.943A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 366 through 378 removed outlier: 3.634A pdb=" N ARG B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.850A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 Processing helix chain 'B' and resid 510 through 535 removed outlier: 3.708A pdb=" N ARG B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 574 removed outlier: 3.532A pdb=" N ALA B 570 " --> pdb=" O GLN B 566 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 4.064A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 Processing helix chain 'B' and resid 624 through 632 removed outlier: 3.593A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 656 removed outlier: 3.595A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 669 Processing helix chain 'B' and resid 669 through 677 Processing helix chain 'B' and resid 679 through 701 removed outlier: 3.969A pdb=" N ARG B 683 " --> pdb=" O GLY B 679 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 717 removed outlier: 3.896A pdb=" N LEU B 707 " --> pdb=" O SER B 703 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 807 removed outlier: 3.609A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 835 Processing helix chain 'B' and resid 836 through 843 removed outlier: 3.561A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 861 Processing helix chain 'B' and resid 905 through 911 Processing helix chain 'B' and resid 948 through 961 removed outlier: 3.605A pdb=" N PHE B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 985 through 1000 removed outlier: 4.434A pdb=" N VAL B 989 " --> pdb=" O GLN B 985 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1012 Processing helix chain 'B' and resid 1013 through 1015 No H-bonds generated for 'chain 'B' and resid 1013 through 1015' Processing helix chain 'B' and resid 1032 through 1044 removed outlier: 4.732A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1050 Processing helix chain 'B' and resid 1089 through 1093 Processing helix chain 'B' and resid 1094 through 1105 Processing helix chain 'B' and resid 1106 through 1126 removed outlier: 4.039A pdb=" N GLN B1110 " --> pdb=" O ARG B1106 " (cutoff:3.500A) Processing helix chain 'B' and resid 1130 through 1134 Processing helix chain 'B' and resid 1161 through 1174 Processing helix chain 'C' and resid 9 through 24 removed outlier: 4.005A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 Processing helix chain 'C' and resid 64 through 77 Processing helix chain 'C' and resid 87 through 103 removed outlier: 3.693A pdb=" N SER C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP C 93 " --> pdb=" O GLN C 89 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR C 97 " --> pdb=" O TRP C 93 " (cutoff:3.500A) Proline residue: C 100 - end of helix Processing helix chain 'C' and resid 108 through 116 Processing helix chain 'C' and resid 121 through 142 Processing helix chain 'C' and resid 142 through 152 removed outlier: 3.859A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 151 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 179 Proline residue: C 167 - end of helix Processing helix chain 'C' and resid 185 through 199 removed outlier: 4.909A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 Processing helix chain 'C' and resid 297 through 304 removed outlier: 3.703A pdb=" N TRP C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 316 removed outlier: 3.539A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 345 Processing helix chain 'C' and resid 354 through 360 removed outlier: 3.610A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.635A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 406 No H-bonds generated for 'chain 'C' and resid 404 through 406' Processing helix chain 'C' and resid 414 through 429 removed outlier: 3.674A pdb=" N TYR C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Proline residue: C 420 - end of helix removed outlier: 3.809A pdb=" N ALA C 429 " --> pdb=" O VAL C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 459 removed outlier: 3.630A pdb=" N LEU C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 475 Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.716A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 501 removed outlier: 3.865A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR C 492 " --> pdb=" O GLU C 488 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 501 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 Processing helix chain 'C' and resid 523 through 537 Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.750A pdb=" N GLY C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 588 removed outlier: 3.537A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 599 Processing helix chain 'C' and resid 604 through 626 removed outlier: 4.411A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 646 removed outlier: 3.731A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 643 " --> pdb=" O ASP C 639 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 removed outlier: 3.607A pdb=" N LEU C 717 " --> pdb=" O ARG C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 758 Processing helix chain 'C' and resid 768 through 780 Processing helix chain 'C' and resid 790 through 795 removed outlier: 3.599A pdb=" N GLN C 795 " --> pdb=" O GLN C 792 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 805 No H-bonds generated for 'chain 'C' and resid 803 through 805' Processing helix chain 'C' and resid 806 through 811 Processing helix chain 'C' and resid 834 through 843 removed outlier: 4.002A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 852 Processing helix chain 'C' and resid 874 through 890 removed outlier: 3.744A pdb=" N GLU C 890 " --> pdb=" O ASN C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 905 removed outlier: 3.935A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 935 removed outlier: 3.800A pdb=" N LEU C 927 " --> pdb=" O GLU C 923 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 991 removed outlier: 3.577A pdb=" N GLY C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 Processing helix chain 'C' and resid 1040 through 1049 Processing helix chain 'C' and resid 1060 through 1077 Processing helix chain 'C' and resid 1087 through 1094 removed outlier: 3.722A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1120 Proline residue: C1115 - end of helix Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.769A pdb=" N GLU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 29 Processing helix chain 'D' and resid 32 through 48 removed outlier: 3.538A pdb=" N THR D 36 " --> pdb=" O HIS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 76 removed outlier: 4.884A pdb=" N SER D 73 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLU D 74 " --> pdb=" O THR D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.637A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 125 removed outlier: 3.514A pdb=" N CYS D 114 " --> pdb=" O ASN D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 145 Processing helix chain 'D' and resid 152 through 164 Processing helix chain 'D' and resid 176 through 192 Processing helix chain 'D' and resid 205 through 223 removed outlier: 3.644A pdb=" N GLN D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 240 through 245 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 275 through 285 removed outlier: 3.605A pdb=" N ALA D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 315 removed outlier: 3.823A pdb=" N ASP D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 319 Processing helix chain 'D' and resid 322 through 334 removed outlier: 3.559A pdb=" N ARG D 327 " --> pdb=" O ALA D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 351 Processing helix chain 'D' and resid 365 through 377 removed outlier: 3.519A pdb=" N GLN D 369 " --> pdb=" O SER D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 388 Processing helix chain 'D' and resid 400 through 424 removed outlier: 4.853A pdb=" N ARG D 417 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TYR D 418 " --> pdb=" O GLY D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.668A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 removed outlier: 3.731A pdb=" N GLU D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 572 Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.619A pdb=" N SER D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 592 " --> pdb=" O ALA D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 606 removed outlier: 3.835A pdb=" N SER D 605 " --> pdb=" O ALA D 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 29 removed outlier: 3.723A pdb=" N ASN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 36 Processing helix chain 'A' and resid 40 through 52 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.260A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N PHE B 127 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.393A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA4, first strand: chain 'B' and resid 494 through 495 Processing sheet with id=AA5, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.543A pdb=" N VAL B 579 " --> pdb=" O ILE B 738 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N THR B 740 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N SER B 814 " --> pdb=" O PRO B 750 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL B 752 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N GLY B 816 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU B 754 " --> pdb=" O GLY B 816 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N MET B 499 " --> pdb=" O ALA B 866 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N GLN B 868 " --> pdb=" O MET B 499 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N MET B 501 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N ALA B 870 " --> pdb=" O MET B 501 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LEU B 503 " --> pdb=" O ALA B 870 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 901 through 904 removed outlier: 6.400A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 9.911A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE B1070 " --> pdb=" O TYR B1077 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N TYR B1076 " --> pdb=" O GLY B1137 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ILE B1139 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 901 through 904 removed outlier: 6.400A pdb=" N ARG B 902 " --> pdb=" O MET B1061 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS B1063 " --> pdb=" O ARG B 902 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N THR B 904 " --> pdb=" O LYS B1063 " (cutoff:3.500A) removed outlier: 9.036A pdb=" N PHE B1065 " --> pdb=" O THR B 904 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL B1058 " --> pdb=" O GLU B1029 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU B1029 " --> pdb=" O VAL B1058 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LEU B1068 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL B1019 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE B1070 " --> pdb=" O LYS B1017 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N LYS B1017 " --> pdb=" O PHE B1070 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 61 removed outlier: 6.201A pdb=" N GLU C 33 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR C 241 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS C 6 " --> pdb=" O LEU C 323 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 365 through 366 removed outlier: 5.930A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 437 through 439 removed outlier: 6.294A pdb=" N ALA C 438 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N THR C 663 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN C 660 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS C 673 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N TYR C 728 " --> pdb=" O LYS C 673 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N VAL C 675 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N SER C 730 " --> pdb=" O VAL C 675 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 677 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N ILE C 732 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 442 through 443 removed outlier: 4.293A pdb=" N ARG C 442 " --> pdb=" O ILE C 650 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 831 through 833 removed outlier: 3.692A pdb=" N THR C 953 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 963 through 968 removed outlier: 6.415A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 1050 through 1051 removed outlier: 3.541A pdb=" N ALA C1056 " --> pdb=" O ASP C1051 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.461A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 238 through 239 removed outlier: 8.978A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY D 171 " --> pdb=" O GLY D 296 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N CYS D 353 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL D 168 " --> pdb=" O CYS D 353 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU D 355 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N SER D 170 " --> pdb=" O LEU D 355 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 393 through 396 removed outlier: 7.891A pdb=" N PHE D 546 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ARG D 576 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N HIS D 548 " --> pdb=" O ARG D 576 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N SER D 578 " --> pdb=" O HIS D 548 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA D 550 " --> pdb=" O SER D 578 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TYR D 580 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE D 552 " --> pdb=" O TYR D 580 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 519 through 522 removed outlier: 4.716A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1135 hydrogen bonds defined for protein. 3324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 5.48 Time building geometry restraints manager: 2.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7353 1.33 - 1.45: 3755 1.45 - 1.57: 13221 1.57 - 1.69: 105 1.69 - 1.81: 173 Bond restraints: 24607 Sorted by residual: bond pdb=" O3A ANP B1501 " pdb=" PB ANP B1501 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" O5' ANP B1501 " pdb=" PA ANP B1501 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C3' DG X 56 " pdb=" C2' DG X 56 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DG X 23 " pdb=" C2' DG X 23 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 ... (remaining 24602 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.65: 33556 3.65 - 7.29: 40 7.29 - 10.94: 5 10.94 - 14.59: 0 14.59 - 18.24: 1 Bond angle restraints: 33602 Sorted by residual: angle pdb=" PB ANP B1501 " pdb=" N3B ANP B1501 " pdb=" PG ANP B1501 " ideal model delta sigma weight residual 126.95 108.71 18.24 3.00e+00 1.11e-01 3.70e+01 angle pdb=" N3 DT X 30 " pdb=" C4 DT X 30 " pdb=" O4 DT X 30 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT X 7 " pdb=" C4 DT X 7 " pdb=" O4 DT X 7 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT X 1 " pdb=" C4 DT X 1 " pdb=" O4 DT X 1 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT X 15 " pdb=" C4 DT X 15 " pdb=" O4 DT X 15 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 33597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.89: 13612 16.89 - 33.78: 731 33.78 - 50.67: 270 50.67 - 67.57: 92 67.57 - 84.46: 7 Dihedral angle restraints: 14712 sinusoidal: 6362 harmonic: 8350 Sorted by residual: dihedral pdb=" CA ASN B1003 " pdb=" C ASN B1003 " pdb=" N GLU B1004 " pdb=" CA GLU B1004 " ideal model delta harmonic sigma weight residual -180.00 -157.59 -22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA TYR D 108 " pdb=" C TYR D 108 " pdb=" N LEU D 109 " pdb=" CA LEU D 109 " ideal model delta harmonic sigma weight residual 180.00 158.61 21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PHE B 127 " pdb=" C PHE B 127 " pdb=" N THR B 128 " pdb=" CA THR B 128 " ideal model delta harmonic sigma weight residual 180.00 161.93 18.07 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 14709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3133 0.050 - 0.101: 462 0.101 - 0.151: 92 0.151 - 0.202: 1 0.202 - 0.252: 1 Chirality restraints: 3689 Sorted by residual: chirality pdb=" C3' ANP B1501 " pdb=" C2' ANP B1501 " pdb=" C4' ANP B1501 " pdb=" O3' ANP B1501 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU C 323 " pdb=" CB LEU C 323 " pdb=" CD1 LEU C 323 " pdb=" CD2 LEU C 323 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CA ILE C 661 " pdb=" N ILE C 661 " pdb=" C ILE C 661 " pdb=" CB ILE C 661 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 3686 not shown) Planarity restraints: 4231 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 657 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.26e+00 pdb=" N PRO C 658 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 658 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 658 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 381 " -0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO C 382 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 382 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 382 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 658 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO B 659 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 659 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 659 " -0.020 5.00e-02 4.00e+02 ... (remaining 4228 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 184 2.63 - 3.20: 21007 3.20 - 3.77: 36354 3.77 - 4.33: 49805 4.33 - 4.90: 82512 Nonbonded interactions: 189862 Sorted by model distance: nonbonded pdb=" OG1 THR B 30 " pdb="MG MG B1502 " model vdw 2.065 2.170 nonbonded pdb=" NH1 ARG B 682 " pdb=" O ARG B 728 " model vdw 2.212 3.120 nonbonded pdb=" OD2 ASP B1044 " pdb=" NE2 GLN B1112 " model vdw 2.223 3.120 nonbonded pdb=" OG SER B1090 " pdb=" OE1 GLN B1153 " model vdw 2.224 3.040 nonbonded pdb=" OD2 ASP B 388 " pdb=" NZ LYS B 745 " model vdw 2.232 3.120 ... (remaining 189857 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.080 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.143 24607 Z= 0.217 Angle : 0.562 18.237 33602 Z= 0.378 Chirality : 0.038 0.252 3689 Planarity : 0.004 0.045 4231 Dihedral : 12.786 84.457 9300 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.05 % Favored : 98.91 % Rotamer: Outliers : 1.44 % Allowed : 3.90 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.14), residues: 2855 helix: -0.22 (0.12), residues: 1481 sheet: -0.71 (0.27), residues: 311 loop : -1.03 (0.17), residues: 1063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 433 TYR 0.018 0.001 TYR B1111 PHE 0.010 0.001 PHE C 857 TRP 0.018 0.001 TRP B 652 HIS 0.003 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.22 (24607) covalent geometry : angle 0.56194 / 0.38 (33602) hydrogen bonds : bond 0.14878 / 10.21 ( 1180) hydrogen bonds : angle 5.76785 / 4.18 ( 3414) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 452 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 289 PHE cc_start: 0.8704 (m-80) cc_final: 0.8381 (m-80) REVERT: B 604 MET cc_start: 0.8116 (tpt) cc_final: 0.7770 (tpt) REVERT: B 672 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: B 709 ARG cc_start: 0.7607 (tpp80) cc_final: 0.7327 (mtm-85) REVERT: B 1079 LEU cc_start: 0.9360 (tp) cc_final: 0.9143 (tt) REVERT: C 42 MET cc_start: 0.8972 (tpt) cc_final: 0.8596 (tpt) REVERT: C 556 LEU cc_start: 0.8817 (mt) cc_final: 0.8536 (mt) REVERT: C 617 GLN cc_start: 0.8214 (tp40) cc_final: 0.7989 (tp40) REVERT: C 924 MET cc_start: 0.8470 (mmp) cc_final: 0.8231 (mmp) REVERT: D 78 LEU cc_start: 0.6377 (mm) cc_final: 0.6134 (tp) REVERT: D 136 LEU cc_start: 0.8316 (tp) cc_final: 0.7905 (tt) outliers start: 35 outliers final: 5 residues processed: 480 average time/residue: 0.1999 time to fit residues: 141.5433 Evaluate side-chains 188 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 182 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 672 GLU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 30.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 162 GLN B 181 GLN B 440 HIS B 458 ASN B 484 ASN B 594 GLN B 650 GLN B 769 HIS B 835 GLN B 843 GLN B 848 GLN B1018 GLN B1072 HIS B1103 GLN B1134 HIS B1161 ASN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 GLN C 336 HIS C 510 ASN C 749 GLN C 979 GLN D 22 GLN D 256 HIS D 399 GLN D 556 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.114617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.086132 restraints weight = 46170.322| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.23 r_work: 0.3077 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 24607 Z= 0.200 Angle : 0.589 11.657 33602 Z= 0.311 Chirality : 0.041 0.188 3689 Planarity : 0.005 0.049 4231 Dihedral : 13.540 83.205 3713 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.13 % Allowed : 8.74 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 2855 helix: 0.93 (0.13), residues: 1507 sheet: -0.23 (0.27), residues: 312 loop : -0.66 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 198 TYR 0.019 0.002 TYR B1111 PHE 0.021 0.002 PHE B 257 TRP 0.029 0.001 TRP B 265 HIS 0.006 0.001 HIS D 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00469 / 0.20 (24607) covalent geometry : angle 0.58922 / 0.31 (33602) hydrogen bonds : bond 0.04764 / 3.20 ( 1180) hydrogen bonds : angle 4.58273 / 3.30 ( 3414) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 194 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: B 310 PHE cc_start: 0.8005 (m-10) cc_final: 0.7797 (m-80) REVERT: B 655 ARG cc_start: 0.8757 (OUTLIER) cc_final: 0.7912 (mpp80) REVERT: B 658 MET cc_start: 0.8693 (tpp) cc_final: 0.8477 (tpp) REVERT: B 709 ARG cc_start: 0.8335 (tpp80) cc_final: 0.7858 (mtm-85) REVERT: B 968 VAL cc_start: 0.7036 (t) cc_final: 0.6744 (t) REVERT: B 1078 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8641 (tt) REVERT: C 30 PHE cc_start: 0.8752 (m-10) cc_final: 0.8464 (m-10) REVERT: C 752 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8691 (tp) REVERT: C 835 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7610 (tm-30) REVERT: C 924 MET cc_start: 0.8783 (mmp) cc_final: 0.8551 (mmp) REVERT: D 78 LEU cc_start: 0.6627 (mm) cc_final: 0.6343 (tp) REVERT: D 384 THR cc_start: 0.8313 (p) cc_final: 0.8049 (t) REVERT: D 407 MET cc_start: 0.7768 (ttp) cc_final: 0.7558 (tmm) REVERT: D 470 ARG cc_start: 0.8044 (ttt180) cc_final: 0.7561 (mtm110) outliers start: 52 outliers final: 24 residues processed: 233 average time/residue: 0.1481 time to fit residues: 57.9257 Evaluate side-chains 183 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 752 ILE Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 399 GLN Chi-restraints excluded: chain D residue 498 ILE Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 33 optimal weight: 7.9990 chunk 284 optimal weight: 50.0000 chunk 56 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 226 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 198 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 463 GLN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 ASN ** 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 = 0.3642 r_free = 0.3642 target = 0.113187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.084308 restraints weight = 45853.208| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.32 r_work: 0.3028 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24607 Z= 0.121 Angle : 0.509 11.595 33602 Z= 0.268 Chirality : 0.038 0.149 3689 Planarity : 0.004 0.047 4231 Dihedral : 13.546 83.688 3710 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.93 % Allowed : 9.52 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.15), residues: 2855 helix: 1.46 (0.13), residues: 1506 sheet: 0.18 (0.28), residues: 308 loop : -0.46 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 575 TYR 0.021 0.001 TYR C 138 PHE 0.017 0.001 PHE B 257 TRP 0.013 0.001 TRP B 265 HIS 0.003 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (24607) covalent geometry : angle 0.50928 / 0.27 (33602) hydrogen bonds : bond 0.04018 / 2.70 ( 1180) hydrogen bonds : angle 4.22977 / 3.07 ( 3414) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.764 Fit side-chains revert: symmetry clash REVERT: B 655 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7760 (mpp80) REVERT: B 709 ARG cc_start: 0.8362 (tpp80) cc_final: 0.7842 (mtm-85) REVERT: B 901 TRP cc_start: 0.8607 (OUTLIER) cc_final: 0.8020 (t60) REVERT: B 968 VAL cc_start: 0.7272 (t) cc_final: 0.7026 (t) REVERT: C 30 PHE cc_start: 0.8758 (m-10) cc_final: 0.8481 (m-10) REVERT: C 42 MET cc_start: 0.9359 (tpp) cc_final: 0.8899 (tpt) REVERT: C 835 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 924 MET cc_start: 0.8946 (mmp) cc_final: 0.8665 (mmp) REVERT: D 78 LEU cc_start: 0.6544 (mm) cc_final: 0.6273 (tp) REVERT: D 407 MET cc_start: 0.8293 (ttp) cc_final: 0.7707 (tmm) REVERT: D 462 MET cc_start: 0.7450 (mmm) cc_final: 0.6850 (mmp) REVERT: D 470 ARG cc_start: 0.8017 (ttt180) cc_final: 0.7438 (mtm110) REVERT: A 18 SER cc_start: 0.8576 (t) cc_final: 0.8329 (t) outliers start: 47 outliers final: 27 residues processed: 215 average time/residue: 0.1408 time to fit residues: 50.4390 Evaluate side-chains 181 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 152 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 901 TRP Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 652 GLN Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 52 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 285 optimal weight: 50.0000 chunk 151 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 184 optimal weight: 0.7980 chunk 219 optimal weight: 0.0770 chunk 211 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 overall best weight: 2.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 705 HIS ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 523 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.111232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.081664 restraints weight = 45894.075| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.41 r_work: 0.2979 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24607 Z= 0.168 Angle : 0.529 11.222 33602 Z= 0.277 Chirality : 0.039 0.146 3689 Planarity : 0.004 0.051 4231 Dihedral : 13.595 84.458 3710 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.59 % Allowed : 9.89 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.15), residues: 2855 helix: 1.57 (0.13), residues: 1509 sheet: 0.29 (0.28), residues: 307 loop : -0.41 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 854 TYR 0.017 0.002 TYR B1111 PHE 0.014 0.001 PHE C 193 TRP 0.009 0.001 TRP C 616 HIS 0.005 0.001 HIS C 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (24607) covalent geometry : angle 0.52882 / 0.28 (33602) hydrogen bonds : bond 0.04143 / 2.78 ( 1180) hydrogen bonds : angle 4.20059 / 3.03 ( 3414) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 163 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 310 PHE cc_start: 0.7941 (m-10) cc_final: 0.7698 (m-10) REVERT: B 332 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8388 (mt) REVERT: B 354 MET cc_start: 0.8054 (mtt) cc_final: 0.7841 (mtt) REVERT: B 655 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.7826 (mpp80) REVERT: B 709 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7680 (mtm-85) REVERT: B 901 TRP cc_start: 0.8505 (OUTLIER) cc_final: 0.7795 (t60) REVERT: B 968 VAL cc_start: 0.7219 (t) cc_final: 0.6969 (t) REVERT: B 1078 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8681 (tt) REVERT: C 30 PHE cc_start: 0.8723 (m-10) cc_final: 0.8502 (m-10) REVERT: C 42 MET cc_start: 0.9260 (tpp) cc_final: 0.8746 (tpt) REVERT: C 835 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7405 (tm-30) REVERT: C 924 MET cc_start: 0.8827 (mmp) cc_final: 0.8480 (mmp) REVERT: D 78 LEU cc_start: 0.6476 (mm) cc_final: 0.6238 (tp) REVERT: D 462 MET cc_start: 0.7473 (mmm) cc_final: 0.6890 (mmp) REVERT: D 470 ARG cc_start: 0.7872 (ttt180) cc_final: 0.7325 (mtm110) REVERT: D 520 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7930 (mtpt) REVERT: A 18 SER cc_start: 0.8681 (t) cc_final: 0.8423 (t) outliers start: 63 outliers final: 42 residues processed: 214 average time/residue: 0.1412 time to fit residues: 49.5332 Evaluate side-chains 199 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 152 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 901 TRP Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 652 GLN Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 896 ARG Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 520 LYS Chi-restraints excluded: chain D residue 523 GLN Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 116 optimal weight: 10.0000 chunk 250 optimal weight: 8.9990 chunk 203 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 282 optimal weight: 30.0000 chunk 226 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 53 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 89 optimal weight: 0.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 834 HIS ** B1112 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 = 0.3609 r_free = 0.3609 target = 0.111063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.081581 restraints weight = 46045.059| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.42 r_work: 0.2975 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24607 Z= 0.157 Angle : 0.509 9.815 33602 Z= 0.268 Chirality : 0.038 0.177 3689 Planarity : 0.004 0.046 4231 Dihedral : 13.596 84.248 3710 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.09 % Allowed : 11.12 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.15), residues: 2855 helix: 1.67 (0.13), residues: 1509 sheet: 0.34 (0.28), residues: 307 loop : -0.38 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 854 TYR 0.017 0.001 TYR B1111 PHE 0.015 0.001 PHE C 193 TRP 0.011 0.001 TRP B 993 HIS 0.004 0.001 HIS C 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (24607) covalent geometry : angle 0.50896 / 0.27 (33602) hydrogen bonds : bond 0.03959 / 2.65 ( 1180) hydrogen bonds : angle 4.12098 / 2.97 ( 3414) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 161 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: B 354 MET cc_start: 0.8098 (mtt) cc_final: 0.7865 (mtt) REVERT: B 655 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8041 (mpp80) REVERT: B 709 ARG cc_start: 0.8250 (tpp80) cc_final: 0.7712 (mtm-85) REVERT: B 901 TRP cc_start: 0.8519 (OUTLIER) cc_final: 0.7752 (t60) REVERT: B 968 VAL cc_start: 0.7153 (t) cc_final: 0.6915 (t) REVERT: B 1078 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8680 (tt) REVERT: C 30 PHE cc_start: 0.8749 (m-10) cc_final: 0.8536 (m-10) REVERT: C 42 MET cc_start: 0.9202 (tpp) cc_final: 0.8703 (tpt) REVERT: C 95 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8934 (mt) REVERT: C 661 ILE cc_start: 0.9159 (OUTLIER) cc_final: 0.8909 (mt) REVERT: C 835 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7381 (tm-30) REVERT: C 924 MET cc_start: 0.8837 (mmp) cc_final: 0.8488 (mmp) REVERT: D 78 LEU cc_start: 0.6471 (mm) cc_final: 0.6234 (tp) REVERT: D 132 VAL cc_start: 0.8686 (m) cc_final: 0.8478 (p) REVERT: D 462 MET cc_start: 0.7557 (mmm) cc_final: 0.6934 (mmp) REVERT: D 470 ARG cc_start: 0.7809 (ttt180) cc_final: 0.7247 (mtm110) REVERT: D 568 THR cc_start: 0.8365 (p) cc_final: 0.8163 (t) REVERT: A 18 SER cc_start: 0.8711 (t) cc_final: 0.8446 (t) outliers start: 51 outliers final: 36 residues processed: 199 average time/residue: 0.1477 time to fit residues: 47.5597 Evaluate side-chains 195 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 154 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 901 TRP Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1078 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain B residue 1098 MET Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 929 ASP Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 108 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 249 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 167 optimal weight: 0.9990 chunk 260 optimal weight: 20.0000 chunk 38 optimal weight: 0.9980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 HIS C1108 GLN D 65 HIS D 523 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.113094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.084335 restraints weight = 46361.647| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.36 r_work: 0.3044 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24607 Z= 0.112 Angle : 0.477 10.196 33602 Z= 0.251 Chirality : 0.037 0.158 3689 Planarity : 0.003 0.050 4231 Dihedral : 13.565 84.931 3708 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.30 % Allowed : 11.41 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.16), residues: 2855 helix: 1.83 (0.13), residues: 1516 sheet: 0.40 (0.28), residues: 307 loop : -0.30 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 365 TYR 0.017 0.001 TYR B1111 PHE 0.016 0.001 PHE C 193 TRP 0.010 0.001 TRP B 710 HIS 0.003 0.001 HIS C 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (24607) covalent geometry : angle 0.47680 / 0.25 (33602) hydrogen bonds : bond 0.03548 / 2.37 ( 1180) hydrogen bonds : angle 3.98822 / 2.88 ( 3414) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 175 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 310 PHE cc_start: 0.7884 (m-10) cc_final: 0.7666 (m-10) REVERT: B 354 MET cc_start: 0.8024 (mtt) cc_final: 0.7786 (mtt) REVERT: B 568 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7132 (tpp80) REVERT: B 655 ARG cc_start: 0.9018 (OUTLIER) cc_final: 0.8003 (mpp80) REVERT: B 709 ARG cc_start: 0.8182 (tpp80) cc_final: 0.7712 (mtm-85) REVERT: B 901 TRP cc_start: 0.8536 (OUTLIER) cc_final: 0.7834 (t60) REVERT: B 968 VAL cc_start: 0.7031 (t) cc_final: 0.6794 (t) REVERT: C 30 PHE cc_start: 0.8679 (m-10) cc_final: 0.8449 (m-10) REVERT: C 835 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7345 (tm-30) REVERT: C 924 MET cc_start: 0.8660 (mmp) cc_final: 0.8361 (mmp) REVERT: D 462 MET cc_start: 0.7620 (mmm) cc_final: 0.6994 (mmp) REVERT: D 470 ARG cc_start: 0.7698 (ttt180) cc_final: 0.7333 (mtm110) REVERT: A 18 SER cc_start: 0.8744 (t) cc_final: 0.8517 (t) outliers start: 56 outliers final: 34 residues processed: 221 average time/residue: 0.1474 time to fit residues: 53.6874 Evaluate side-chains 192 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 901 TRP Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 929 ASP Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 367 ILE Chi-restraints excluded: chain D residue 523 GLN Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 151 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 261 optimal weight: 8.9990 chunk 290 optimal weight: 20.0000 chunk 131 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B1112 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 = 0.3648 r_free = 0.3648 target = 0.112375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.084252 restraints weight = 46700.322| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.41 r_work: 0.3034 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24607 Z= 0.139 Angle : 0.494 10.164 33602 Z= 0.258 Chirality : 0.038 0.177 3689 Planarity : 0.003 0.047 4231 Dihedral : 13.563 85.072 3706 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.17 % Allowed : 11.74 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.16), residues: 2855 helix: 1.86 (0.13), residues: 1517 sheet: 0.39 (0.28), residues: 307 loop : -0.32 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 13 TYR 0.016 0.001 TYR B1111 PHE 0.015 0.001 PHE C 193 TRP 0.010 0.001 TRP B 710 HIS 0.004 0.001 HIS C 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (24607) covalent geometry : angle 0.49430 / 0.26 (33602) hydrogen bonds : bond 0.03672 / 2.46 ( 1180) hydrogen bonds : angle 3.98633 / 2.88 ( 3414) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 160 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: B 354 MET cc_start: 0.8289 (mtt) cc_final: 0.8043 (mtt) REVERT: B 431 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8289 (mpp) REVERT: B 639 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8450 (t0) REVERT: B 655 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8177 (mpp80) REVERT: B 709 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7846 (mtm-85) REVERT: B 901 TRP cc_start: 0.8654 (OUTLIER) cc_final: 0.7910 (t60) REVERT: B 968 VAL cc_start: 0.7044 (t) cc_final: 0.6788 (t) REVERT: C 30 PHE cc_start: 0.8804 (m-10) cc_final: 0.8509 (m-10) REVERT: C 661 ILE cc_start: 0.9173 (OUTLIER) cc_final: 0.8967 (mt) REVERT: C 835 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7655 (tm-30) REVERT: C 924 MET cc_start: 0.8803 (mmp) cc_final: 0.8521 (mmp) REVERT: D 407 MET cc_start: 0.8167 (tmm) cc_final: 0.7852 (tmm) REVERT: D 462 MET cc_start: 0.7704 (mmm) cc_final: 0.7071 (mmp) REVERT: D 470 ARG cc_start: 0.7798 (ttt180) cc_final: 0.7341 (mtm110) REVERT: A 18 SER cc_start: 0.8789 (t) cc_final: 0.8547 (t) outliers start: 53 outliers final: 37 residues processed: 200 average time/residue: 0.1523 time to fit residues: 49.9744 Evaluate side-chains 198 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 901 TRP Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 661 ILE Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 929 ASP Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 225 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 70 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 115 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 282 optimal weight: 30.0000 chunk 161 optimal weight: 0.0770 overall best weight: 1.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.112391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.083987 restraints weight = 46413.533| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.50 r_work: 0.3033 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24607 Z= 0.130 Angle : 0.490 10.084 33602 Z= 0.257 Chirality : 0.038 0.152 3689 Planarity : 0.003 0.049 4231 Dihedral : 13.563 85.043 3706 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.09 % Allowed : 11.94 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.16), residues: 2855 helix: 1.93 (0.13), residues: 1515 sheet: 0.41 (0.29), residues: 303 loop : -0.31 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 365 TYR 0.016 0.001 TYR B1111 PHE 0.016 0.001 PHE B 310 TRP 0.010 0.001 TRP B 710 HIS 0.004 0.001 HIS C 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (24607) covalent geometry : angle 0.48980 / 0.26 (33602) hydrogen bonds : bond 0.03606 / 2.41 ( 1180) hydrogen bonds : angle 3.95700 / 2.85 ( 3414) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 158 time to evaluate : 0.974 Fit side-chains revert: symmetry clash REVERT: B 354 MET cc_start: 0.8069 (mtt) cc_final: 0.7840 (mtt) REVERT: B 431 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8090 (mpp) REVERT: B 639 ASP cc_start: 0.8724 (OUTLIER) cc_final: 0.8511 (t0) REVERT: B 655 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8096 (mpp80) REVERT: B 709 ARG cc_start: 0.8202 (tpp80) cc_final: 0.7703 (mtm-85) REVERT: B 901 TRP cc_start: 0.8533 (OUTLIER) cc_final: 0.7803 (t60) REVERT: B 968 VAL cc_start: 0.7032 (t) cc_final: 0.6779 (t) REVERT: C 30 PHE cc_start: 0.8722 (m-10) cc_final: 0.8489 (m-10) REVERT: C 835 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7335 (tm-30) REVERT: C 924 MET cc_start: 0.8627 (mmp) cc_final: 0.8324 (mmp) REVERT: D 407 MET cc_start: 0.8082 (tmm) cc_final: 0.7751 (tmm) REVERT: D 462 MET cc_start: 0.7765 (mmm) cc_final: 0.7122 (mmp) REVERT: D 470 ARG cc_start: 0.7633 (ttt180) cc_final: 0.7346 (mtm110) REVERT: A 18 SER cc_start: 0.8769 (t) cc_final: 0.8543 (t) outliers start: 51 outliers final: 41 residues processed: 195 average time/residue: 0.1535 time to fit residues: 49.4080 Evaluate side-chains 200 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 155 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 499 MET Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 639 ASP Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 727 MET Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 901 TRP Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 324 ASP Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 375 THR Chi-restraints excluded: chain C residue 448 HIS Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 519 THR Chi-restraints excluded: chain C residue 594 MET Chi-restraints excluded: chain C residue 641 LEU Chi-restraints excluded: chain C residue 929 ASP Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 136 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 250 SER Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 155 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 130 optimal weight: 0.5980 chunk 134 optimal weight: 3.9990 chunk 257 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 167 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 243 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 843 GLN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN D 523 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.113734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085771 restraints weight = 46559.354| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.49 r_work: 0.3062 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24607 Z= 0.096 Angle : 0.469 10.166 33602 Z= 0.246 Chirality : 0.037 0.151 3689 Planarity : 0.003 0.047 4231 Dihedral : 13.508 85.530 3706 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.72 % Allowed : 12.35 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.16), residues: 2855 helix: 2.06 (0.13), residues: 1513 sheet: 0.57 (0.29), residues: 291 loop : -0.26 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 728 TYR 0.016 0.001 TYR B1111 PHE 0.017 0.001 PHE C 193 TRP 0.031 0.001 TRP B 993 HIS 0.003 0.001 HIS C 759 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 (24607) covalent geometry : angle 0.46925 / 0.25 (33602) hydrogen bonds : bond 0.03245 / 2.17 ( 1180) hydrogen bonds : angle 3.85331 / 2.78 ( 3414) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: B 431 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8057 (mpp) REVERT: B 568 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7183 (tpp80) REVERT: B 655 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8061 (mpp80) REVERT: B 709 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7660 (mtm-85) REVERT: B 901 TRP cc_start: 0.8512 (OUTLIER) cc_final: 0.7793 (t60) REVERT: B 968 VAL cc_start: 0.7050 (t) cc_final: 0.6810 (t) REVERT: C 30 PHE cc_start: 0.8642 (m-10) cc_final: 0.8407 (m-10) REVERT: C 835 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7262 (tm-30) REVERT: C 924 MET cc_start: 0.8627 (mmp) cc_final: 0.8321 (mmp) REVERT: D 407 MET cc_start: 0.8089 (tmm) cc_final: 0.7719 (tmm) REVERT: D 462 MET cc_start: 0.7748 (mmm) cc_final: 0.7112 (mmp) REVERT: D 470 ARG cc_start: 0.7608 (ttt180) cc_final: 0.7267 (mtm110) REVERT: A 18 SER cc_start: 0.8718 (t) cc_final: 0.8000 (p) outliers start: 42 outliers final: 31 residues processed: 204 average time/residue: 0.1545 time to fit residues: 52.2144 Evaluate side-chains 199 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 901 TRP Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 896 ARG Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain C residue 1081 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 62 optimal weight: 8.9990 chunk 27 optimal weight: 0.0970 chunk 188 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 129 optimal weight: 0.0060 chunk 74 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 273 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 843 GLN B 848 GLN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.113623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.085656 restraints weight = 46487.065| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.48 r_work: 0.3057 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24607 Z= 0.107 Angle : 0.479 10.128 33602 Z= 0.251 Chirality : 0.037 0.207 3689 Planarity : 0.003 0.049 4231 Dihedral : 13.486 85.693 3706 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.60 % Allowed : 12.64 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.16), residues: 2855 helix: 2.08 (0.13), residues: 1511 sheet: 0.46 (0.29), residues: 303 loop : -0.24 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 706 TYR 0.016 0.001 TYR B1111 PHE 0.021 0.001 PHE B 310 TRP 0.031 0.001 TRP B 993 HIS 0.002 0.001 HIS B 171 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (24607) covalent geometry : angle 0.47904 / 0.25 (33602) hydrogen bonds : bond 0.03280 / 2.19 ( 1180) hydrogen bonds : angle 3.85179 / 2.78 ( 3414) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5710 Ramachandran restraints generated. 2855 Oldfield, 0 Emsley, 2855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 167 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 431 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.8060 (mpp) REVERT: B 453 MET cc_start: 0.7948 (mmm) cc_final: 0.7696 (mmt) REVERT: B 655 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8113 (mpp80) REVERT: B 709 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7676 (mtm-85) REVERT: B 901 TRP cc_start: 0.8524 (OUTLIER) cc_final: 0.7816 (t60) REVERT: B 968 VAL cc_start: 0.7047 (t) cc_final: 0.6802 (t) REVERT: C 667 MET cc_start: 0.8639 (mmt) cc_final: 0.8427 (mmt) REVERT: C 835 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7279 (tm-30) REVERT: C 924 MET cc_start: 0.8611 (mmp) cc_final: 0.8318 (mmp) REVERT: D 407 MET cc_start: 0.8070 (tmm) cc_final: 0.7709 (tmm) REVERT: D 462 MET cc_start: 0.7731 (mmm) cc_final: 0.7111 (mmp) REVERT: D 470 ARG cc_start: 0.7614 (ttt180) cc_final: 0.7281 (mtm110) REVERT: A 18 SER cc_start: 0.8740 (t) cc_final: 0.8033 (p) outliers start: 39 outliers final: 32 residues processed: 196 average time/residue: 0.1546 time to fit residues: 50.0388 Evaluate side-chains 200 residues out of total 2437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 382 MET Chi-restraints excluded: chain B residue 407 THR Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 655 ARG Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 699 THR Chi-restraints excluded: chain B residue 716 LEU Chi-restraints excluded: chain B residue 815 LEU Chi-restraints excluded: chain B residue 880 VAL Chi-restraints excluded: chain B residue 901 TRP Chi-restraints excluded: chain B residue 979 LEU Chi-restraints excluded: chain B residue 990 LEU Chi-restraints excluded: chain B residue 1002 LEU Chi-restraints excluded: chain B residue 1096 GLN Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 896 ARG Chi-restraints excluded: chain C residue 947 CYS Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 314 CYS Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain A residue 19 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 214 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 chunk 287 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 210 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 122 optimal weight: 0.4980 chunk 87 optimal weight: 20.0000 chunk 74 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 843 GLN ** B1112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 518 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.112944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.084847 restraints weight = 46469.598| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.47 r_work: 0.3047 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24607 Z= 0.128 Angle : 0.484 10.106 33602 Z= 0.254 Chirality : 0.037 0.173 3689 Planarity : 0.003 0.048 4231 Dihedral : 13.479 85.589 3706 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.60 % Allowed : 12.64 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.16), residues: 2855 helix: 2.06 (0.13), residues: 1512 sheet: 0.42 (0.29), residues: 303 loop : -0.26 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 706 TYR 0.016 0.001 TYR B1111 PHE 0.016 0.001 PHE C 193 TRP 0.025 0.001 TRP B 993 HIS 0.003 0.001 HIS C 6 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (24607) covalent geometry : angle 0.48424 / 0.25 (33602) hydrogen bonds : bond 0.03411 / 2.28 ( 1180) hydrogen bonds : angle 3.87274 / 2.79 ( 3414) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4923.97 seconds wall clock time: 85 minutes 11.24 seconds (5111.24 seconds total)