Starting phenix.real_space_refine on Fri Sep 19 06:52:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ld2_4038/09_2025/5ld2_4038_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ld2_4038/09_2025/5ld2_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_2025/5ld2_4038_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ld2_4038/09_2025/5ld2_4038_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ld2_4038/09_2025/5ld2_4038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ld2_4038/09_2025/5ld2_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-2.0-5805/lib/python3.9/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: 5.22, per 1000 atoms: 0.22 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: 1.63 Conformation dependent library (CDL) restraints added in 934.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 2.37 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: 3.90 Time building geometry restraints manager: 2.20 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: 33063 3.28 - 6.56: 474 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: 3492 0.101 - 0.202: 194 0.202 - 0.303: 6 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: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.030 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 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= 0.465 Angle : 1.047 16.402 33606 Z= 0.601 Chirality : 0.052 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 aren 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 covalent geometry : bond 0.00951 (24601) covalent geometry : angle 1.04674 (33603) hydrogen bonds : bond 0.17210 ( 1068) hydrogen bonds : angle 9.68105 ( 3066) link_TRANS : bond 0.00303 ( 1) link_TRANS : angle 0.93974 ( 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 : 0.940 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: 0.1755 time to fit residues: 99.6253 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 : 0.858 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 138 ASN 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 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 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 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 = 0.3277 r_free = 0.3277 target = 0.064519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.050585 restraints weight = 96350.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.052259 restraints weight = 49915.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.053417 restraints weight = 32305.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.054193 restraints weight = 23956.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.054587 restraints weight = 19501.835| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2388 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= 0.175 Angle : 0.720 9.638 33606 Z= 0.370 Chirality : 0.042 0.220 3694 Planarity : 0.005 0.048 4237 Dihedral : 14.606 77.920 3740 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.16 % Favored : 96.73 % Rotamer: Outliers : 1.07 % Allowed : 7.51 % Favored : 91.42 % 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 aren not related in a simple way. whole: -1.20 (0.14), residues: 2847 helix: -0.47 (0.13), residues: 1407 sheet: -0.49 (0.27), residues: 297 loop : -1.12 (0.17), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 425 TYR 0.030 0.002 TYR B1111 PHE 0.029 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 covalent geometry : bond 0.00383 (24601) covalent geometry : angle 0.71958 (33603) hydrogen bonds : bond 0.04827 ( 1068) hydrogen bonds : angle 5.39475 ( 3066) link_TRANS : bond 0.00017 ( 1) link_TRANS : angle 0.13363 ( 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 262 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.976 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 37 TYR cc_start: 0.9168 (t80) cc_final: 0.8951 (t80) REVERT: B 133 CYS cc_start: 0.8944 (m) cc_final: 0.8172 (p) REVERT: B 384 ASP cc_start: 0.9059 (t0) cc_final: 0.8567 (t0) REVERT: B 385 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7896 (mm-30) REVERT: B 499 MET cc_start: 0.8635 (tmm) cc_final: 0.7643 (tmm) REVERT: B 518 MET cc_start: 0.8779 (mmm) cc_final: 0.8201 (mmm) REVERT: B 589 GLU cc_start: 0.8584 (tt0) cc_final: 0.8132 (tm-30) REVERT: B 610 ASN cc_start: 0.9037 (t0) cc_final: 0.8770 (t0) REVERT: B 728 ARG cc_start: 0.6463 (OUTLIER) cc_final: 0.6161 (ptt180) REVERT: B 793 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8625 (mt-10) REVERT: B 865 ILE cc_start: 0.9528 (mt) cc_final: 0.9284 (mt) REVERT: B 1061 MET cc_start: 0.8714 (mmt) cc_final: 0.8093 (mmt) REVERT: C 1 MET cc_start: 0.7187 (tmm) cc_final: 0.6895 (tmm) REVERT: C 91 MET cc_start: 0.9060 (mtp) cc_final: 0.8745 (mtp) REVERT: C 516 LEU cc_start: 0.9356 (mt) cc_final: 0.9118 (mp) REVERT: C 643 GLN cc_start: 0.9189 (tt0) cc_final: 0.8952 (tm-30) REVERT: C 718 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8299 (mt-10) REVERT: C 781 THR cc_start: 0.9439 (m) cc_final: 0.8911 (p) REVERT: C 851 MET cc_start: 0.8521 (mmm) cc_final: 0.8229 (mmm) REVERT: C 879 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8716 (mp10) REVERT: C 978 MET cc_start: 0.8760 (tpp) cc_final: 0.8047 (tpp) REVERT: C 983 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7991 (pm20) REVERT: C 1031 MET cc_start: 0.9355 (mmp) cc_final: 0.9039 (mmm) REVERT: C 1079 MET cc_start: 0.8175 (ppp) cc_final: 0.7306 (ppp) REVERT: C 1080 MET cc_start: 0.7665 (mmm) cc_final: 0.7377 (mmm) REVERT: D 284 ASP cc_start: 0.9086 (m-30) cc_final: 0.8678 (p0) REVERT: D 359 TYR cc_start: 0.7688 (m-80) cc_final: 0.7488 (m-10) REVERT: D 393 ILE cc_start: 0.8898 (tp) cc_final: 0.8642 (mp) REVERT: D 551 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8841 (tp) outliers start: 26 outliers final: 9 residues processed: 257 average time/residue: 0.1541 time to fit residues: 62.1493 Evaluate side-chains 182 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 169 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 C residue 8 ASN 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 551 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 249 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 241 optimal weight: 9.9990 chunk 162 optimal weight: 9.9990 chunk 49 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 284 optimal weight: 20.0000 chunk 56 optimal weight: 0.0870 chunk 195 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 overall best weight: 6.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 HIS B 610 ASN ** B 714 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 768 ASN C 792 GLN C 793 ASN C 993 ASN C1078 ASN D 255 HIS ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.061678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.047532 restraints weight = 98649.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.049138 restraints weight = 52530.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.050237 restraints weight = 34721.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.050968 restraints weight = 26140.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.051469 restraints weight = 21503.651| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 24602 Z= 0.294 Angle : 0.730 9.518 33606 Z= 0.372 Chirality : 0.042 0.169 3694 Planarity : 0.005 0.059 4237 Dihedral : 14.265 75.020 3738 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.39 % Favored : 95.50 % Rotamer: Outliers : 1.81 % Allowed : 8.62 % Favored : 89.57 % 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 aren not related in a simple way. whole: -0.41 (0.15), residues: 2847 helix: 0.46 (0.13), residues: 1424 sheet: -0.44 (0.27), residues: 301 loop : -1.09 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 425 TYR 0.023 0.002 TYR B1111 PHE 0.022 0.002 PHE C 912 TRP 0.037 0.002 TRP B 652 HIS 0.012 0.002 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00644 (24601) covalent geometry : angle 0.72986 (33603) hydrogen bonds : bond 0.04698 ( 1068) hydrogen bonds : angle 5.13262 ( 3066) link_TRANS : bond 0.00100 ( 1) link_TRANS : angle 0.29759 ( 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 213 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 169 time to evaluate : 0.722 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: B 136 MET cc_start: 0.8561 (tpp) cc_final: 0.8337 (tpp) REVERT: B 499 MET cc_start: 0.8754 (tmm) cc_final: 0.7751 (tmm) REVERT: B 518 MET cc_start: 0.8805 (mmm) cc_final: 0.8317 (mmm) REVERT: B 589 GLU cc_start: 0.8603 (tt0) cc_final: 0.8190 (tm-30) REVERT: B 604 MET cc_start: 0.9287 (tpp) cc_final: 0.8597 (ttt) REVERT: B 728 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.6290 (ptt180) REVERT: B 793 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8624 (mt-10) REVERT: B 865 ILE cc_start: 0.9505 (mt) cc_final: 0.9140 (mt) REVERT: B 1086 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.6979 (pt) REVERT: C 1 MET cc_start: 0.7424 (tmm) cc_final: 0.6866 (tmm) REVERT: C 91 MET cc_start: 0.9111 (mtp) cc_final: 0.8807 (mtp) REVERT: C 189 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9204 (mt) REVERT: C 287 PHE cc_start: 0.8159 (t80) cc_final: 0.7415 (m-80) REVERT: C 697 MET cc_start: 0.8823 (mtm) cc_final: 0.8338 (mtm) REVERT: C 718 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8317 (tp30) REVERT: C 781 THR cc_start: 0.9508 (m) cc_final: 0.9135 (p) REVERT: C 851 MET cc_start: 0.8561 (mmm) cc_final: 0.8230 (mmm) REVERT: C 978 MET cc_start: 0.8740 (tpp) cc_final: 0.8163 (tpp) REVERT: C 1031 MET cc_start: 0.9393 (mmp) cc_final: 0.8650 (mmm) REVERT: C 1079 MET cc_start: 0.8197 (ppp) cc_final: 0.7443 (ppp) REVERT: C 1080 MET cc_start: 0.7693 (mmm) cc_final: 0.7417 (mmm) REVERT: D 37 LEU cc_start: 0.9261 (tp) cc_final: 0.8940 (pp) REVERT: D 284 ASP cc_start: 0.9100 (m-30) cc_final: 0.8626 (p0) REVERT: D 359 TYR cc_start: 0.7877 (m-80) cc_final: 0.7636 (m-10) outliers start: 44 outliers final: 21 residues processed: 203 average time/residue: 0.1432 time to fit residues: 48.3931 Evaluate side-chains 167 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 82 GLU Chi-restraints excluded: chain B residue 87 CYS 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 282 LEU Chi-restraints excluded: chain B residue 431 MET 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 729 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 189 LEU 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 879 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 272 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 262 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 404 GLN B 562 GLN B 714 HIS 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** ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.062068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.047826 restraints weight = 97787.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.049495 restraints weight = 51032.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.050611 restraints weight = 33258.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.051370 restraints weight = 24924.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.051834 restraints weight = 20375.431| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24602 Z= 0.206 Angle : 0.636 9.592 33606 Z= 0.325 Chirality : 0.040 0.179 3694 Planarity : 0.004 0.060 4237 Dihedral : 14.096 74.191 3738 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.97 % Favored : 95.96 % Rotamer: Outliers : 1.81 % Allowed : 9.28 % Favored : 88.91 % 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 aren not related in a simple way. whole: -0.01 (0.15), residues: 2847 helix: 0.88 (0.14), residues: 1423 sheet: -0.31 (0.28), residues: 301 loop : -1.01 (0.18), residues: 1123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 425 TYR 0.021 0.002 TYR B1111 PHE 0.018 0.002 PHE C 68 TRP 0.033 0.001 TRP B 652 HIS 0.009 0.001 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00457 (24601) covalent geometry : angle 0.63631 (33603) hydrogen bonds : bond 0.04168 ( 1068) hydrogen bonds : angle 4.74212 ( 3066) link_TRANS : bond 0.00054 ( 1) link_TRANS : angle 0.19396 ( 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 205 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.730 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: B 136 MET cc_start: 0.8555 (tpp) cc_final: 0.8338 (tpp) REVERT: B 146 MET cc_start: 0.8705 (mmm) cc_final: 0.8414 (mmm) REVERT: B 385 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8082 (mm-30) REVERT: B 499 MET cc_start: 0.8803 (tmm) cc_final: 0.7642 (tmm) REVERT: B 518 MET cc_start: 0.8752 (mmm) cc_final: 0.8225 (mmm) REVERT: B 589 GLU cc_start: 0.8605 (tt0) cc_final: 0.8162 (tm-30) REVERT: B 604 MET cc_start: 0.9269 (tpp) cc_final: 0.8531 (ttt) REVERT: B 728 ARG cc_start: 0.6632 (OUTLIER) cc_final: 0.6270 (ptt180) REVERT: B 793 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8619 (mt-10) REVERT: B 865 ILE cc_start: 0.9543 (mt) cc_final: 0.9074 (mt) REVERT: C 1 MET cc_start: 0.7437 (tmm) cc_final: 0.6901 (tmm) REVERT: C 91 MET cc_start: 0.9062 (mtp) cc_final: 0.8816 (mtp) REVERT: C 189 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9231 (mt) REVERT: C 287 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7472 (m-80) REVERT: C 650 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8852 (tt) REVERT: C 697 MET cc_start: 0.8806 (mtm) cc_final: 0.8294 (mtm) REVERT: C 718 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8320 (tp30) REVERT: C 781 THR cc_start: 0.9512 (m) cc_final: 0.9164 (p) REVERT: C 851 MET cc_start: 0.8632 (mmm) cc_final: 0.8339 (mmm) REVERT: C 978 MET cc_start: 0.8691 (tpp) cc_final: 0.8098 (tpp) REVERT: C 1031 MET cc_start: 0.9312 (mmp) cc_final: 0.9083 (mmp) REVERT: C 1079 MET cc_start: 0.8170 (ppp) cc_final: 0.7350 (ppp) REVERT: D 261 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8565 (pp) REVERT: D 284 ASP cc_start: 0.9071 (m-30) cc_final: 0.8577 (p0) REVERT: D 359 TYR cc_start: 0.7884 (m-80) cc_final: 0.7475 (m-10) outliers start: 44 outliers final: 25 residues processed: 197 average time/residue: 0.1358 time to fit residues: 45.1163 Evaluate side-chains 172 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 142 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 82 GLU 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 453 MET 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 813 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 906 TYR Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 106 GLU Chi-restraints excluded: chain C residue 189 LEU 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 533 LEU Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 650 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 236 optimal weight: 7.9990 chunk 229 optimal weight: 9.9990 chunk 161 optimal weight: 0.9990 chunk 266 optimal weight: 0.6980 chunk 160 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 125 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 843 GLN C 185 HIS C 228 GLN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 GLN ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.062795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.048620 restraints weight = 96655.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.050274 restraints weight = 50997.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.051408 restraints weight = 33447.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.052159 restraints weight = 24967.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.052673 restraints weight = 20459.315| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24602 Z= 0.146 Angle : 0.591 9.778 33606 Z= 0.300 Chirality : 0.039 0.156 3694 Planarity : 0.004 0.065 4237 Dihedral : 13.879 77.782 3738 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.07 % Favored : 95.82 % Rotamer: Outliers : 2.06 % Allowed : 9.65 % 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 aren not related in a simple way. whole: 0.34 (0.16), residues: 2847 helix: 1.17 (0.14), residues: 1435 sheet: -0.15 (0.29), residues: 302 loop : -0.86 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 396 TYR 0.022 0.001 TYR B1111 PHE 0.016 0.001 PHE B 461 TRP 0.029 0.001 TRP B 652 HIS 0.006 0.001 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00321 (24601) covalent geometry : angle 0.59097 (33603) hydrogen bonds : bond 0.03781 ( 1068) hydrogen bonds : angle 4.45554 ( 3066) link_TRANS : bond 0.00045 ( 1) link_TRANS : angle 0.17194 ( 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 220 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 170 time to evaluate : 0.852 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: B 133 CYS cc_start: 0.8974 (m) cc_final: 0.8237 (p) REVERT: B 146 MET cc_start: 0.8826 (mmm) cc_final: 0.8585 (mmm) REVERT: B 307 HIS cc_start: 0.8447 (OUTLIER) cc_final: 0.7565 (p90) REVERT: B 385 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8027 (mm-30) REVERT: B 499 MET cc_start: 0.8832 (tmm) cc_final: 0.7730 (tmm) REVERT: B 518 MET cc_start: 0.8730 (mmm) cc_final: 0.8191 (mmm) REVERT: B 589 GLU cc_start: 0.8546 (tt0) cc_final: 0.8077 (tm-30) REVERT: B 604 MET cc_start: 0.9260 (tpp) cc_final: 0.8567 (ttt) REVERT: B 728 ARG cc_start: 0.6779 (ttp-170) cc_final: 0.6422 (ptt180) REVERT: B 1086 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.6999 (pt) REVERT: B 1098 MET cc_start: 0.8165 (ptp) cc_final: 0.7777 (ptp) REVERT: C 1 MET cc_start: 0.7406 (tmm) cc_final: 0.7136 (tmm) REVERT: C 72 MET cc_start: 0.8830 (mtp) cc_final: 0.8235 (mmp) REVERT: C 91 MET cc_start: 0.8994 (mtp) cc_final: 0.8747 (mtp) REVERT: C 287 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: C 396 MET cc_start: 0.9169 (mmm) cc_final: 0.8957 (mtt) REVERT: C 650 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8818 (tt) REVERT: C 781 THR cc_start: 0.9478 (m) cc_final: 0.9090 (p) REVERT: C 851 MET cc_start: 0.8594 (mmm) cc_final: 0.8159 (mmm) REVERT: C 978 MET cc_start: 0.8623 (tpp) cc_final: 0.8404 (tpp) REVERT: C 983 GLU cc_start: 0.8337 (pt0) cc_final: 0.8034 (pm20) REVERT: C 1031 MET cc_start: 0.9166 (mmp) cc_final: 0.8854 (mmm) REVERT: C 1079 MET cc_start: 0.8129 (ppp) cc_final: 0.7431 (pmm) REVERT: D 191 MET cc_start: 0.8709 (tpp) cc_final: 0.8474 (tpp) REVERT: D 261 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8753 (pp) REVERT: D 284 ASP cc_start: 0.9005 (m-30) cc_final: 0.8674 (p0) REVERT: D 359 TYR cc_start: 0.7961 (m-80) cc_final: 0.7591 (m-10) outliers start: 50 outliers final: 24 residues processed: 207 average time/residue: 0.1390 time to fit residues: 48.5529 Evaluate side-chains 182 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 153 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 56 VAL Chi-restraints excluded: chain B residue 82 GLU 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 453 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 715 ILE Chi-restraints excluded: chain B residue 721 ASN Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain B residue 813 CYS Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 34 MET 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 533 LEU Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 261 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: 10.0000 chunk 104 optimal weight: 8.9990 chunk 276 optimal weight: 10.0000 chunk 122 optimal weight: 0.2980 chunk 215 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 103 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN B 258 ASN B 261 ASN B 531 GLN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.061629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.047550 restraints weight = 98294.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.049154 restraints weight = 52348.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.050242 restraints weight = 34500.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.050947 restraints weight = 25934.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.051469 restraints weight = 21361.641| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 24602 Z= 0.237 Angle : 0.651 13.753 33606 Z= 0.327 Chirality : 0.040 0.156 3694 Planarity : 0.004 0.062 4237 Dihedral : 13.821 79.117 3738 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.99 % Favored : 94.91 % Rotamer: Outliers : 1.65 % Allowed : 11.13 % Favored : 87.22 % 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 aren not related in a simple way. whole: 0.32 (0.16), residues: 2847 helix: 1.16 (0.14), residues: 1444 sheet: -0.05 (0.30), residues: 292 loop : -0.93 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 425 TYR 0.021 0.002 TYR B 648 PHE 0.019 0.002 PHE C 912 TRP 0.034 0.001 TRP B 652 HIS 0.010 0.001 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00524 (24601) covalent geometry : angle 0.65100 (33603) hydrogen bonds : bond 0.03999 ( 1068) hydrogen bonds : angle 4.56992 ( 3066) link_TRANS : bond 0.00113 ( 1) link_TRANS : angle 0.23074 ( 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 196 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.964 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: B 133 CYS cc_start: 0.8985 (m) cc_final: 0.8296 (p) REVERT: B 146 MET cc_start: 0.8889 (mmm) cc_final: 0.8660 (mmm) REVERT: B 307 HIS cc_start: 0.8383 (OUTLIER) cc_final: 0.7406 (p90) REVERT: B 384 ASP cc_start: 0.8879 (t0) cc_final: 0.8490 (t0) REVERT: B 385 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8099 (mm-30) REVERT: B 499 MET cc_start: 0.8903 (tmm) cc_final: 0.7751 (tmm) REVERT: B 518 MET cc_start: 0.8772 (mmm) cc_final: 0.8398 (tpp) REVERT: B 589 GLU cc_start: 0.8542 (tt0) cc_final: 0.8152 (tm-30) REVERT: B 596 MET cc_start: 0.9031 (mmm) cc_final: 0.8476 (mtm) REVERT: B 604 MET cc_start: 0.9170 (tpp) cc_final: 0.8512 (ttt) REVERT: B 660 MET cc_start: 0.9156 (ppp) cc_final: 0.8927 (ppp) REVERT: B 728 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6233 (ptt180) REVERT: B 832 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7945 (t70) REVERT: C 1 MET cc_start: 0.7448 (tmm) cc_final: 0.7159 (tmm) REVERT: C 72 MET cc_start: 0.8857 (mtp) cc_final: 0.8253 (mmp) REVERT: C 189 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9231 (mt) REVERT: C 287 PHE cc_start: 0.8220 (OUTLIER) cc_final: 0.7458 (m-80) REVERT: C 396 MET cc_start: 0.9180 (mmm) cc_final: 0.8897 (mtt) REVERT: C 650 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8916 (tt) REVERT: C 781 THR cc_start: 0.9457 (m) cc_final: 0.9094 (p) REVERT: C 851 MET cc_start: 0.8649 (mmm) cc_final: 0.8286 (mmm) REVERT: C 978 MET cc_start: 0.8711 (tpp) cc_final: 0.8490 (tpp) REVERT: C 983 GLU cc_start: 0.8300 (pt0) cc_final: 0.8025 (pm20) REVERT: C 1031 MET cc_start: 0.9299 (mmp) cc_final: 0.8373 (mmm) REVERT: D 261 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8858 (pp) REVERT: D 284 ASP cc_start: 0.9075 (m-30) cc_final: 0.8768 (p0) REVERT: D 359 TYR cc_start: 0.7964 (m-80) cc_final: 0.7587 (m-10) outliers start: 40 outliers final: 24 residues processed: 187 average time/residue: 0.1425 time to fit residues: 44.7849 Evaluate side-chains 181 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 54 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 82 GLU 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 453 MET Chi-restraints excluded: chain B residue 549 VAL 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 813 CYS Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain D residue 151 ILE 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: 3.9990 chunk 135 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 255 optimal weight: 10.0000 chunk 251 optimal weight: 1.9990 chunk 277 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3216 r_free = 0.3216 target = 0.061997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.047861 restraints weight = 98140.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.049491 restraints weight = 52399.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.050607 restraints weight = 34523.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.051276 restraints weight = 25824.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.051818 restraints weight = 21424.310| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24602 Z= 0.179 Angle : 0.604 8.723 33606 Z= 0.304 Chirality : 0.039 0.157 3694 Planarity : 0.004 0.063 4237 Dihedral : 13.735 80.950 3738 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.57 % Rotamer: Outliers : 1.81 % Allowed : 11.38 % 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 aren not related in a simple way. whole: 0.48 (0.16), residues: 2847 helix: 1.26 (0.14), residues: 1445 sheet: 0.19 (0.32), residues: 273 loop : -0.84 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 655 TYR 0.021 0.002 TYR B 648 PHE 0.016 0.001 PHE B 461 TRP 0.030 0.001 TRP B 652 HIS 0.011 0.001 HIS C 448 Details of bonding type rmsd covalent geometry : bond 0.00396 (24601) covalent geometry : angle 0.60396 (33603) hydrogen bonds : bond 0.03762 ( 1068) hydrogen bonds : angle 4.41402 ( 3066) link_TRANS : bond 0.00078 ( 1) link_TRANS : angle 0.28197 ( 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 201 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.720 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 55 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8829 (p) REVERT: B 133 CYS cc_start: 0.8982 (m) cc_final: 0.8304 (p) REVERT: B 146 MET cc_start: 0.8889 (mmm) cc_final: 0.8657 (mmm) REVERT: B 307 HIS cc_start: 0.8372 (OUTLIER) cc_final: 0.7427 (p90) REVERT: B 384 ASP cc_start: 0.8945 (t0) cc_final: 0.8533 (t0) REVERT: B 385 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8041 (mm-30) REVERT: B 389 THR cc_start: 0.9469 (m) cc_final: 0.9176 (p) REVERT: B 499 MET cc_start: 0.8881 (tmm) cc_final: 0.7798 (tmm) REVERT: B 589 GLU cc_start: 0.8528 (tt0) cc_final: 0.8101 (tm-30) REVERT: B 596 MET cc_start: 0.9025 (mmm) cc_final: 0.8439 (ttm) REVERT: B 604 MET cc_start: 0.9246 (tpp) cc_final: 0.8728 (ttt) REVERT: B 658 MET cc_start: 0.9143 (mmm) cc_final: 0.8776 (tpp) REVERT: B 660 MET cc_start: 0.9132 (ppp) cc_final: 0.8894 (ppp) REVERT: B 728 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.6352 (ptt180) REVERT: B 832 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.7941 (t70) REVERT: B 1061 MET cc_start: 0.8902 (mmm) cc_final: 0.8671 (mmt) REVERT: B 1086 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7100 (pt) REVERT: C 1 MET cc_start: 0.7461 (tmm) cc_final: 0.7154 (tmm) REVERT: C 72 MET cc_start: 0.8869 (mtp) cc_final: 0.8220 (mmp) REVERT: C 287 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: C 396 MET cc_start: 0.9134 (mmm) cc_final: 0.8889 (mtt) REVERT: C 609 MET cc_start: 0.9480 (mmm) cc_final: 0.9222 (mmm) REVERT: C 650 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8968 (tt) REVERT: C 781 THR cc_start: 0.9469 (m) cc_final: 0.9109 (p) REVERT: C 851 MET cc_start: 0.8644 (mmm) cc_final: 0.8273 (mmm) REVERT: C 978 MET cc_start: 0.8650 (tpp) cc_final: 0.8429 (tpp) REVERT: C 1031 MET cc_start: 0.9236 (mmp) cc_final: 0.8265 (mmm) REVERT: D 261 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8887 (pp) REVERT: D 284 ASP cc_start: 0.9048 (m-30) cc_final: 0.8726 (p0) REVERT: D 359 TYR cc_start: 0.7982 (m-80) cc_final: 0.7604 (m-10) outliers start: 44 outliers final: 32 residues processed: 193 average time/residue: 0.1436 time to fit residues: 46.6028 Evaluate side-chains 188 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 54 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 82 GLU 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 304 THR Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 549 VAL 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 813 CYS Chi-restraints excluded: chain B residue 832 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 259 LYS 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 533 LEU Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 872 LEU 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 261 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 290 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 283 optimal weight: 3.9990 chunk 285 optimal weight: 0.2980 chunk 242 optimal weight: 10.0000 chunk 280 optimal weight: 0.9990 chunk 226 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3245 r_free = 0.3245 target = 0.063154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.048997 restraints weight = 96576.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.050675 restraints weight = 50541.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.051820 restraints weight = 32908.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.052583 restraints weight = 24459.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.053086 restraints weight = 19974.237| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4322 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= 0.121 Angle : 0.588 9.534 33606 Z= 0.295 Chirality : 0.039 0.157 3694 Planarity : 0.004 0.064 4237 Dihedral : 13.648 81.459 3738 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.11 % Favored : 95.79 % Rotamer: Outliers : 1.81 % Allowed : 11.63 % Favored : 86.56 % 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 aren not related in a simple way. whole: 0.61 (0.16), residues: 2847 helix: 1.36 (0.14), residues: 1447 sheet: 0.26 (0.32), residues: 274 loop : -0.77 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 396 TYR 0.020 0.001 TYR B 648 PHE 0.015 0.001 PHE B 461 TRP 0.024 0.001 TRP B 652 HIS 0.005 0.001 HIS C 448 Details of bonding type rmsd covalent geometry : bond 0.00264 (24601) covalent geometry : angle 0.58769 (33603) hydrogen bonds : bond 0.03497 ( 1068) hydrogen bonds : angle 4.22873 ( 3066) link_TRANS : bond 0.00086 ( 1) link_TRANS : angle 0.16975 ( 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: 44 poor density : 161 time to evaluate : 0.910 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: B 55 THR cc_start: 0.9202 (OUTLIER) cc_final: 0.8994 (p) REVERT: B 133 CYS cc_start: 0.8950 (m) cc_final: 0.8272 (p) REVERT: B 136 MET cc_start: 0.8569 (tpp) cc_final: 0.8286 (tpp) REVERT: B 146 MET cc_start: 0.8865 (mmm) cc_final: 0.8655 (mmm) REVERT: B 307 HIS cc_start: 0.8333 (OUTLIER) cc_final: 0.7481 (p90) REVERT: B 385 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8021 (mm-30) REVERT: B 389 THR cc_start: 0.9428 (m) cc_final: 0.9138 (p) REVERT: B 499 MET cc_start: 0.8860 (tmm) cc_final: 0.7662 (tmm) REVERT: B 589 GLU cc_start: 0.8521 (tt0) cc_final: 0.8073 (tm-30) REVERT: B 604 MET cc_start: 0.9243 (tpp) cc_final: 0.8725 (ttt) REVERT: B 658 MET cc_start: 0.9172 (mmm) cc_final: 0.8848 (tpp) REVERT: B 660 MET cc_start: 0.9152 (ppp) cc_final: 0.8902 (ppp) REVERT: B 714 HIS cc_start: 0.9209 (OUTLIER) cc_final: 0.8953 (m90) REVERT: B 728 ARG cc_start: 0.6680 (OUTLIER) cc_final: 0.6332 (ptt180) REVERT: B 832 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.7956 (t70) REVERT: B 1056 MET cc_start: 0.9041 (mmm) cc_final: 0.8769 (mmm) REVERT: B 1086 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7111 (pt) REVERT: B 1098 MET cc_start: 0.8141 (ptp) cc_final: 0.7730 (ptp) REVERT: B 1168 MET cc_start: 0.9238 (ttm) cc_final: 0.8962 (ttm) REVERT: C 1 MET cc_start: 0.7364 (tmm) cc_final: 0.7055 (tmm) REVERT: C 17 MET cc_start: 0.9180 (ttp) cc_final: 0.8923 (ppp) REVERT: C 72 MET cc_start: 0.8858 (mtp) cc_final: 0.8205 (mmp) REVERT: C 158 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9033 (tt) REVERT: C 287 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7439 (m-80) REVERT: C 396 MET cc_start: 0.9137 (mmm) cc_final: 0.8898 (mtt) REVERT: C 462 ASP cc_start: 0.8837 (m-30) cc_final: 0.8406 (p0) REVERT: C 594 MET cc_start: 0.9083 (tpp) cc_final: 0.8807 (mmm) REVERT: C 781 THR cc_start: 0.9457 (m) cc_final: 0.9090 (p) REVERT: C 851 MET cc_start: 0.8639 (mmm) cc_final: 0.8227 (mmm) REVERT: C 978 MET cc_start: 0.8660 (tpp) cc_final: 0.8419 (tpp) REVERT: C 1031 MET cc_start: 0.9135 (mmp) cc_final: 0.8832 (mmm) REVERT: D 261 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8809 (pp) REVERT: D 284 ASP cc_start: 0.8983 (m-30) cc_final: 0.8703 (p0) REVERT: D 359 TYR cc_start: 0.7975 (m-80) cc_final: 0.7644 (m-80) outliers start: 44 outliers final: 28 residues processed: 196 average time/residue: 0.1370 time to fit residues: 45.3198 Evaluate side-chains 188 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 54 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 82 GLU 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 453 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 714 HIS 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 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 158 LEU 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 606 GLU Chi-restraints excluded: chain C residue 872 LEU 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 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: 4.9990 chunk 60 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 261 optimal weight: 8.9990 chunk 37 optimal weight: 0.4980 chunk 191 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 8 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.062131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.047843 restraints weight = 98159.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.049493 restraints weight = 51198.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.050630 restraints weight = 33326.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.051402 restraints weight = 24738.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.051924 restraints weight = 20109.437| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24602 Z= 0.149 Angle : 0.605 11.013 33606 Z= 0.303 Chirality : 0.039 0.156 3694 Planarity : 0.004 0.063 4237 Dihedral : 13.628 81.370 3738 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.54 % Rotamer: Outliers : 1.90 % Allowed : 11.71 % Favored : 86.39 % 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 aren not related in a simple way. whole: 0.63 (0.16), residues: 2847 helix: 1.37 (0.14), residues: 1445 sheet: 0.20 (0.33), residues: 257 loop : -0.72 (0.18), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 396 TYR 0.020 0.001 TYR B1111 PHE 0.015 0.001 PHE B 461 TRP 0.031 0.001 TRP B 652 HIS 0.008 0.001 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00332 (24601) covalent geometry : angle 0.60550 (33603) hydrogen bonds : bond 0.03626 ( 1068) hydrogen bonds : angle 4.21011 ( 3066) link_TRANS : bond 0.00083 ( 1) link_TRANS : angle 0.16407 ( 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 198 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 152 time to evaluate : 0.750 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: B 55 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8921 (p) REVERT: B 133 CYS cc_start: 0.9075 (m) cc_final: 0.8396 (p) REVERT: B 146 MET cc_start: 0.8893 (mmm) cc_final: 0.8656 (mmm) REVERT: B 307 HIS cc_start: 0.8349 (OUTLIER) cc_final: 0.7473 (p90) REVERT: B 385 GLU cc_start: 0.8394 (mm-30) cc_final: 0.8045 (mm-30) REVERT: B 389 THR cc_start: 0.9421 (m) cc_final: 0.9149 (p) REVERT: B 499 MET cc_start: 0.8884 (tmm) cc_final: 0.7708 (tmm) REVERT: B 589 GLU cc_start: 0.8579 (tt0) cc_final: 0.8129 (tm-30) REVERT: B 596 MET cc_start: 0.9050 (mtp) cc_final: 0.8755 (ttm) REVERT: B 604 MET cc_start: 0.9263 (tpp) cc_final: 0.8767 (ttt) REVERT: B 658 MET cc_start: 0.9227 (mmm) cc_final: 0.8899 (tpp) REVERT: B 660 MET cc_start: 0.9259 (ppp) cc_final: 0.9032 (ppp) REVERT: B 728 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6456 (ptt180) REVERT: B 793 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8668 (mt-10) REVERT: B 832 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8021 (t70) REVERT: B 1056 MET cc_start: 0.9145 (mmm) cc_final: 0.8848 (mmm) REVERT: B 1086 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7185 (pt) REVERT: B 1098 MET cc_start: 0.8139 (ptp) cc_final: 0.7739 (ptp) REVERT: B 1168 MET cc_start: 0.9316 (ttm) cc_final: 0.9033 (ttm) REVERT: C 1 MET cc_start: 0.7341 (tmm) cc_final: 0.7011 (tmm) REVERT: C 17 MET cc_start: 0.9304 (ttp) cc_final: 0.8969 (ppp) REVERT: C 72 MET cc_start: 0.8913 (mtp) cc_final: 0.8255 (mmp) REVERT: C 158 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9051 (tt) REVERT: C 287 PHE cc_start: 0.8269 (OUTLIER) cc_final: 0.7517 (m-80) REVERT: C 396 MET cc_start: 0.9168 (mmm) cc_final: 0.8927 (mtt) REVERT: C 594 MET cc_start: 0.9101 (tpp) cc_final: 0.8793 (mmm) REVERT: C 680 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.8848 (mpp) REVERT: C 781 THR cc_start: 0.9443 (m) cc_final: 0.9082 (p) REVERT: C 851 MET cc_start: 0.8746 (mmm) cc_final: 0.8305 (mmm) REVERT: C 1031 MET cc_start: 0.9178 (mmp) cc_final: 0.8864 (mmm) REVERT: D 261 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8819 (pp) REVERT: D 284 ASP cc_start: 0.9042 (m-30) cc_final: 0.8723 (p0) REVERT: D 359 TYR cc_start: 0.8007 (m-80) cc_final: 0.7656 (m-80) outliers start: 46 outliers final: 32 residues processed: 187 average time/residue: 0.1352 time to fit residues: 43.2079 Evaluate side-chains 188 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.900 ------------------------------------------------------------------------------- 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 54 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 82 GLU 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 453 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 549 VAL 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 832 ASP Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain C residue 8 ASN Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 259 LYS 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 606 GLU Chi-restraints excluded: chain C residue 665 MET Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 261 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 236 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 258 optimal weight: 20.0000 chunk 96 optimal weight: 1.9990 chunk 90 optimal weight: 50.0000 chunk 264 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 202 optimal weight: 5.9990 chunk 229 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3200 r_free = 0.3200 target = 0.061890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.047684 restraints weight = 98184.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.049327 restraints weight = 51148.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.050451 restraints weight = 33167.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.051217 restraints weight = 24619.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.051694 restraints weight = 20049.980| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 24602 Z= 0.166 Angle : 0.619 11.018 33606 Z= 0.308 Chirality : 0.039 0.165 3694 Planarity : 0.004 0.063 4237 Dihedral : 13.624 81.479 3738 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.54 % Rotamer: Outliers : 1.73 % Allowed : 12.08 % Favored : 86.19 % 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 aren not related in a simple way. whole: 0.64 (0.16), residues: 2847 helix: 1.38 (0.14), residues: 1446 sheet: 0.20 (0.33), residues: 255 loop : -0.71 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 57 TYR 0.027 0.001 TYR B1114 PHE 0.015 0.001 PHE B 461 TRP 0.030 0.001 TRP B 652 HIS 0.007 0.001 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00368 (24601) covalent geometry : angle 0.61897 (33603) hydrogen bonds : bond 0.03617 ( 1068) hydrogen bonds : angle 4.22943 ( 3066) link_TRANS : bond 0.00102 ( 1) link_TRANS : angle 0.14796 ( 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 190 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 148 time to evaluate : 0.908 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: B 55 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8913 (p) REVERT: B 136 MET cc_start: 0.8636 (tpp) cc_final: 0.8415 (tpp) REVERT: B 146 MET cc_start: 0.8892 (mmm) cc_final: 0.8673 (mmm) REVERT: B 307 HIS cc_start: 0.8211 (OUTLIER) cc_final: 0.7294 (p90) REVERT: B 385 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8066 (mm-30) REVERT: B 389 THR cc_start: 0.9313 (m) cc_final: 0.9027 (p) REVERT: B 499 MET cc_start: 0.8859 (tmm) cc_final: 0.7743 (tmm) REVERT: B 541 MET cc_start: 0.7939 (pmm) cc_final: 0.7675 (pmm) REVERT: B 589 GLU cc_start: 0.8577 (tt0) cc_final: 0.8171 (tm-30) REVERT: B 596 MET cc_start: 0.9065 (mtp) cc_final: 0.8772 (ttm) REVERT: B 604 MET cc_start: 0.9286 (tpp) cc_final: 0.8781 (ttt) REVERT: B 658 MET cc_start: 0.9222 (mmm) cc_final: 0.8912 (tpp) REVERT: B 660 MET cc_start: 0.9292 (ppp) cc_final: 0.9064 (ppp) REVERT: B 728 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6468 (ptt180) REVERT: B 793 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8668 (mt-10) REVERT: B 832 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8037 (t70) REVERT: B 1056 MET cc_start: 0.9148 (mmm) cc_final: 0.8849 (mmm) REVERT: B 1086 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7178 (pt) REVERT: B 1098 MET cc_start: 0.8144 (ptp) cc_final: 0.7747 (ptp) REVERT: B 1168 MET cc_start: 0.9316 (ttm) cc_final: 0.9047 (ttm) REVERT: C 1 MET cc_start: 0.7324 (tmm) cc_final: 0.7074 (tmm) REVERT: C 17 MET cc_start: 0.9319 (ttp) cc_final: 0.8982 (ppp) REVERT: C 72 MET cc_start: 0.8928 (mtp) cc_final: 0.8265 (mmp) REVERT: C 158 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9055 (tt) REVERT: C 287 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: C 396 MET cc_start: 0.9170 (mmm) cc_final: 0.8928 (mtt) REVERT: C 594 MET cc_start: 0.9102 (tpp) cc_final: 0.8793 (mmm) REVERT: C 781 THR cc_start: 0.9441 (m) cc_final: 0.9078 (p) REVERT: C 851 MET cc_start: 0.8751 (mmm) cc_final: 0.8312 (mmm) REVERT: C 978 MET cc_start: 0.8804 (tpt) cc_final: 0.8448 (tpp) REVERT: C 1031 MET cc_start: 0.9203 (mmp) cc_final: 0.8875 (mmm) REVERT: C 1079 MET cc_start: 0.8426 (pmm) cc_final: 0.7908 (pmm) REVERT: C 1080 MET cc_start: 0.8365 (mpp) cc_final: 0.7102 (mpp) REVERT: D 263 LEU cc_start: 0.9183 (mp) cc_final: 0.8704 (tt) REVERT: D 284 ASP cc_start: 0.9052 (m-30) cc_final: 0.8731 (p0) REVERT: D 359 TYR cc_start: 0.8026 (m-80) cc_final: 0.7680 (m-80) outliers start: 42 outliers final: 33 residues processed: 182 average time/residue: 0.1394 time to fit residues: 42.7157 Evaluate side-chains 185 residues out of total 2425 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 54 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 82 GLU 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 453 MET Chi-restraints excluded: chain B residue 464 THR Chi-restraints excluded: chain B residue 549 VAL 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 853 LEU Chi-restraints excluded: chain B residue 888 LEU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 158 LEU Chi-restraints excluded: chain C residue 259 LYS 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 606 GLU Chi-restraints excluded: chain C residue 665 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 78 LEU Chi-restraints excluded: chain D residue 151 ILE 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: 20.0000 chunk 144 optimal weight: 0.9990 chunk 253 optimal weight: 7.9990 chunk 219 optimal weight: 0.9990 chunk 136 optimal weight: 0.0170 chunk 79 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 220 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 216 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 overall best weight: 0.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 793 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.063606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.049510 restraints weight = 96539.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.051207 restraints weight = 49790.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.052352 restraints weight = 32081.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.053142 restraints weight = 23627.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.053677 restraints weight = 19092.212| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24602 Z= 0.108 Angle : 0.594 10.503 33606 Z= 0.294 Chirality : 0.038 0.156 3694 Planarity : 0.004 0.065 4237 Dihedral : 13.543 82.260 3738 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.65 % Favored : 96.24 % Rotamer: Outliers : 1.53 % Allowed : 12.33 % Favored : 86.14 % 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 aren not related in a simple way. whole: 0.71 (0.16), residues: 2847 helix: 1.43 (0.14), residues: 1445 sheet: 0.22 (0.33), residues: 256 loop : -0.67 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 396 TYR 0.031 0.001 TYR B1114 PHE 0.015 0.001 PHE C 193 TRP 0.023 0.001 TRP B 652 HIS 0.004 0.001 HIS C 984 Details of bonding type rmsd covalent geometry : bond 0.00231 (24601) covalent geometry : angle 0.59422 (33603) hydrogen bonds : bond 0.03308 ( 1068) hydrogen bonds : angle 4.07802 ( 3066) link_TRANS : bond 0.00043 ( 1) link_TRANS : angle 0.10827 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3164.99 seconds wall clock time: 55 minutes 41.72 seconds (3341.72 seconds total)