Starting phenix.real_space_refine on Sun Sep 13 14:24:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ld2_4038/09_2026/5ld2_4038_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ld2_4038/09_2026/5ld2_4038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5ld2_4038/09_2026/5ld2_4038_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ld2_4038/09_2026/5ld2_4038_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ld2_4038/09_2026/5ld2_4038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ld2_4038/09_2026/5ld2_4038.map" } resolution = 3.83 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= 0.009 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 101 5.16 5 C 14991 2.51 5 N 4229 2.21 5 O 4606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 101 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23981 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 7143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 894, 7143 Classifications: {'peptide': 894} Link IDs: {'PTRANS': 36, 'TRANS': 857} Chain breaks: 1 Chain: "B" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2021 Classifications: {'peptide': 257} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 17} Link IDs: {'PTRANS': 15, 'TRANS': 241} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 9078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1121, 9078 Classifications: {'peptide': 1121} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1053} Chain: "D" Number of atoms: 4672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4672 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 25, 'TRANS': 579} 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: "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} Residues with excluded nonbonded symmetry interactions: 20 residue: pdb=" N UNK B 913 " occ=0.00 ... (2 atoms not shown) pdb=" O UNK B 913 " occ=0.00 residue: pdb=" N UNK B 914 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 914 " occ=0.00 residue: pdb=" N UNK B 915 " occ=0.00 ... (2 atoms not shown) pdb=" O UNK B 915 " occ=0.00 residue: pdb=" N UNK B 916 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 916 " occ=0.00 residue: pdb=" N UNK B 917 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 917 " occ=0.00 residue: pdb=" N UNK B 918 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 918 " occ=0.00 residue: pdb=" N UNK B 919 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 919 " occ=0.00 residue: pdb=" N UNK B 920 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 920 " occ=0.00 residue: pdb=" N UNK B 921 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 921 " occ=0.00 residue: pdb=" N UNK B 922 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 922 " occ=0.00 residue: pdb=" N UNK B 923 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 923 " occ=0.00 residue: pdb=" N UNK B 924 " occ=0.00 ... (3 atoms not shown) pdb=" CB UNK B 924 " occ=0.00 ... (remaining 8 not shown) Time building chain proxies: 4.95, per 1000 atoms: 0.21 Number of scatterers: 23981 At special positions: 0 Unit cell: (152.76, 148.74, 127.3, 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 101 16.00 P 53 15.00 Mg 1 11.99 O 4606 8.00 N 4229 7.00 C 14991 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 Links applied TRANS " UNK B 913 " - " ARG B 912 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.1 seconds 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5426 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 20 sheets defined 54.7% alpha, 10.0% beta 18 base pairs and 34 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'B' and resid 28 through 43 removed outlier: 3.707A pdb=" N ILE B 33 " --> pdb=" O LYS B 29 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) removed outlier: 4.335A 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 59 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 128 through 140 removed outlier: 3.901A pdb=" N GLN B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 135 " --> pdb=" O GLY B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.968A pdb=" N SER B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 171 Processing helix chain 'B' and resid 176 through 187 removed outlier: 3.636A pdb=" N VAL B 182 " --> pdb=" O GLU B 178 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU B 185 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 202 removed outlier: 3.592A pdb=" N ARG B 195 " --> pdb=" O GLN B 191 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG B 199 " --> pdb=" O ARG B 195 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N TYR B 200 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN B 202 " --> pdb=" O ASN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 240 removed outlier: 3.989A pdb=" N VAL B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.821A pdb=" N ASN B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG B 259 " --> pdb=" O ARG B 255 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 281 Processing helix chain 'B' and resid 282 through 289 removed outlier: 3.729A pdb=" N LYS B 288 " --> pdb=" O GLU B 284 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.594A pdb=" N GLU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASP B 314 " --> pdb=" O PHE B 310 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N GLU B 319 " --> pdb=" O GLN B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 347 removed outlier: 3.722A pdb=" N ARG B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 364 Processing helix chain 'B' and resid 366 through 378 removed outlier: 3.819A pdb=" N LEU B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 414 through 418 removed outlier: 3.525A pdb=" N ALA B 418 " --> pdb=" O PRO B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 424 Processing helix chain 'B' and resid 426 through 437 removed outlier: 3.766A pdb=" N TYR B 430 " --> pdb=" O ASP B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 462 removed outlier: 3.664A pdb=" N ASN B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 535 removed outlier: 3.570A pdb=" N ARG B 535 " --> pdb=" O GLN B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 574 removed outlier: 3.842A pdb=" N ALA B 570 " --> pdb=" O GLN B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 589 Processing helix chain 'B' and resid 590 through 605 removed outlier: 4.119A pdb=" N GLN B 594 " --> pdb=" O THR B 590 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 605 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 617 removed outlier: 4.140A pdb=" N ALA B 615 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 632 Processing helix chain 'B' and resid 634 through 656 removed outlier: 3.626A pdb=" N TRP B 638 " --> pdb=" O ASP B 634 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 650 " --> pdb=" O ASP B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 669 Processing helix chain 'B' and resid 669 through 677 removed outlier: 3.938A pdb=" N LEU B 675 " --> pdb=" O ALA B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 701 removed outlier: 3.889A pdb=" N ARG B 683 " --> pdb=" O GLY B 679 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN B 700 " --> pdb=" O GLU B 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 717 removed outlier: 3.969A pdb=" N VAL B 708 " --> pdb=" O GLU B 704 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 712 " --> pdb=" O VAL B 708 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 745 Processing helix chain 'B' and resid 783 through 808 removed outlier: 3.682A pdb=" N VAL B 787 " --> pdb=" O ALA B 783 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 835 removed outlier: 4.199A pdb=" N HIS B 834 " --> pdb=" O THR B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 836 through 843 removed outlier: 3.704A pdb=" N LEU B 841 " --> pdb=" O ALA B 837 " (cutoff:3.500A) Processing helix chain 'B' and resid 849 through 860 removed outlier: 3.998A pdb=" N LEU B 860 " --> pdb=" O CYS B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 906 through 911 removed outlier: 3.571A pdb=" N GLN B 911 " --> pdb=" O SER B 907 " (cutoff:3.500A) Processing helix chain 'B' and resid 948 through 962 removed outlier: 3.690A pdb=" N PHE B 959 " --> pdb=" O LEU B 955 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP B 961 " --> pdb=" O SER B 957 " (cutoff:3.500A) Processing helix chain 'B' and resid 969 through 981 Processing helix chain 'B' and resid 986 through 1000 removed outlier: 4.094A pdb=" N GLU B 992 " --> pdb=" O PRO B 988 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TRP B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR B 995 " --> pdb=" O THR B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1010 through 1012 No H-bonds generated for 'chain 'B' and resid 1010 through 1012' Processing helix chain 'B' and resid 1033 through 1044 removed outlier: 3.612A pdb=" N THR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU B1039 " --> pdb=" O GLN B1035 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B1043 " --> pdb=" O LEU B1039 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1049 removed outlier: 3.506A pdb=" N GLY B1049 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing helix chain 'B' and resid 1094 through 1106 removed outlier: 3.503A pdb=" N ALA B1099 " --> pdb=" O GLN B1095 " (cutoff:3.500A) Processing helix chain 'B' and resid 1106 through 1126 removed outlier: 3.778A 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 1163 through 1174 removed outlier: 3.806A pdb=" N LEU B1167 " --> pdb=" O GLY B1163 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B1170 " --> pdb=" O ALA B1166 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 24 removed outlier: 3.808A pdb=" N LEU C 13 " --> pdb=" O ARG C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 55 removed outlier: 3.894A pdb=" N ALA C 43 " --> pdb=" O SER C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 77 removed outlier: 3.583A pdb=" N VAL C 74 " --> pdb=" O TRP C 70 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG C 75 " --> pdb=" O ASP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 103 removed outlier: 3.516A pdb=" N TRP C 93 " --> pdb=" O GLN C 89 " (cutoff:3.500A) removed outlier: 3.604A 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: 3.803A pdb=" N LEU C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 3.540A 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: 3.611A pdb=" N TYR C 190 " --> pdb=" O ARG C 186 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ARG C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 231 removed outlier: 3.597A pdb=" N LEU C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 304 through 315 removed outlier: 3.927A pdb=" N ASP C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 344 Processing helix chain 'C' and resid 354 through 360 removed outlier: 4.336A pdb=" N ARG C 360 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 400 removed outlier: 3.527A pdb=" N ASP C 391 " --> pdb=" O GLU C 387 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP C 400 " --> pdb=" O MET C 396 " (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: 3.739A pdb=" N TYR C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) Proline residue: C 420 - end of helix Processing helix chain 'C' and resid 447 through 459 removed outlier: 4.216A pdb=" N LEU C 451 " --> pdb=" O SER C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 476 removed outlier: 3.594A pdb=" N LEU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 474 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N VAL C 476 " --> pdb=" O ALA C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 483 removed outlier: 3.817A pdb=" N PHE C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 491 removed outlier: 3.549A pdb=" N ARG C 491 " --> pdb=" O GLU C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 500 removed outlier: 3.595A pdb=" N GLN C 495 " --> pdb=" O ARG C 491 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL C 497 " --> pdb=" O LEU C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.562A pdb=" N VAL C 511 " --> pdb=" O ASP C 507 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 514 " --> pdb=" O ASN C 510 " (cutoff:3.500A) 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: 3.752A pdb=" N GLY C 562 " --> pdb=" O ALA C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 589 through 599 Processing helix chain 'C' and resid 604 through 626 removed outlier: 4.305A pdb=" N ALA C 608 " --> pdb=" O GLU C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 646 removed outlier: 3.948A pdb=" N LEU C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASP C 639 " --> pdb=" O SER C 635 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLN C 643 " --> pdb=" O ASP C 639 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 722 removed outlier: 3.721A 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 Processing helix chain 'C' and resid 806 through 811 Processing helix chain 'C' and resid 834 through 843 removed outlier: 4.423A pdb=" N HIS C 843 " --> pdb=" O ARG C 839 " (cutoff:3.500A) Processing helix chain 'C' and resid 843 through 851 removed outlier: 3.761A pdb=" N PHE C 848 " --> pdb=" O PRO C 844 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE C 849 " --> pdb=" O VAL C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 873 through 890 removed outlier: 3.722A pdb=" N ARG C 877 " --> pdb=" O GLU C 873 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE C 880 " --> pdb=" O SER C 876 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU C 890 " --> pdb=" O ASN C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 893 through 904 removed outlier: 4.076A pdb=" N LEU C 897 " --> pdb=" O ASP C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 935 removed outlier: 3.612A pdb=" N GLY C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN C 926 " --> pdb=" O GLN C 922 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 930 " --> pdb=" O GLN C 926 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N CYS C 934 " --> pdb=" O ARG C 930 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 935 " --> pdb=" O VAL C 931 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 990 removed outlier: 3.548A pdb=" N TYR C 987 " --> pdb=" O GLU C 983 " (cutoff:3.500A) Processing helix chain 'C' and resid 1012 through 1033 removed outlier: 3.651A pdb=" N SER C1032 " --> pdb=" O ARG C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1049 Processing helix chain 'C' and resid 1060 through 1065 Processing helix chain 'C' and resid 1065 through 1076 removed outlier: 3.665A pdb=" N THR C1069 " --> pdb=" O GLN C1065 " (cutoff:3.500A) Processing helix chain 'C' and resid 1087 through 1094 removed outlier: 4.213A pdb=" N LEU C1093 " --> pdb=" O TRP C1089 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TRP C1094 " --> pdb=" O TYR C1090 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1120 removed outlier: 3.835A pdb=" N LEU C1114 " --> pdb=" O GLN C1110 " (cutoff:3.500A) Proline residue: C1115 - end of helix Processing helix chain 'D' and resid 3 through 13 removed outlier: 3.746A pdb=" N GLU D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA D 10 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL D 11 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 3.925A 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: 3.626A pdb=" N THR D 36 " --> pdb=" O HIS D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 62 removed outlier: 3.722A pdb=" N GLU D 62 " --> pdb=" O LEU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 72 Processing helix chain 'D' and resid 80 through 88 removed outlier: 3.657A pdb=" N SER D 88 " --> pdb=" O CYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 124 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: 3.592A pdb=" N GLN D 222 " --> pdb=" O LYS D 218 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU D 223 " --> pdb=" O ALA D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 233 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 284 Processing helix chain 'D' and resid 309 through 315 Processing helix chain 'D' and resid 316 through 320 Processing helix chain 'D' and resid 322 through 333 removed outlier: 3.674A 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 375 removed outlier: 4.035A pdb=" N ASN D 375 " --> pdb=" O ALA D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 387 removed outlier: 3.866A pdb=" N ALA D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS D 383 " --> pdb=" O LYS D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 415 removed outlier: 4.008A pdb=" N ALA D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 413 " --> pdb=" O GLU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 424 Processing helix chain 'D' and resid 427 through 436 removed outlier: 3.613A pdb=" N ILE D 431 " --> pdb=" O GLU D 427 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN D 436 " --> pdb=" O ILE D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 465 removed outlier: 4.047A pdb=" N GLU D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 465 " --> pdb=" O PHE D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 542 Processing helix chain 'D' and resid 562 through 572 removed outlier: 3.788A pdb=" N VAL D 566 " --> pdb=" O THR D 562 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 592 removed outlier: 3.788A pdb=" N ALA D 591 " --> pdb=" O SER D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 604 Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 7 removed outlier: 6.484A pdb=" N GLU B 6 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLY B 17 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU B 411 " --> pdb=" O GLY B 17 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARG B 19 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA B 381 " --> pdb=" O LEU B 410 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ILE B 412 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE B 383 " --> pdb=" O ILE B 412 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU B 60 " --> pdb=" O MET B 382 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL B 61 " --> pdb=" O PHE B 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 151 through 152 removed outlier: 6.944A pdb=" N GLN B 151 " --> pdb=" O LEU B 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 208 removed outlier: 6.556A pdb=" N VAL B 207 " --> pdb=" O LEU B 778 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 445 through 446 Processing sheet with id=AA5, first strand: chain 'B' and resid 487 through 490 Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 580 removed outlier: 6.835A pdb=" N ILE B 554 " --> pdb=" O GLN B 737 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL B 739 " --> pdb=" O ILE B 554 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N VAL B 556 " --> pdb=" O VAL B 739 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N SER B 814 " --> pdb=" O PRO B 750 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL B 752 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N GLY B 816 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU B 754 " --> pdb=" O GLY B 816 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 904 through 905 removed outlier: 9.903A pdb=" N ILE B1066 " --> pdb=" O TYR B1081 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N TYR B1081 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE B1070 " --> pdb=" O TYR B1077 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N TYR B1076 " --> pdb=" O GLY B1137 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N ILE B1139 " --> pdb=" O TYR B1076 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU B1078 " --> pdb=" O ILE B1139 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B1141 " --> pdb=" O LEU B1078 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ALA B1080 " --> pdb=" O LEU B1141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 904 through 905 removed outlier: 3.680A pdb=" N VAL B1058 " --> pdb=" O LEU B1031 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N GLY B1060 " --> pdb=" O GLU B1029 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N GLU B1029 " --> pdb=" O GLY B1060 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N LEU B1062 " --> pdb=" O ILE B1027 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE B1027 " --> pdb=" O LEU B1062 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLY B1064 " --> pdb=" O LEU B1025 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU B1025 " --> pdb=" O GLY B1064 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE B1066 " --> pdb=" O PHE B1023 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE B1023 " --> pdb=" O ILE B1066 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B1068 " --> pdb=" O MET B1021 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B1021 " --> pdb=" O LEU B1068 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N PHE B1070 " --> pdb=" O VAL B1019 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N VAL B1019 " --> pdb=" O PHE B1070 " (cutoff:3.500A) removed outlier: 10.488A pdb=" N HIS B1072 " --> pdb=" O LYS B1017 " (cutoff:3.500A) removed outlier: 11.253A pdb=" N LYS B1017 " --> pdb=" O HIS B1072 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 57 " --> pdb=" O TYR B1024 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AB1, first strand: chain 'C' and resid 60 through 61 removed outlier: 4.273A pdb=" N MET C 34 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C 211 " --> pdb=" O HIS C 237 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N LEU C 239 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE C 213 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N THR C 241 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU C 2 " --> pdb=" O GLN C 321 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU C 323 " --> pdb=" O LEU C 2 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N VAL C 4 " --> pdb=" O LEU C 323 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ALA C 325 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N HIS C 6 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 365 through 366 removed outlier: 6.158A pdb=" N ARG C 365 " --> pdb=" O TYR C 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 437 through 439 removed outlier: 6.306A pdb=" N ALA C 438 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N THR C 663 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE C 408 " --> pdb=" O ASN C 660 " (cutoff:3.500A) removed outlier: 8.285A pdb=" N CYS C 662 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL C 410 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N PHE C 672 " --> pdb=" O GLN C 724 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LYS C 726 " --> pdb=" O PHE C 672 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL C 674 " --> pdb=" O LYS C 726 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N TYR C 728 " --> pdb=" O VAL C 674 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS C 676 " --> pdb=" O TYR C 728 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N SER C 730 " --> pdb=" O CYS C 676 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU C 678 " --> pdb=" O SER C 730 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE C 732 " --> pdb=" O LEU C 678 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N THR C 375 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N TYR C 731 " --> pdb=" O THR C 375 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N HIS C 377 " --> pdb=" O TYR C 731 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 734 through 735 removed outlier: 3.699A pdb=" N SER C 740 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 831 through 833 removed outlier: 3.747A pdb=" N THR C 953 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN C 958 " --> pdb=" O GLN C 939 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLN C 939 " --> pdb=" O GLN C 958 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 963 through 967 removed outlier: 6.271A pdb=" N LEU C 964 " --> pdb=" O ARG C 997 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE C 999 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ARG C 966 " --> pdb=" O PHE C 999 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1050 through 1051 Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.193A pdb=" N SER D 92 " --> pdb=" O LEU D 102 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 237 through 239 removed outlier: 9.139A pdb=" N SER D 238 " --> pdb=" O ILE D 199 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU D 201 " --> pdb=" O SER D 238 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY D 296 " --> pdb=" O ILE D 169 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N CYS D 353 " --> pdb=" O ILE D 166 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL D 168 " --> pdb=" O CYS D 353 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LEU D 355 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N SER D 170 " --> pdb=" O LEU D 355 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 395 through 396 removed outlier: 7.544A pdb=" N PHE D 546 " --> pdb=" O ARG D 574 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ARG D 576 " --> pdb=" O PHE D 546 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N HIS D 548 " --> pdb=" O ARG D 576 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N SER D 578 " --> pdb=" O HIS D 548 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ALA D 550 " --> pdb=" O SER D 578 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TYR D 580 " --> pdb=" O ALA D 550 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ILE D 552 " --> pdb=" O TYR D 580 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N MET D 536 " --> pdb=" O TYR D 438 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU D 440 " --> pdb=" O MET D 536 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 519 through 522 removed outlier: 4.844A pdb=" N ALA D 513 " --> pdb=" O ILE D 498 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ILE D 498 " --> pdb=" O ALA D 513 " (cutoff:3.500A) 1025 hydrogen bonds defined for protein. 2976 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 34 stacking parallelities Total time for adding SS restraints: 5.83 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6316 1.33 - 1.45: 4644 1.45 - 1.57: 13368 1.57 - 1.69: 102 1.69 - 1.81: 171 Bond restraints: 24601 Sorted by residual: bond pdb=" C LYS C 259 " pdb=" N LEU C 260 " ideal model delta sigma weight residual 1.331 1.537 -0.207 1.48e-02 4.57e+03 1.95e+02 bond pdb=" C LEU C 260 " pdb=" N LEU C 261 " ideal model delta sigma weight residual 1.332 1.490 -0.158 1.52e-02 4.33e+03 1.09e+02 bond pdb=" C TYR D 359 " pdb=" N ARG D 360 " ideal model delta sigma weight residual 1.334 1.460 -0.126 1.27e-02 6.20e+03 9.82e+01 bond pdb=" O3A ANP B1501 " pdb=" PB ANP B1501 " ideal model delta sigma weight residual 1.700 1.547 0.153 2.00e-02 2.50e+03 5.89e+01 bond pdb=" O1B ANP B1501 " pdb=" PB ANP B1501 " ideal model delta sigma weight residual 1.501 1.378 0.123 2.00e-02 2.50e+03 3.80e+01 ... (remaining 24596 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 33059 3.28 - 6.56: 478 6.56 - 9.84: 53 9.84 - 13.12: 8 13.12 - 16.40: 5 Bond angle restraints: 33603 Sorted by residual: angle pdb=" N ILE B 738 " pdb=" CA ILE B 738 " pdb=" C ILE B 738 " ideal model delta sigma weight residual 107.75 91.35 16.40 1.46e+00 4.69e-01 1.26e+02 angle pdb=" N ILE B 738 " pdb=" CA ILE B 738 " pdb=" CB ILE B 738 " ideal model delta sigma weight residual 111.64 122.21 -10.57 1.30e+00 5.92e-01 6.61e+01 angle pdb=" N GLN C 688 " pdb=" CA GLN C 688 " pdb=" C GLN C 688 " ideal model delta sigma weight residual 108.41 119.44 -11.03 1.63e+00 3.76e-01 4.58e+01 angle pdb=" N GLN B 737 " pdb=" CA GLN B 737 " pdb=" C GLN B 737 " ideal model delta sigma weight residual 107.62 94.56 13.06 1.97e+00 2.58e-01 4.39e+01 angle pdb=" N GLN C 854 " pdb=" CA GLN C 854 " pdb=" C GLN C 854 " ideal model delta sigma weight residual 113.23 120.87 -7.64 1.22e+00 6.72e-01 3.92e+01 ... (remaining 33598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.82: 13767 16.82 - 33.65: 569 33.65 - 50.47: 260 50.47 - 67.29: 108 67.29 - 84.11: 33 Dihedral angle restraints: 14737 sinusoidal: 6364 harmonic: 8373 Sorted by residual: dihedral pdb=" CA SER B 720 " pdb=" C SER B 720 " pdb=" N ASN B 721 " pdb=" CA ASN B 721 " ideal model delta harmonic sigma weight residual -180.00 -144.28 -35.72 0 5.00e+00 4.00e-02 5.10e+01 dihedral pdb=" C GLN B 737 " pdb=" N GLN B 737 " pdb=" CA GLN B 737 " pdb=" CB GLN B 737 " ideal model delta harmonic sigma weight residual -122.60 -106.02 -16.58 0 2.50e+00 1.60e-01 4.40e+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 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 14734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 3476 0.101 - 0.202: 209 0.202 - 0.303: 7 0.303 - 0.404: 1 0.404 - 0.504: 1 Chirality restraints: 3694 Sorted by residual: chirality pdb=" CA GLN B 737 " pdb=" N GLN B 737 " pdb=" C GLN B 737 " pdb=" CB GLN B 737 " both_signs ideal model delta sigma weight residual False 2.51 3.01 -0.50 2.00e-01 2.50e+01 6.36e+00 chirality pdb=" CA GLN C 854 " pdb=" N GLN C 854 " pdb=" C GLN C 854 " pdb=" CB GLN C 854 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA GLN C 688 " pdb=" N GLN C 688 " pdb=" C GLN C 688 " pdb=" CB GLN C 688 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 ... (remaining 3691 not shown) Planarity restraints: 4238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS C 259 " 0.035 2.00e-02 2.50e+03 6.95e-02 4.83e+01 pdb=" C LYS C 259 " -0.120 2.00e-02 2.50e+03 pdb=" O LYS C 259 " 0.049 2.00e-02 2.50e+03 pdb=" N LEU C 260 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 260 " -0.028 2.00e-02 2.50e+03 5.09e-02 2.60e+01 pdb=" C LEU C 260 " 0.088 2.00e-02 2.50e+03 pdb=" O LEU C 260 " -0.033 2.00e-02 2.50e+03 pdb=" N LEU C 261 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS D 530 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C HIS D 530 " -0.050 2.00e-02 2.50e+03 pdb=" O HIS D 530 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU D 531 " 0.017 2.00e-02 2.50e+03 ... (remaining 4235 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 217 2.56 - 3.14: 21528 3.14 - 3.73: 36532 3.73 - 4.31: 51960 4.31 - 4.90: 83382 Nonbonded interactions: 193619 Sorted by model distance: nonbonded pdb=" OG1 THR B 30 " pdb="MG MG B1502 " model vdw 1.975 2.170 nonbonded pdb=" O HIS C1018 " pdb=" OG SER C1021 " model vdw 2.036 3.040 nonbonded pdb=" O GLY C 577 " pdb=" NH2 ARG C 582 " model vdw 2.098 3.120 nonbonded pdb=" OE1 GLU C 398 " pdb=" OH TYR C 802 " model vdw 2.099 3.040 nonbonded pdb=" NH2 ARG D 425 " pdb=" O ASP D 503 " model vdw 2.104 3.120 ... (remaining 193614 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 25.710 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 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 : 0.010 0.207 24602 Z= 0.502 Angle : 1.057 16.402 33606 Z= 0.639 Chirality : 0.053 0.504 3694 Planarity : 0.005 0.070 4237 Dihedral : 13.275 84.114 9308 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.73 % Favored : 94.03 % Rotamer: Outliers : 0.25 % Allowed : 1.24 % Favored : 98.52 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.86 (0.12), residues: 2847 helix: -3.31 (0.09), residues: 1369 sheet: -0.97 (0.28), residues: 270 loop : -1.78 (0.15), residues: 1208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 306 TYR 0.035 0.003 TYR B1111 PHE 0.034 0.003 PHE C 376 TRP 0.040 0.003 TRP B 598 HIS 0.018 0.003 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00956 / 0.50 (24601) covalent geometry : angle 1.05731 / 0.64 (33603) hydrogen bonds : bond 0.17210 / 11.53 ( 1068) hydrogen bonds : angle 9.68105 / 7.04 ( 3066) link_TRANS : bond 0.00303 / 0.16 ( 1) link_TRANS : angle 0.93974 / 0.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 371 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLU cc_start: 0.9067 (tp30) cc_final: 0.8824 (tm-30) REVERT: B 133 CYS cc_start: 0.8763 (m) cc_final: 0.8263 (p) REVERT: B 518 MET cc_start: 0.8906 (mmm) cc_final: 0.8635 (mmm) REVERT: B 589 GLU cc_start: 0.9507 (tt0) cc_final: 0.9273 (tm-30) REVERT: B 596 MET cc_start: 0.8841 (mmm) cc_final: 0.8611 (mmm) REVERT: B 793 GLU cc_start: 0.9654 (mt-10) cc_final: 0.9300 (mt-10) REVERT: B 1061 MET cc_start: 0.8405 (mmt) cc_final: 0.7717 (mmm) REVERT: B 1150 HIS cc_start: 0.8153 (m-70) cc_final: 0.7766 (m90) REVERT: C 34 MET cc_start: 0.8830 (mmt) cc_final: 0.8484 (mmt) REVERT: C 643 GLN cc_start: 0.9516 (tt0) cc_final: 0.9059 (tm-30) REVERT: C 781 THR cc_start: 0.9509 (m) cc_final: 0.9204 (p) REVERT: C 1031 MET cc_start: 0.9247 (mmp) cc_final: 0.8934 (mmm) REVERT: D 284 ASP cc_start: 0.9624 (m-30) cc_final: 0.9124 (p0) REVERT: D 359 TYR cc_start: 0.7794 (m-80) cc_final: 0.6830 (p90) REVERT: D 409 GLU cc_start: 0.9613 (mt-10) cc_final: 0.9394 (mm-30) outliers start: 6 outliers final: 1 residues processed: 376 average time/residue: 0.1911 time to fit residues: 109.6174 Evaluate side-chains 185 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 354 LEU 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: 7.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 134 GLN B 138 ASN B 150 GLN B 181 GLN B 262 GLN B 278 ASN ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 HIS B 458 ASN B 463 GLN B 484 ASN B 610 ASN B 695 GLN B 700 GLN ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 721 ASN B 848 GLN B 879 GLN C 8 ASN ** C 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 HIS C 510 ASN C 522 HIS C 660 ASN C 768 ASN C 920 GLN C 951 GLN C 979 GLN ** D 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 13 HIS D 22 GLN D 50 HIS D 473 HIS D 523 GLN D 548 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.064408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.050268 restraints weight = 96683.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.051979 restraints weight = 49972.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.053155 restraints weight = 32325.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.053931 restraints weight = 23933.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.054455 restraints weight = 19491.212| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24602 Z= 0.188 Angle : 0.765 10.027 33606 Z= 0.394 Chirality : 0.045 0.204 3694 Planarity : 0.005 0.057 4237 Dihedral : 14.836 74.842 3740 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 1.28 % Allowed : 7.34 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.38 (0.14), residues: 2847 helix: -0.70 (0.12), residues: 1418 sheet: -0.55 (0.27), residues: 297 loop : -1.10 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 947 TYR 0.032 0.002 TYR B1111 PHE 0.026 0.002 PHE C 73 TRP 0.033 0.002 TRP B 652 HIS 0.008 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.19 (24601) covalent geometry : angle 0.76499 / 0.39 (33603) hydrogen bonds : bond 0.05308 / 3.50 ( 1068) hydrogen bonds : angle 5.68183 / 4.20 ( 3066) link_TRANS : bond 0.00031 / 0.02 ( 1) link_TRANS : angle 0.15982 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 229 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.8986 (m) cc_final: 0.8168 (p) REVERT: B 499 MET cc_start: 0.8712 (tmm) cc_final: 0.7674 (tmm) REVERT: B 518 MET cc_start: 0.8774 (mmm) cc_final: 0.8166 (mmm) REVERT: B 589 GLU cc_start: 0.8589 (tt0) cc_final: 0.8125 (tm-30) REVERT: B 728 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.6279 (ptt180) REVERT: B 793 GLU cc_start: 0.8920 (mt-10) cc_final: 0.8675 (mt-10) REVERT: B 865 ILE cc_start: 0.9518 (mt) cc_final: 0.9210 (mt) REVERT: B 1061 MET cc_start: 0.8747 (mmt) cc_final: 0.8036 (mmp) REVERT: C 1 MET cc_start: 0.7288 (tmm) cc_final: 0.6547 (tmm) REVERT: C 91 MET cc_start: 0.9040 (mtp) cc_final: 0.8731 (mtp) REVERT: C 643 GLN cc_start: 0.9085 (tt0) cc_final: 0.8832 (tm-30) REVERT: C 697 MET cc_start: 0.8813 (mtm) cc_final: 0.8061 (mtm) REVERT: C 718 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8311 (mt-10) REVERT: C 781 THR cc_start: 0.9454 (m) cc_final: 0.8934 (p) REVERT: C 851 MET cc_start: 0.8520 (mmm) cc_final: 0.8221 (mmm) REVERT: C 906 ASP cc_start: 0.8921 (t0) cc_final: 0.8578 (p0) REVERT: C 978 MET cc_start: 0.8744 (tpp) cc_final: 0.8042 (tpp) REVERT: C 983 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: C 1031 MET cc_start: 0.9425 (mmp) cc_final: 0.9046 (mmm) REVERT: C 1079 MET cc_start: 0.8109 (ppp) cc_final: 0.7428 (ppp) REVERT: C 1080 MET cc_start: 0.7566 (mmm) cc_final: 0.7274 (mmm) REVERT: D 284 ASP cc_start: 0.9126 (m-30) cc_final: 0.8665 (p0) REVERT: D 359 TYR cc_start: 0.7671 (m-80) cc_final: 0.7039 (p90) REVERT: D 393 ILE cc_start: 0.8907 (tp) cc_final: 0.8648 (mp) REVERT: D 551 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8856 (tp) outliers start: 31 outliers final: 15 residues processed: 254 average time/residue: 0.1720 time to fit residues: 69.6743 Evaluate side-chains 185 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 318 GLU Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 738 ASP Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain C residue 983 GLU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 551 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 249 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 241 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 195 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 HIS B 404 GLN B 485 GLN ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 HIS C 768 ASN C 993 ASN D 4 GLN D 255 HIS D 256 HIS D 542 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.061923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.047820 restraints weight = 98666.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.049434 restraints weight = 52397.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.050493 restraints weight = 34512.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.051275 restraints weight = 26093.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.051781 restraints weight = 21393.953| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 24602 Z= 0.281 Angle : 0.752 10.237 33606 Z= 0.381 Chirality : 0.043 0.204 3694 Planarity : 0.005 0.058 4237 Dihedral : 14.504 71.756 3738 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.29 % Favored : 95.57 % Rotamer: Outliers : 1.57 % Allowed : 8.82 % Favored : 89.61 % 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: -0.59 (0.15), residues: 2847 helix: 0.25 (0.13), residues: 1419 sheet: -0.48 (0.27), residues: 312 loop : -1.10 (0.18), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 425 TYR 0.027 0.002 TYR B 648 PHE 0.021 0.002 PHE C 73 TRP 0.035 0.002 TRP B 652 HIS 0.013 0.002 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.28 (24601) covalent geometry : angle 0.75196 / 0.38 (33603) hydrogen bonds : bond 0.04956 / 3.29 ( 1068) hydrogen bonds : angle 5.32219 / 3.91 ( 3066) link_TRANS : bond 0.00114 / 0.06 ( 1) link_TRANS : angle 0.32001 / 0.18 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 167 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.9021 (m) cc_final: 0.8811 (m) REVERT: B 136 MET cc_start: 0.8482 (tpp) cc_final: 0.8217 (tpp) REVERT: B 146 MET cc_start: 0.8857 (mmm) cc_final: 0.8532 (mmm) REVERT: B 499 MET cc_start: 0.8643 (tmm) cc_final: 0.7651 (tmm) REVERT: B 518 MET cc_start: 0.8791 (mmm) cc_final: 0.8202 (mmm) REVERT: B 589 GLU cc_start: 0.8619 (tt0) cc_final: 0.8230 (tm-30) REVERT: B 658 MET cc_start: 0.9232 (tpp) cc_final: 0.8918 (tpp) REVERT: B 660 MET cc_start: 0.9119 (ppp) cc_final: 0.8863 (ppp) REVERT: B 728 ARG cc_start: 0.6652 (OUTLIER) cc_final: 0.6162 (ptt180) REVERT: B 793 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8623 (mt-10) REVERT: B 865 ILE cc_start: 0.9465 (mt) cc_final: 0.9030 (mt) REVERT: B 1061 MET cc_start: 0.8698 (mmt) cc_final: 0.8158 (mmm) REVERT: C 1 MET cc_start: 0.7320 (tmm) cc_final: 0.6729 (tmm) REVERT: C 91 MET cc_start: 0.9085 (mtp) cc_final: 0.8772 (mtp) REVERT: C 287 PHE cc_start: 0.8067 (t80) cc_final: 0.7325 (m-80) REVERT: C 643 GLN cc_start: 0.9144 (tt0) cc_final: 0.8864 (tm-30) REVERT: C 697 MET cc_start: 0.8772 (mtm) cc_final: 0.8361 (mtm) REVERT: C 718 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8388 (tp30) REVERT: C 781 THR cc_start: 0.9546 (m) cc_final: 0.9154 (p) REVERT: C 851 MET cc_start: 0.8524 (mmm) cc_final: 0.8197 (mmm) REVERT: C 978 MET cc_start: 0.8804 (tpp) cc_final: 0.8588 (tpp) REVERT: C 1031 MET cc_start: 0.9413 (mmp) cc_final: 0.8688 (mmm) REVERT: C 1079 MET cc_start: 0.8221 (ppp) cc_final: 0.7483 (ppp) REVERT: C 1080 MET cc_start: 0.7766 (mmm) cc_final: 0.7426 (mmm) REVERT: D 37 LEU cc_start: 0.9249 (tp) cc_final: 0.8939 (pp) REVERT: D 269 ASP cc_start: 0.8394 (t0) cc_final: 0.8146 (t0) REVERT: D 284 ASP cc_start: 0.9113 (m-30) cc_final: 0.8620 (p0) REVERT: D 359 TYR cc_start: 0.7642 (m-80) cc_final: 0.7440 (m-10) outliers start: 38 outliers final: 18 residues processed: 196 average time/residue: 0.1545 time to fit residues: 50.2458 Evaluate side-chains 161 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain B residue 1032 ILE Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 537 MET Chi-restraints excluded: chain C residue 647 GLN Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain D residue 188 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 5.9990 chunk 179 optimal weight: 0.0870 chunk 272 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 262 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 241 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 307 HIS B 404 GLN B 714 HIS B 721 ASN C 185 HIS ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.062970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.048864 restraints weight = 96897.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.050546 restraints weight = 50763.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051682 restraints weight = 33050.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.052443 restraints weight = 24638.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052965 restraints weight = 20165.393| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24602 Z= 0.153 Angle : 0.629 10.047 33606 Z= 0.325 Chirality : 0.041 0.165 3694 Planarity : 0.004 0.060 4237 Dihedral : 14.299 70.129 3738 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.69 % Favored : 96.21 % Rotamer: Outliers : 1.69 % Allowed : 9.44 % Favored : 88.87 % 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: -0.16 (0.15), residues: 2847 helix: 0.70 (0.13), residues: 1422 sheet: -0.23 (0.29), residues: 301 loop : -1.04 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 425 TYR 0.023 0.002 TYR B1111 PHE 0.027 0.002 PHE C 68 TRP 0.029 0.001 TRP B 652 HIS 0.006 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (24601) covalent geometry : angle 0.62855 / 0.33 (33603) hydrogen bonds : bond 0.04267 / 2.82 ( 1068) hydrogen bonds : angle 4.81006 / 3.54 ( 3066) link_TRANS : bond 0.00027 / 0.01 ( 1) link_TRANS : angle 0.17541 / 0.11 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 173 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 CYS cc_start: 0.8939 (m) cc_final: 0.8709 (m) REVERT: B 136 MET cc_start: 0.8480 (tpp) cc_final: 0.8260 (tpp) REVERT: B 146 MET cc_start: 0.8911 (mmm) cc_final: 0.8629 (mmm) REVERT: B 385 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8010 (mm-30) REVERT: B 499 MET cc_start: 0.8780 (tmm) cc_final: 0.7754 (tmm) REVERT: B 518 MET cc_start: 0.8778 (mmm) cc_final: 0.8246 (mmm) REVERT: B 589 GLU cc_start: 0.8627 (tt0) cc_final: 0.8146 (tm-30) REVERT: B 610 ASN cc_start: 0.8914 (t0) cc_final: 0.8613 (t0) REVERT: B 660 MET cc_start: 0.9070 (ppp) cc_final: 0.8809 (ppp) REVERT: B 728 ARG cc_start: 0.6535 (OUTLIER) cc_final: 0.6186 (ptt180) REVERT: B 865 ILE cc_start: 0.9508 (mt) cc_final: 0.9125 (mt) REVERT: B 1098 MET cc_start: 0.8255 (ptp) cc_final: 0.7895 (ptp) REVERT: B 1102 MET cc_start: 0.8855 (tpp) cc_final: 0.8535 (tpp) REVERT: C 1 MET cc_start: 0.7343 (tmm) cc_final: 0.7075 (tmm) REVERT: C 91 MET cc_start: 0.9031 (mtp) cc_final: 0.8719 (mtp) REVERT: C 287 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: C 606 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: C 643 GLN cc_start: 0.9236 (tt0) cc_final: 0.8966 (tm-30) REVERT: C 697 MET cc_start: 0.8807 (mtm) cc_final: 0.8390 (mtm) REVERT: C 718 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8240 (tp30) REVERT: C 781 THR cc_start: 0.9497 (m) cc_final: 0.9108 (p) REVERT: C 851 MET cc_start: 0.8544 (mmm) cc_final: 0.8257 (mmm) REVERT: C 978 MET cc_start: 0.8705 (tpp) cc_final: 0.8111 (tpp) REVERT: C 983 GLU cc_start: 0.8161 (pt0) cc_final: 0.7879 (pm20) REVERT: C 1031 MET cc_start: 0.9265 (mmp) cc_final: 0.9013 (mmp) REVERT: C 1079 MET cc_start: 0.8160 (ppp) cc_final: 0.7287 (ppp) REVERT: C 1080 MET cc_start: 0.7500 (mmm) cc_final: 0.7248 (mmm) REVERT: D 37 LEU cc_start: 0.9217 (tp) cc_final: 0.8903 (pp) REVERT: D 269 ASP cc_start: 0.8403 (t0) cc_final: 0.8132 (t0) REVERT: D 278 MET cc_start: 0.9033 (tpp) cc_final: 0.8692 (tpt) REVERT: D 284 ASP cc_start: 0.9041 (m-30) cc_final: 0.8586 (p0) REVERT: D 359 TYR cc_start: 0.7802 (m-80) cc_final: 0.7541 (m-10) outliers start: 41 outliers final: 18 residues processed: 202 average time/residue: 0.1479 time to fit residues: 50.4298 Evaluate side-chains 171 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 404 GLN Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 261 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 236 optimal weight: 9.9990 chunk 229 optimal weight: 20.0000 chunk 161 optimal weight: 5.9990 chunk 266 optimal weight: 0.3980 chunk 160 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 199 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 ASN B 261 ASN ** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 520 GLN B 562 GLN ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1078 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.062123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.048132 restraints weight = 97108.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.049726 restraints weight = 51330.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.050849 restraints weight = 33780.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051600 restraints weight = 25192.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.052114 restraints weight = 20616.805| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 24602 Z= 0.208 Angle : 0.646 9.844 33606 Z= 0.330 Chirality : 0.041 0.187 3694 Planarity : 0.004 0.061 4237 Dihedral : 14.131 69.496 3738 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.21 % Favored : 95.68 % Rotamer: Outliers : 1.81 % Allowed : 9.90 % Favored : 88.29 % 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: -0.02 (0.15), residues: 2847 helix: 0.87 (0.14), residues: 1431 sheet: -0.26 (0.29), residues: 289 loop : -1.04 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 425 TYR 0.021 0.002 TYR C 190 PHE 0.017 0.002 PHE C 376 TRP 0.030 0.001 TRP B 652 HIS 0.009 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.21 (24601) covalent geometry : angle 0.64590 / 0.33 (33603) hydrogen bonds : bond 0.04234 / 2.81 ( 1068) hydrogen bonds : angle 4.74321 / 3.47 ( 3066) link_TRANS : bond 0.00058 / 0.03 ( 1) link_TRANS : angle 0.20132 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.8943 (m) cc_final: 0.8205 (p) REVERT: B 136 MET cc_start: 0.8564 (tpp) cc_final: 0.8315 (tpp) REVERT: B 146 MET cc_start: 0.8912 (mmm) cc_final: 0.8644 (mmm) REVERT: B 385 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8076 (mm-30) REVERT: B 499 MET cc_start: 0.8775 (tmm) cc_final: 0.7734 (tmm) REVERT: B 518 MET cc_start: 0.8791 (mmm) cc_final: 0.8293 (mmm) REVERT: B 541 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7732 (mpp) REVERT: B 589 GLU cc_start: 0.8590 (tt0) cc_final: 0.8173 (tm-30) REVERT: B 596 MET cc_start: 0.8948 (mmm) cc_final: 0.8621 (ttm) REVERT: B 660 MET cc_start: 0.9148 (ppp) cc_final: 0.8904 (ppp) REVERT: B 727 MET cc_start: 0.8309 (mtt) cc_final: 0.8028 (mtt) REVERT: B 728 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.6176 (ptt180) REVERT: B 865 ILE cc_start: 0.9545 (mt) cc_final: 0.9252 (mt) REVERT: B 1102 MET cc_start: 0.8864 (tpp) cc_final: 0.8618 (tpp) REVERT: B 1168 MET cc_start: 0.9183 (ttm) cc_final: 0.8943 (ttm) REVERT: C 1 MET cc_start: 0.7404 (tmm) cc_final: 0.7106 (tmm) REVERT: C 72 MET cc_start: 0.8746 (mtp) cc_final: 0.8103 (mmp) REVERT: C 287 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7480 (m-80) REVERT: C 643 GLN cc_start: 0.9215 (tt0) cc_final: 0.8957 (tm-30) REVERT: C 697 MET cc_start: 0.8801 (mtm) cc_final: 0.8369 (mtm) REVERT: C 718 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8296 (tp30) REVERT: C 781 THR cc_start: 0.9475 (m) cc_final: 0.9101 (p) REVERT: C 851 MET cc_start: 0.8609 (mmm) cc_final: 0.8348 (mmm) REVERT: C 978 MET cc_start: 0.8717 (tpp) cc_final: 0.8126 (tpp) REVERT: C 1031 MET cc_start: 0.9277 (mmp) cc_final: 0.9006 (mmp) REVERT: C 1079 MET cc_start: 0.8152 (ppp) cc_final: 0.7251 (ppp) REVERT: C 1080 MET cc_start: 0.7505 (mmm) cc_final: 0.7293 (mmm) REVERT: D 37 LEU cc_start: 0.9240 (tp) cc_final: 0.8908 (pp) REVERT: D 269 ASP cc_start: 0.8507 (t0) cc_final: 0.8282 (t0) REVERT: D 278 MET cc_start: 0.9063 (tpp) cc_final: 0.8542 (tpp) REVERT: D 284 ASP cc_start: 0.9017 (m-30) cc_final: 0.8539 (p0) REVERT: D 359 TYR cc_start: 0.7875 (m-80) cc_final: 0.7631 (m-10) outliers start: 44 outliers final: 24 residues processed: 187 average time/residue: 0.1428 time to fit residues: 45.8098 Evaluate side-chains 171 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 431 MET Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 541 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 188 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 21 optimal weight: 20.0000 chunk 163 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 276 optimal weight: 10.0000 chunk 122 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 190 optimal weight: 0.4980 chunk 246 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 GLN ** C 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.063223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.049169 restraints weight = 96765.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.050842 restraints weight = 50825.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.051965 restraints weight = 33088.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.052667 restraints weight = 24698.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.053230 restraints weight = 20308.369| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24602 Z= 0.134 Angle : 0.593 9.252 33606 Z= 0.305 Chirality : 0.040 0.156 3694 Planarity : 0.004 0.063 4237 Dihedral : 13.953 73.977 3738 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 1.94 % Allowed : 10.52 % Favored : 87.55 % 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: 0.24 (0.15), residues: 2847 helix: 1.07 (0.14), residues: 1434 sheet: -0.10 (0.30), residues: 292 loop : -0.93 (0.18), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 396 TYR 0.022 0.001 TYR C 190 PHE 0.014 0.001 PHE B 461 TRP 0.027 0.001 TRP B 652 HIS 0.005 0.001 HIS C 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (24601) covalent geometry : angle 0.59279 / 0.30 (33603) hydrogen bonds : bond 0.03825 / 2.53 ( 1068) hydrogen bonds : angle 4.44800 / 3.26 ( 3066) link_TRANS : bond 0.00028 / 0.01 ( 1) link_TRANS : angle 0.13609 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 160 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 146 MET cc_start: 0.8918 (mmm) cc_final: 0.8638 (mmm) REVERT: B 307 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7581 (p90) REVERT: B 385 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7988 (mm-30) REVERT: B 389 THR cc_start: 0.9429 (m) cc_final: 0.8998 (p) REVERT: B 499 MET cc_start: 0.8726 (tmm) cc_final: 0.7621 (tmm) REVERT: B 518 MET cc_start: 0.8804 (mmm) cc_final: 0.8290 (mmm) REVERT: B 589 GLU cc_start: 0.8568 (tt0) cc_final: 0.8093 (tm-30) REVERT: B 660 MET cc_start: 0.9138 (ppp) cc_final: 0.8902 (ppp) REVERT: B 727 MET cc_start: 0.8256 (mtt) cc_final: 0.8001 (mtt) REVERT: B 728 ARG cc_start: 0.6552 (ttp-170) cc_final: 0.6216 (ptt180) REVERT: B 1168 MET cc_start: 0.9189 (ttm) cc_final: 0.8962 (ttm) REVERT: C 1 MET cc_start: 0.7376 (tmm) cc_final: 0.7065 (tmm) REVERT: C 72 MET cc_start: 0.8869 (mtp) cc_final: 0.8203 (mmp) REVERT: C 287 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: C 643 GLN cc_start: 0.9259 (tt0) cc_final: 0.8986 (tm-30) REVERT: C 697 MET cc_start: 0.8806 (mtm) cc_final: 0.8375 (mtm) REVERT: C 781 THR cc_start: 0.9463 (m) cc_final: 0.9093 (p) REVERT: C 851 MET cc_start: 0.8617 (mmm) cc_final: 0.8260 (mmm) REVERT: C 978 MET cc_start: 0.8679 (tpp) cc_final: 0.8413 (tpp) REVERT: C 1031 MET cc_start: 0.9178 (mmp) cc_final: 0.8886 (mmm) REVERT: D 37 LEU cc_start: 0.9208 (tp) cc_final: 0.8846 (pp) REVERT: D 261 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8539 (pp) REVERT: D 278 MET cc_start: 0.9036 (tpp) cc_final: 0.8676 (tpt) REVERT: D 284 ASP cc_start: 0.8967 (m-30) cc_final: 0.8505 (p0) REVERT: D 359 TYR cc_start: 0.7857 (m-80) cc_final: 0.7469 (m-10) outliers start: 47 outliers final: 22 residues processed: 196 average time/residue: 0.1361 time to fit residues: 45.9838 Evaluate side-chains 176 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 261 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 212 optimal weight: 8.9990 chunk 135 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 255 optimal weight: 7.9990 chunk 251 optimal weight: 0.4980 chunk 277 optimal weight: 0.2980 chunk 14 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** 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 = 0.3241 r_free = 0.3241 target = 0.062996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.048952 restraints weight = 97112.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.050611 restraints weight = 51037.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051730 restraints weight = 33291.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.052477 restraints weight = 24830.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.052878 restraints weight = 20334.340| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24602 Z= 0.143 Angle : 0.597 9.186 33606 Z= 0.305 Chirality : 0.039 0.155 3694 Planarity : 0.004 0.063 4237 Dihedral : 13.867 74.744 3738 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.00 % Favored : 95.89 % Rotamer: Outliers : 1.65 % Allowed : 11.18 % Favored : 87.18 % 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: 0.35 (0.16), residues: 2847 helix: 1.13 (0.14), residues: 1441 sheet: 0.01 (0.30), residues: 292 loop : -0.84 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 57 TYR 0.022 0.001 TYR D 580 PHE 0.015 0.001 PHE B 461 TRP 0.026 0.001 TRP B 652 HIS 0.009 0.001 HIS C 448 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (24601) covalent geometry : angle 0.59664 / 0.31 (33603) hydrogen bonds : bond 0.03833 / 2.52 ( 1068) hydrogen bonds : angle 4.41462 / 3.23 ( 3066) link_TRANS : bond 0.00032 / 0.02 ( 1) link_TRANS : angle 0.13139 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 157 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.8931 (m) cc_final: 0.8223 (p) REVERT: B 146 MET cc_start: 0.8900 (mmm) cc_final: 0.8653 (mmm) REVERT: B 307 HIS cc_start: 0.8353 (OUTLIER) cc_final: 0.7533 (p90) REVERT: B 385 GLU cc_start: 0.8375 (mm-30) cc_final: 0.8009 (mm-30) REVERT: B 389 THR cc_start: 0.9444 (m) cc_final: 0.9016 (p) REVERT: B 499 MET cc_start: 0.8518 (tmm) cc_final: 0.7505 (tmm) REVERT: B 518 MET cc_start: 0.8888 (mmm) cc_final: 0.8430 (mmm) REVERT: B 589 GLU cc_start: 0.8544 (tt0) cc_final: 0.8066 (tm-30) REVERT: B 660 MET cc_start: 0.9168 (ppp) cc_final: 0.8922 (ppp) REVERT: B 727 MET cc_start: 0.8169 (mtt) cc_final: 0.7916 (mtt) REVERT: B 728 ARG cc_start: 0.6598 (OUTLIER) cc_final: 0.6263 (ptt180) REVERT: B 832 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7857 (t70) REVERT: B 1098 MET cc_start: 0.8138 (ptp) cc_final: 0.7757 (ptp) REVERT: B 1102 MET cc_start: 0.9066 (tpp) cc_final: 0.8708 (tpp) REVERT: C 1 MET cc_start: 0.7367 (tmm) cc_final: 0.7065 (tmm) REVERT: C 72 MET cc_start: 0.8874 (mtp) cc_final: 0.8214 (mmp) REVERT: C 287 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7522 (m-80) REVERT: C 643 GLN cc_start: 0.9260 (tt0) cc_final: 0.8977 (tm-30) REVERT: C 680 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.9115 (mpp) REVERT: C 697 MET cc_start: 0.8798 (mtm) cc_final: 0.8353 (mtm) REVERT: C 781 THR cc_start: 0.9454 (m) cc_final: 0.9080 (p) REVERT: C 851 MET cc_start: 0.8653 (mmm) cc_final: 0.8298 (mmm) REVERT: C 978 MET cc_start: 0.8634 (tpp) cc_final: 0.8378 (tpp) REVERT: C 1031 MET cc_start: 0.9152 (mmp) cc_final: 0.8851 (mmm) REVERT: C 1079 MET cc_start: 0.7999 (ppp) cc_final: 0.6636 (ppp) REVERT: D 37 LEU cc_start: 0.9242 (tp) cc_final: 0.8904 (pp) REVERT: D 261 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8521 (pp) REVERT: D 278 MET cc_start: 0.9023 (tpp) cc_final: 0.8666 (tpt) REVERT: D 284 ASP cc_start: 0.8983 (m-30) cc_final: 0.8692 (p0) REVERT: D 359 TYR cc_start: 0.7968 (m-80) cc_final: 0.7608 (m-10) outliers start: 40 outliers final: 29 residues processed: 188 average time/residue: 0.1341 time to fit residues: 43.5473 Evaluate side-chains 182 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 261 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 290 optimal weight: 50.0000 chunk 199 optimal weight: 5.9990 chunk 283 optimal weight: 7.9990 chunk 285 optimal weight: 0.0170 chunk 242 optimal weight: 4.9990 chunk 280 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 36 optimal weight: 0.0170 chunk 157 optimal weight: 20.0000 overall best weight: 2.4062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** 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 = 0.3242 r_free = 0.3242 target = 0.062988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.048955 restraints weight = 96692.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.050623 restraints weight = 50960.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.051738 restraints weight = 33219.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.052434 restraints weight = 24802.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.052992 restraints weight = 20443.659| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24602 Z= 0.141 Angle : 0.595 8.449 33606 Z= 0.304 Chirality : 0.039 0.175 3694 Planarity : 0.004 0.064 4237 Dihedral : 13.798 76.606 3738 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 1.94 % Allowed : 11.26 % Favored : 86.80 % 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: 0.43 (0.16), residues: 2847 helix: 1.20 (0.14), residues: 1442 sheet: 0.09 (0.31), residues: 292 loop : -0.81 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1082 TYR 0.023 0.001 TYR C 190 PHE 0.015 0.001 PHE B 461 TRP 0.026 0.001 TRP B 652 HIS 0.006 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (24601) covalent geometry : angle 0.59515 / 0.30 (33603) hydrogen bonds : bond 0.03698 / 2.44 ( 1068) hydrogen bonds : angle 4.34430 / 3.17 ( 3066) link_TRANS : bond 0.00035 / 0.02 ( 1) link_TRANS : angle 0.12470 / 0.07 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 158 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.8924 (m) cc_final: 0.8234 (p) REVERT: B 146 MET cc_start: 0.8887 (mmm) cc_final: 0.8654 (mmm) REVERT: B 307 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7578 (p90) REVERT: B 385 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7996 (mm-30) REVERT: B 389 THR cc_start: 0.9465 (m) cc_final: 0.9050 (p) REVERT: B 499 MET cc_start: 0.8518 (tmm) cc_final: 0.7520 (tmm) REVERT: B 504 MET cc_start: 0.8306 (mmm) cc_final: 0.8078 (ttt) REVERT: B 518 MET cc_start: 0.8875 (mmm) cc_final: 0.8575 (mmm) REVERT: B 589 GLU cc_start: 0.8537 (tt0) cc_final: 0.8049 (tm-30) REVERT: B 595 GLU cc_start: 0.9230 (tp30) cc_final: 0.8957 (tp30) REVERT: B 660 MET cc_start: 0.9164 (ppp) cc_final: 0.8911 (ppp) REVERT: B 728 ARG cc_start: 0.6609 (OUTLIER) cc_final: 0.6267 (ptt180) REVERT: B 832 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7855 (t70) REVERT: B 1061 MET cc_start: 0.8499 (mmt) cc_final: 0.7845 (mmp) REVERT: B 1098 MET cc_start: 0.8119 (ptp) cc_final: 0.7748 (ptp) REVERT: B 1102 MET cc_start: 0.9051 (tpp) cc_final: 0.8727 (tpp) REVERT: B 1112 GLN cc_start: 0.9248 (mt0) cc_final: 0.8940 (mp10) REVERT: C 1 MET cc_start: 0.7312 (tmm) cc_final: 0.7039 (tmm) REVERT: C 72 MET cc_start: 0.8698 (mtp) cc_final: 0.8075 (mmp) REVERT: C 287 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: C 609 MET cc_start: 0.9375 (mmm) cc_final: 0.9155 (mmm) REVERT: C 643 GLN cc_start: 0.9245 (tt0) cc_final: 0.8956 (tm-30) REVERT: C 680 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.8928 (mpp) REVERT: C 697 MET cc_start: 0.8793 (mtm) cc_final: 0.8336 (mtm) REVERT: C 781 THR cc_start: 0.9456 (m) cc_final: 0.9070 (p) REVERT: C 851 MET cc_start: 0.8659 (mmm) cc_final: 0.8307 (mmm) REVERT: C 978 MET cc_start: 0.8610 (tpp) cc_final: 0.8350 (tpp) REVERT: C 1031 MET cc_start: 0.9159 (mmp) cc_final: 0.8854 (mmm) REVERT: D 37 LEU cc_start: 0.9230 (tp) cc_final: 0.8894 (pp) REVERT: D 261 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8497 (pp) REVERT: D 278 MET cc_start: 0.9036 (tpp) cc_final: 0.8683 (tpt) REVERT: D 284 ASP cc_start: 0.8978 (m-30) cc_final: 0.8704 (p0) REVERT: D 359 TYR cc_start: 0.7970 (m-80) cc_final: 0.7614 (m-10) outliers start: 47 outliers final: 32 residues processed: 194 average time/residue: 0.1394 time to fit residues: 46.8177 Evaluate side-chains 184 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 853 LEU Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 261 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 112 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 221 optimal weight: 10.0000 chunk 101 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 0.0470 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 GLN ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 531 GLN ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.061874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.047771 restraints weight = 98078.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.049368 restraints weight = 52319.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.050468 restraints weight = 34463.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.051197 restraints weight = 25920.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.051647 restraints weight = 21318.345| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 24602 Z= 0.225 Angle : 0.653 11.374 33606 Z= 0.328 Chirality : 0.040 0.155 3694 Planarity : 0.004 0.062 4237 Dihedral : 13.778 76.808 3738 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.29 % Rotamer: Outliers : 1.77 % Allowed : 11.88 % Favored : 86.35 % 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: 0.45 (0.16), residues: 2847 helix: 1.25 (0.14), residues: 1442 sheet: 0.10 (0.31), residues: 291 loop : -0.88 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 504 TYR 0.020 0.002 TYR D 580 PHE 0.019 0.002 PHE C 912 TRP 0.037 0.001 TRP B 652 HIS 0.009 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 (24601) covalent geometry : angle 0.65266 / 0.33 (33603) hydrogen bonds : bond 0.03936 / 2.60 ( 1068) hydrogen bonds : angle 4.46713 / 3.25 ( 3066) link_TRANS : bond 0.00088 / 0.05 ( 1) link_TRANS : angle 0.14909 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.8926 (m) cc_final: 0.8275 (p) REVERT: B 146 MET cc_start: 0.8883 (mmm) cc_final: 0.8658 (mmm) REVERT: B 307 HIS cc_start: 0.8402 (OUTLIER) cc_final: 0.7579 (p90) REVERT: B 385 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8014 (mm-30) REVERT: B 389 THR cc_start: 0.9519 (m) cc_final: 0.9147 (p) REVERT: B 499 MET cc_start: 0.8511 (tmm) cc_final: 0.7611 (tmm) REVERT: B 518 MET cc_start: 0.8940 (mmm) cc_final: 0.8400 (tpp) REVERT: B 589 GLU cc_start: 0.8544 (tt0) cc_final: 0.8164 (tm-30) REVERT: B 595 GLU cc_start: 0.9262 (tp30) cc_final: 0.8950 (tp30) REVERT: B 604 MET cc_start: 0.9258 (tpp) cc_final: 0.8594 (ttt) REVERT: B 660 MET cc_start: 0.9198 (ppp) cc_final: 0.8953 (ppp) REVERT: B 728 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.6437 (ptt180) REVERT: B 793 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8669 (mt-10) REVERT: B 832 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.7893 (t70) REVERT: B 1061 MET cc_start: 0.8576 (mmt) cc_final: 0.7923 (mmp) REVERT: B 1098 MET cc_start: 0.8121 (ptp) cc_final: 0.7748 (ptp) REVERT: B 1102 MET cc_start: 0.9038 (tpp) cc_final: 0.8741 (tpp) REVERT: C 1 MET cc_start: 0.7354 (tmm) cc_final: 0.7087 (tmm) REVERT: C 72 MET cc_start: 0.8701 (mtp) cc_final: 0.8016 (mmp) REVERT: C 287 PHE cc_start: 0.8351 (OUTLIER) cc_final: 0.7592 (m-80) REVERT: C 643 GLN cc_start: 0.9243 (tt0) cc_final: 0.8966 (tm-30) REVERT: C 680 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8735 (mpp) REVERT: C 697 MET cc_start: 0.8784 (mtm) cc_final: 0.8315 (mtm) REVERT: C 781 THR cc_start: 0.9456 (m) cc_final: 0.9092 (p) REVERT: C 851 MET cc_start: 0.8679 (mmm) cc_final: 0.8324 (mmm) REVERT: C 978 MET cc_start: 0.8685 (tpp) cc_final: 0.8027 (tpp) REVERT: C 1031 MET cc_start: 0.9294 (mmp) cc_final: 0.8927 (mmm) REVERT: D 37 LEU cc_start: 0.9236 (tp) cc_final: 0.8887 (pp) REVERT: D 278 MET cc_start: 0.9112 (tpp) cc_final: 0.8617 (tpp) REVERT: D 284 ASP cc_start: 0.9041 (m-30) cc_final: 0.8792 (p0) REVERT: D 359 TYR cc_start: 0.7964 (m-80) cc_final: 0.7594 (m-10) outliers start: 43 outliers final: 31 residues processed: 180 average time/residue: 0.1400 time to fit residues: 42.6547 Evaluate side-chains 176 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 500 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 236 optimal weight: 5.9990 chunk 217 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 258 optimal weight: 8.9990 chunk 96 optimal weight: 0.5980 chunk 90 optimal weight: 50.0000 chunk 264 optimal weight: 0.9990 chunk 235 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 229 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 8 ASN C 228 GLN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 793 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.063485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.049343 restraints weight = 96731.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.051007 restraints weight = 50875.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.052145 restraints weight = 33198.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052905 restraints weight = 24840.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.053428 restraints weight = 20325.680| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 24602 Z= 0.114 Angle : 0.608 12.889 33606 Z= 0.306 Chirality : 0.039 0.170 3694 Planarity : 0.004 0.064 4237 Dihedral : 13.696 78.978 3738 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.79 % Favored : 96.10 % Rotamer: Outliers : 1.32 % Allowed : 12.16 % Favored : 86.52 % 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: 0.55 (0.16), residues: 2847 helix: 1.27 (0.14), residues: 1447 sheet: 0.20 (0.31), residues: 293 loop : -0.74 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 252 TYR 0.024 0.002 TYR C 190 PHE 0.015 0.001 PHE C 193 TRP 0.029 0.001 TRP B 638 HIS 0.004 0.001 HIS C 563 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (24601) covalent geometry : angle 0.60782 / 0.31 (33603) hydrogen bonds : bond 0.03584 / 2.37 ( 1068) hydrogen bonds : angle 4.23555 / 3.09 ( 3066) link_TRANS : bond 0.00054 / 0.03 ( 1) link_TRANS : angle 0.14549 / 0.07 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5694 Ramachandran restraints generated. 2847 Oldfield, 0 Emsley, 2847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 133 CYS cc_start: 0.8864 (m) cc_final: 0.8228 (p) REVERT: B 146 MET cc_start: 0.8898 (mmm) cc_final: 0.8588 (mmm) REVERT: B 307 HIS cc_start: 0.8340 (OUTLIER) cc_final: 0.7602 (p90) REVERT: B 384 ASP cc_start: 0.8939 (t0) cc_final: 0.8509 (t0) REVERT: B 385 GLU cc_start: 0.8272 (mm-30) cc_final: 0.8008 (mm-30) REVERT: B 389 THR cc_start: 0.9475 (m) cc_final: 0.9087 (p) REVERT: B 499 MET cc_start: 0.8494 (tmm) cc_final: 0.7598 (tmm) REVERT: B 518 MET cc_start: 0.8922 (mmm) cc_final: 0.8685 (tpp) REVERT: B 589 GLU cc_start: 0.8537 (tt0) cc_final: 0.8078 (tm-30) REVERT: B 595 GLU cc_start: 0.9247 (tp30) cc_final: 0.8611 (tp30) REVERT: B 604 MET cc_start: 0.9239 (tpp) cc_final: 0.8514 (ttt) REVERT: B 660 MET cc_start: 0.9150 (ppp) cc_final: 0.8916 (ppp) REVERT: B 728 ARG cc_start: 0.6736 (OUTLIER) cc_final: 0.6395 (ptt180) REVERT: B 832 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.7889 (t70) REVERT: B 1061 MET cc_start: 0.8468 (mmt) cc_final: 0.7814 (mmp) REVERT: B 1086 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.6925 (pt) REVERT: B 1098 MET cc_start: 0.8142 (ptp) cc_final: 0.7763 (ptp) REVERT: B 1102 MET cc_start: 0.8981 (tpp) cc_final: 0.8720 (tpp) REVERT: B 1112 GLN cc_start: 0.9250 (mt0) cc_final: 0.8995 (mp10) REVERT: C 1 MET cc_start: 0.7305 (tmm) cc_final: 0.7022 (tmm) REVERT: C 72 MET cc_start: 0.8756 (mtp) cc_final: 0.8130 (mmp) REVERT: C 287 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7515 (m-80) REVERT: C 594 MET cc_start: 0.9038 (tpp) cc_final: 0.8788 (mmm) REVERT: C 643 GLN cc_start: 0.9269 (tt0) cc_final: 0.8996 (tm-30) REVERT: C 680 MET cc_start: 0.9063 (mpp) cc_final: 0.8558 (mpp) REVERT: C 697 MET cc_start: 0.8795 (mtm) cc_final: 0.8323 (mtm) REVERT: C 781 THR cc_start: 0.9446 (m) cc_final: 0.9088 (p) REVERT: C 851 MET cc_start: 0.8643 (mmm) cc_final: 0.8298 (mmm) REVERT: C 978 MET cc_start: 0.8630 (tpp) cc_final: 0.8363 (tpp) REVERT: C 1031 MET cc_start: 0.9140 (mmp) cc_final: 0.8825 (mmm) REVERT: D 278 MET cc_start: 0.9037 (tpp) cc_final: 0.8597 (tpp) REVERT: D 284 ASP cc_start: 0.8965 (m-30) cc_final: 0.8690 (p0) REVERT: D 359 TYR cc_start: 0.7968 (m-80) cc_final: 0.7610 (m-10) outliers start: 32 outliers final: 25 residues processed: 183 average time/residue: 0.1426 time to fit residues: 44.2985 Evaluate side-chains 178 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 187 TRP Chi-restraints excluded: chain B residue 304 THR Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 354 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1094 THR Chi-restraints excluded: chain B residue 1116 LEU Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 474 LEU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 879 GLN Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 236 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 149 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 chunk 253 optimal weight: 0.3980 chunk 219 optimal weight: 10.0000 chunk 136 optimal weight: 0.2980 chunk 79 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 216 optimal weight: 6.9990 chunk 184 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 233 HIS ** 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 = 0.3263 r_free = 0.3263 target = 0.063870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.049726 restraints weight = 96116.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.051404 restraints weight = 50776.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.052522 restraints weight = 33213.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.053266 restraints weight = 24854.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053794 restraints weight = 20390.332| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24602 Z= 0.115 Angle : 0.606 12.733 33606 Z= 0.301 Chirality : 0.039 0.171 3694 Planarity : 0.004 0.067 4237 Dihedral : 13.605 78.647 3738 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.93 % Favored : 95.96 % Rotamer: Outliers : 1.36 % Allowed : 12.41 % Favored : 86.23 % 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: 0.64 (0.16), residues: 2847 helix: 1.35 (0.14), residues: 1443 sheet: 0.31 (0.31), residues: 289 loop : -0.73 (0.19), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 252 TYR 0.024 0.001 TYR C 190 PHE 0.014 0.001 PHE D 386 TRP 0.027 0.001 TRP B 652 HIS 0.004 0.001 HIS C 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (24601) covalent geometry : angle 0.60565 / 0.30 (33603) hydrogen bonds : bond 0.03496 / 2.31 ( 1068) hydrogen bonds : angle 4.18394 / 3.05 ( 3066) link_TRANS : bond 0.00176 / 0.09 ( 1) link_TRANS : angle 0.60463 / 0.30 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3405.78 seconds wall clock time: 59 minutes 58.47 seconds (3598.47 seconds total)