Starting phenix.real_space_refine on Sun Jul 5 15:23:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8re4_19079/07_2026/8re4_19079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8re4_19079/07_2026/8re4_19079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8re4_19079/07_2026/8re4_19079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8re4_19079/07_2026/8re4_19079.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8re4_19079/07_2026/8re4_19079.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8re4_19079/07_2026/8re4_19079.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8re4_19079/07_2026/8re4_19079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8re4_19079/07_2026/8re4_19079.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 102 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 17981 2.51 5 N 5167 2.21 5 O 5810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29165 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2365 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1733 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'HIS:plan': 2, 'TYR:plan': 1, 'ASP:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 10080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10080 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 22, 'ARG:plan': 18, 'HIS:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 15, 'PHE:plan': 5, 'TYR:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 338 Chain: "D" Number of atoms: 9685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 9685 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PTRANS': 53, 'TRANS': 1276} Chain breaks: 5 Unresolved non-hydrogen bonds: 688 Unresolved non-hydrogen angles: 836 Unresolved non-hydrogen dihedrals: 583 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 15, 'ASP:plan': 18, 'GLU:plan': 31, 'ASN:plan1': 5, 'PHE:plan': 9, 'ARG:plan': 18, 'HIS:plan': 1, 'TYR:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 441 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2657 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 16, 'TRANS': 363} Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 436 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASN:plan1': 8, 'ASP:plan': 14, 'TYR:plan': 2, 'GLN:plan1': 8, 'GLU:plan': 12, 'HIS:plan': 2, 'PHE:plan': 2, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 217 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 960 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain breaks: 1 Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Chain breaks: 1 Chain: "T" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1030 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14701 SG CYS D 70 103.972 112.746 93.290 1.00 58.66 S ATOM 14715 SG CYS D 72 102.253 116.852 95.537 1.00 47.22 S ATOM 14830 SG CYS D 88 102.041 113.314 96.978 1.00 51.38 S ATOM 20946 SG CYS D 898 93.575 45.025 89.115 1.00 44.84 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.58 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.58 Time building chain proxies: 5.73, per 1000 atoms: 0.20 Number of scatterers: 29165 At special positions: 0 Unit cell: (140.8, 169.4, 166.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 102 16.00 P 102 15.00 Mg 1 11.99 O 5810 8.00 N 5167 7.00 C 17981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6802 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 45 sheets defined 41.4% alpha, 14.0% beta 38 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.842A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.760A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.363A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.573A pdb=" N ALA A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.985A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.526A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.721A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.515A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.695A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.752A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 48 through 57 removed outlier: 4.079A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.712A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.771A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.612A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.844A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.681A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 491 Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.340A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.743A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.602A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.547A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.528A pdb=" N SER C 863 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.554A pdb=" N LEU C 946 " --> pdb=" O ASP C 942 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.658A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1000 removed outlier: 3.834A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.626A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.563A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.298A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.638A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.765A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1239 through 1241 No H-bonds generated for 'chain 'C' and resid 1239 through 1241' Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.846A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.768A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 13 removed outlier: 3.747A pdb=" N THR D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 removed outlier: 4.003A pdb=" N LYS D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.984A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.442A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.647A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.737A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.515A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 612 removed outlier: 3.922A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.651A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.672A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.538A pdb=" N GLY D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.067A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.857A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.591A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.556A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.507A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.757A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.157A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1295 through 1299 removed outlier: 3.561A pdb=" N GLY D1299 " --> pdb=" O GLY D1296 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1314 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.728A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.563A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1376 Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.792A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.623A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 119 through 130 Processing helix chain 'M' and resid 134 through 147 removed outlier: 3.732A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 171 through 184 removed outlier: 3.597A pdb=" N ALA M 177 " --> pdb=" O GLU M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 205 removed outlier: 3.903A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 218 removed outlier: 4.348A pdb=" N LEU M 218 " --> pdb=" O GLU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 230 Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 242 through 256 removed outlier: 3.544A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 311 removed outlier: 3.883A pdb=" N GLY M 307 " --> pdb=" O TYR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 322 through 351 removed outlier: 3.658A pdb=" N ARG M 327 " --> pdb=" O LEU M 323 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TRP M 328 " --> pdb=" O GLN M 324 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 356 removed outlier: 3.628A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.757A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 removed outlier: 3.550A pdb=" N ILE M 381 " --> pdb=" O HIS M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 399 through 404 removed outlier: 3.710A pdb=" N SER M 404 " --> pdb=" O TYR M 401 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 466 removed outlier: 3.526A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 8.794A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.534A pdb=" N VAL A 98 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.729A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.386A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 61 removed outlier: 7.133A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.224A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.779A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.779A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.663A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.102A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.213A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.606A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 723 through 727 removed outlier: 6.685A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC4, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.222A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.713A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.713A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.798A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1243 through 1246 Processing sheet with id=AD1, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.731A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD3, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.760A pdb=" N LYS D 50 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 104 through 111 removed outlier: 10.330A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.774A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 removed outlier: 7.097A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 572 " --> pdb=" O VAL D 548 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 570 " --> pdb=" O VAL D 550 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.654A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 848 through 849 removed outlier: 7.181A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 958 Processing sheet with id=AE5, first strand: chain 'D' and resid 974 through 975 removed outlier: 4.071A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1059 through 1060 removed outlier: 3.801A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1174 through 1177 removed outlier: 4.306A pdb=" N VAL D1176 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU D1188 " --> pdb=" O VAL D1176 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE9, first strand: chain 'M' and resid 277 through 278 removed outlier: 7.023A pdb=" N LEU M 277 " --> pdb=" O HIS M 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 1181 hydrogen bonds defined for protein. 3285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 7.87 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8484 1.34 - 1.46: 4728 1.46 - 1.58: 16210 1.58 - 1.70: 199 1.70 - 1.82: 177 Bond restraints: 29798 Sorted by residual: bond pdb=" N GLU C1316 " pdb=" CA GLU C1316 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 2.05e+01 bond pdb=" N GLY D 742 " pdb=" CA GLY D 742 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.99e+01 bond pdb=" CE1 HIS C1237 " pdb=" NE2 HIS C1237 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.77e+01 bond pdb=" CE1 HIS C 628 " pdb=" NE2 HIS C 628 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.77e+01 bond pdb=" CE1 HIS D 430 " pdb=" NE2 HIS D 430 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.76e+01 ... (remaining 29793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 40364 2.88 - 5.75: 508 5.75 - 8.63: 26 8.63 - 11.51: 5 11.51 - 14.38: 2 Bond angle restraints: 40905 Sorted by residual: angle pdb=" C3' DT N 2 " pdb=" O3' DT N 2 " pdb=" P DA N 3 " ideal model delta sigma weight residual 120.20 108.30 11.90 1.50e+00 4.44e-01 6.29e+01 angle pdb=" C3' DA N 3 " pdb=" O3' DA N 3 " pdb=" P DG N 4 " ideal model delta sigma weight residual 120.20 111.82 8.38 1.50e+00 4.44e-01 3.12e+01 angle pdb=" O4' DC T -2 " pdb=" C4' DC T -2 " pdb=" C3' DC T -2 " ideal model delta sigma weight residual 106.00 102.87 3.13 6.00e-01 2.78e+00 2.73e+01 angle pdb=" CA GLY C 48 " pdb=" C GLY C 48 " pdb=" O GLY C 48 " ideal model delta sigma weight residual 122.29 118.08 4.21 8.10e-01 1.52e+00 2.71e+01 angle pdb=" C ARG A 235 " pdb=" CA ARG A 235 " pdb=" CB ARG A 235 " ideal model delta sigma weight residual 116.54 110.77 5.77 1.15e+00 7.56e-01 2.52e+01 ... (remaining 40900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.30: 16902 34.30 - 68.60: 977 68.60 - 102.90: 36 102.90 - 137.20: 0 137.20 - 171.50: 3 Dihedral angle restraints: 17918 sinusoidal: 7374 harmonic: 10544 Sorted by residual: dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 137.49 42.51 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CD ARG A 235 " pdb=" NE ARG A 235 " pdb=" CZ ARG A 235 " pdb=" NH1 ARG A 235 " ideal model delta sinusoidal sigma weight residual 0.00 -57.78 57.78 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CA PHE C 15 " pdb=" C PHE C 15 " pdb=" N GLY C 16 " pdb=" CA GLY C 16 " ideal model delta harmonic sigma weight residual 180.00 154.39 25.61 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 17915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4339 0.098 - 0.197: 501 0.197 - 0.295: 9 0.295 - 0.394: 0 0.394 - 0.492: 2 Chirality restraints: 4851 Sorted by residual: chirality pdb=" P DT N 2 " pdb=" OP1 DT N 2 " pdb=" OP2 DT N 2 " pdb=" O5' DT N 2 " both_signs ideal model delta sigma weight residual True 2.34 -2.83 -0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" P DA N 3 " pdb=" OP1 DA N 3 " pdb=" OP2 DA N 3 " pdb=" O5' DA N 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.81 -0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA ILE D 856 " pdb=" N ILE D 856 " pdb=" C ILE D 856 " pdb=" CB ILE D 856 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 4848 not shown) Planarity restraints: 5004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 235 " -0.920 9.50e-02 1.11e+02 4.13e-01 1.03e+02 pdb=" NE ARG A 235 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG A 235 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 235 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 235 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1330 " 0.544 9.50e-02 1.11e+02 2.44e-01 3.64e+01 pdb=" NE ARG D1330 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG D1330 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D1330 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D1330 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 535 " -0.420 9.50e-02 1.11e+02 1.88e-01 2.17e+01 pdb=" NE ARG D 535 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 535 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 535 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 535 " -0.014 2.00e-02 2.50e+03 ... (remaining 5001 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 113 2.52 - 3.12: 22072 3.12 - 3.71: 46098 3.71 - 4.31: 62752 4.31 - 4.90: 103319 Nonbonded interactions: 234354 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 1.931 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.088 2.170 nonbonded pdb=" OG1 THR D 980 " pdb=" O VAL D 997 " model vdw 2.188 3.040 nonbonded pdb=" OH TYR C 179 " pdb=" OE2 GLU C 458 " model vdw 2.202 3.040 nonbonded pdb=" O TYR C 810 " pdb=" OG SER C1077 " model vdw 2.206 3.040 ... (remaining 234349 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 33.790 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:9.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.008 0.684 29802 Z= 0.497 Angle : 0.857 14.383 40905 Z= 0.613 Chirality : 0.058 0.492 4851 Planarity : 0.010 0.413 5004 Dihedral : 18.842 171.503 11116 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.09 % Favored : 93.66 % Rotamer: Outliers : 1.66 % Allowed : 24.96 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.14), residues: 3643 helix: 0.92 (0.15), residues: 1323 sheet: 0.30 (0.27), residues: 396 loop : -1.39 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 279 TYR 0.021 0.001 TYR A 177 PHE 0.023 0.001 PHE M 354 TRP 0.017 0.002 TRP D 115 HIS 0.005 0.001 HIS C1116 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.47 (29798) covalent geometry : angle 0.85741 / 0.61 (40905) hydrogen bonds : bond 0.18451 / 13.27 ( 1263) hydrogen bonds : angle 6.50588 / 4.61 ( 3481) metal coordination : bond 0.40579 / 20.79 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: C 1240 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6552 (m-30) outliers start: 45 outliers final: 12 residues processed: 220 average time/residue: 0.6041 time to fit residues: 156.8414 Evaluate side-chains 135 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 294 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN D 300 GLN D 450 HIS D 739 GLN D1249 ASN D1259 GLN ** M 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 406 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.068968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.044175 restraints weight = 107291.209| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 3.32 r_work: 0.2733 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2730 r_free = 0.2730 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29802 Z= 0.199 Angle : 0.638 10.084 40905 Z= 0.337 Chirality : 0.044 0.355 4851 Planarity : 0.005 0.069 5004 Dihedral : 16.496 175.848 5113 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.57 % Favored : 94.40 % Rotamer: Outliers : 3.99 % Allowed : 22.64 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.14), residues: 3643 helix: 1.15 (0.14), residues: 1351 sheet: 0.61 (0.27), residues: 374 loop : -1.40 (0.13), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 478 TYR 0.016 0.001 TYR M 112 PHE 0.016 0.001 PHE A 231 TRP 0.016 0.002 TRP M 212 HIS 0.008 0.001 HIS C 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (29798) covalent geometry : angle 0.63766 / 0.34 (40905) hydrogen bonds : bond 0.04947 / 3.42 ( 1263) hydrogen bonds : angle 4.69597 / 3.26 ( 3481) metal coordination : bond 0.01889 / 0.99 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 129 time to evaluate : 0.907 Fit side-chains REVERT: A 25 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8594 (mmmm) REVERT: A 93 GLN cc_start: 0.7651 (mp10) cc_final: 0.7350 (mp-120) REVERT: B 215 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8388 (tm-30) REVERT: C 246 LEU cc_start: 0.9738 (OUTLIER) cc_final: 0.9515 (pp) REVERT: C 1069 ARG cc_start: 0.9176 (OUTLIER) cc_final: 0.8565 (ptt-90) REVERT: D 115 TRP cc_start: 0.8556 (OUTLIER) cc_final: 0.7020 (m-90) REVERT: D 1222 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8647 (ttm-80) REVERT: E 8 ASP cc_start: 0.9091 (m-30) cc_final: 0.8828 (m-30) REVERT: E 69 ARG cc_start: 0.8696 (mmm160) cc_final: 0.8124 (tpm-80) outliers start: 108 outliers final: 33 residues processed: 228 average time/residue: 0.5158 time to fit residues: 141.6766 Evaluate side-chains 160 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 547 ARG Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 140 optimal weight: 0.6980 chunk 365 optimal weight: 80.0000 chunk 150 optimal weight: 40.0000 chunk 372 optimal weight: 50.0000 chunk 76 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 192 optimal weight: 0.0270 chunk 48 optimal weight: 5.9990 chunk 283 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 299 optimal weight: 50.0000 overall best weight: 3.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN C 518 ASN D1289 ASN M 290 ASN ** M 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 406 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.068199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.043131 restraints weight = 109104.754| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 3.41 r_work: 0.2711 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2709 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2709 r_free = 0.2709 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (19 function evaluations) r_final: 0.2709 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29802 Z= 0.161 Angle : 0.581 9.181 40905 Z= 0.308 Chirality : 0.043 0.281 4851 Planarity : 0.004 0.063 5004 Dihedral : 16.361 175.280 5102 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 3.77 % Allowed : 22.49 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3643 helix: 1.37 (0.15), residues: 1358 sheet: 0.50 (0.26), residues: 388 loop : -1.32 (0.13), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 407 TYR 0.023 0.001 TYR M 361 PHE 0.011 0.001 PHE M 403 TRP 0.012 0.001 TRP D 115 HIS 0.005 0.001 HIS C 832 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (29798) covalent geometry : angle 0.58121 / 0.31 (40905) hydrogen bonds : bond 0.04441 / 3.09 ( 1263) hydrogen bonds : angle 4.36249 / 3.01 ( 3481) metal coordination : bond 0.01685 / 0.85 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 125 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 GLN cc_start: 0.9085 (tp40) cc_final: 0.8410 (mm110) REVERT: B 102 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8377 (tm) REVERT: B 137 ASN cc_start: 0.8807 (m-40) cc_final: 0.8171 (p0) REVERT: B 215 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: C 470 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8839 (mtt-85) REVERT: C 492 MET cc_start: 0.8030 (mmp) cc_final: 0.7754 (mmm) REVERT: C 1069 ARG cc_start: 0.9154 (OUTLIER) cc_final: 0.8265 (ptt-90) REVERT: C 1220 GLN cc_start: 0.9286 (OUTLIER) cc_final: 0.9016 (tt0) REVERT: D 115 TRP cc_start: 0.8537 (OUTLIER) cc_final: 0.7066 (m-90) REVERT: D 160 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9115 (pp) REVERT: D 179 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8889 (mppt) REVERT: D 255 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8279 (mm) REVERT: D 1222 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.8733 (ttm-80) REVERT: E 42 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: M 361 TYR cc_start: 0.9252 (m-80) cc_final: 0.8764 (m-10) outliers start: 102 outliers final: 38 residues processed: 215 average time/residue: 0.5554 time to fit residues: 142.1728 Evaluate side-chains 172 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 123 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 349 GLU Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 104 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 184 optimal weight: 7.9990 chunk 129 optimal weight: 10.0000 chunk 243 optimal weight: 0.6980 chunk 231 optimal weight: 10.0000 chunk 84 optimal weight: 2.9990 chunk 286 optimal weight: 40.0000 chunk 114 optimal weight: 10.0000 chunk 195 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 139 ASN C 622 ASN D 430 HIS D 739 GLN D1289 ASN ** M 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 391 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.066747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.041639 restraints weight = 108704.382| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.38 r_work: 0.2664 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 29802 Z= 0.208 Angle : 0.601 9.953 40905 Z= 0.315 Chirality : 0.043 0.244 4851 Planarity : 0.004 0.060 5004 Dihedral : 16.350 176.619 5101 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.02 % Rotamer: Outliers : 4.32 % Allowed : 22.30 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3643 helix: 1.43 (0.14), residues: 1365 sheet: 0.38 (0.27), residues: 385 loop : -1.28 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 69 TYR 0.016 0.001 TYR D 631 PHE 0.013 0.001 PHE D 49 TRP 0.013 0.001 TRP D 115 HIS 0.010 0.001 HIS M 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (29798) covalent geometry : angle 0.60108 / 0.31 (40905) hydrogen bonds : bond 0.04362 / 2.98 ( 1263) hydrogen bonds : angle 4.17646 / 2.87 ( 3481) metal coordination : bond 0.01147 / 0.58 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 124 time to evaluate : 0.880 Fit side-chains revert: symmetry clash REVERT: A 59 VAL cc_start: 0.9723 (OUTLIER) cc_final: 0.9491 (p) REVERT: A 206 GLU cc_start: 0.8689 (OUTLIER) cc_final: 0.8429 (tt0) REVERT: B 93 GLN cc_start: 0.9108 (tp40) cc_final: 0.8428 (mm110) REVERT: B 215 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8406 (tm-30) REVERT: C 105 TYR cc_start: 0.8449 (m-10) cc_final: 0.7854 (m-80) REVERT: C 246 LEU cc_start: 0.9746 (OUTLIER) cc_final: 0.9519 (pp) REVERT: C 470 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8883 (mtt-85) REVERT: C 492 MET cc_start: 0.8096 (mmp) cc_final: 0.7867 (mmm) REVERT: C 1069 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8330 (ptt-90) REVERT: C 1233 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9254 (mt) REVERT: D 115 TRP cc_start: 0.8642 (OUTLIER) cc_final: 0.6881 (m-90) REVERT: D 160 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9074 (pp) REVERT: D 179 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8887 (mppt) REVERT: D 255 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8461 (mm) REVERT: D 901 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.7862 (ptp-170) REVERT: D 1222 ARG cc_start: 0.9469 (OUTLIER) cc_final: 0.8818 (ttm-80) REVERT: D 1330 ARG cc_start: 0.9189 (OUTLIER) cc_final: 0.8881 (tmm-80) REVERT: E 42 GLU cc_start: 0.9164 (OUTLIER) cc_final: 0.8462 (mp0) REVERT: M 361 TYR cc_start: 0.9303 (m-80) cc_final: 0.8775 (m-10) outliers start: 117 outliers final: 37 residues processed: 229 average time/residue: 0.5232 time to fit residues: 143.9355 Evaluate side-chains 171 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 119 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 388 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 311 optimal weight: 0.4980 chunk 313 optimal weight: 6.9990 chunk 300 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 191 optimal weight: 8.9990 chunk 133 optimal weight: 0.8980 chunk 181 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 299 optimal weight: 30.0000 chunk 195 optimal weight: 8.9990 overall best weight: 5.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS M 357 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.066552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.041471 restraints weight = 108758.283| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.32 r_work: 0.2664 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29802 Z= 0.182 Angle : 0.579 9.378 40905 Z= 0.303 Chirality : 0.043 0.274 4851 Planarity : 0.004 0.059 5004 Dihedral : 16.318 177.957 5099 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 4.17 % Allowed : 22.78 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.14), residues: 3643 helix: 1.53 (0.14), residues: 1365 sheet: 0.40 (0.27), residues: 385 loop : -1.24 (0.14), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 678 TYR 0.014 0.001 TYR D 140 PHE 0.011 0.001 PHE D 49 TRP 0.012 0.001 TRP D 115 HIS 0.006 0.001 HIS M 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (29798) covalent geometry : angle 0.57920 / 0.30 (40905) hydrogen bonds : bond 0.04134 / 2.83 ( 1263) hydrogen bonds : angle 4.07392 / 2.80 ( 3481) metal coordination : bond 0.01158 / 0.58 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 124 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8424 (tt0) REVERT: B 93 GLN cc_start: 0.9167 (tp40) cc_final: 0.8510 (mm110) REVERT: B 215 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: C 105 TYR cc_start: 0.8484 (m-10) cc_final: 0.7855 (m-80) REVERT: C 246 LEU cc_start: 0.9757 (OUTLIER) cc_final: 0.9532 (pp) REVERT: C 470 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8858 (mtt-85) REVERT: C 492 MET cc_start: 0.8117 (mmp) cc_final: 0.7878 (mmm) REVERT: C 548 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.7594 (mtp85) REVERT: C 1069 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8266 (ptt-90) REVERT: C 1220 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8975 (tt0) REVERT: C 1233 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9259 (mt) REVERT: D 160 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9078 (pp) REVERT: D 179 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8856 (mppt) REVERT: D 255 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8480 (mm) REVERT: D 747 MET cc_start: 0.8585 (pmm) cc_final: 0.8352 (pmm) REVERT: D 901 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7820 (ptp-170) REVERT: D 1222 ARG cc_start: 0.9523 (OUTLIER) cc_final: 0.8848 (ttm-80) REVERT: D 1330 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8923 (tmm-80) REVERT: E 8 ASP cc_start: 0.9022 (m-30) cc_final: 0.8721 (m-30) REVERT: E 42 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8531 (mp0) REVERT: M 361 TYR cc_start: 0.9255 (m-80) cc_final: 0.8556 (m-10) outliers start: 113 outliers final: 46 residues processed: 224 average time/residue: 0.5196 time to fit residues: 141.4376 Evaluate side-chains 184 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 123 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 971 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 118 optimal weight: 3.9990 chunk 84 optimal weight: 40.0000 chunk 166 optimal weight: 9.9990 chunk 302 optimal weight: 0.4980 chunk 24 optimal weight: 30.0000 chunk 256 optimal weight: 6.9990 chunk 75 optimal weight: 30.0000 chunk 170 optimal weight: 10.0000 chunk 12 optimal weight: 9.9990 chunk 88 optimal weight: 0.0030 chunk 234 optimal weight: 3.9990 overall best weight: 3.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN D 430 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.066952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.041784 restraints weight = 108306.818| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.38 r_work: 0.2675 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29802 Z= 0.135 Angle : 0.561 11.297 40905 Z= 0.292 Chirality : 0.042 0.254 4851 Planarity : 0.004 0.061 5004 Dihedral : 16.273 178.867 5099 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 3.55 % Allowed : 23.60 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3643 helix: 1.63 (0.15), residues: 1365 sheet: 0.50 (0.27), residues: 384 loop : -1.22 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 69 TYR 0.018 0.001 TYR M 361 PHE 0.008 0.001 PHE D1325 TRP 0.009 0.001 TRP M 126 HIS 0.004 0.001 HIS M 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (29798) covalent geometry : angle 0.56084 / 0.29 (40905) hydrogen bonds : bond 0.03778 / 2.60 ( 1263) hydrogen bonds : angle 3.95423 / 2.72 ( 3481) metal coordination : bond 0.01271 / 0.64 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 123 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8418 (tt0) REVERT: B 76 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8080 (mt-10) REVERT: B 93 GLN cc_start: 0.9178 (tp40) cc_final: 0.8529 (mm110) REVERT: B 215 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: C 105 TYR cc_start: 0.8482 (m-10) cc_final: 0.7814 (m-80) REVERT: C 246 LEU cc_start: 0.9750 (OUTLIER) cc_final: 0.9528 (pp) REVERT: C 370 MET cc_start: 0.8529 (tmm) cc_final: 0.8317 (ppp) REVERT: C 459 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8893 (mtp) REVERT: C 470 ARG cc_start: 0.9115 (OUTLIER) cc_final: 0.8876 (mtt-85) REVERT: C 492 MET cc_start: 0.8102 (mmp) cc_final: 0.7901 (mmm) REVERT: C 1069 ARG cc_start: 0.9192 (OUTLIER) cc_final: 0.8274 (ptt-90) REVERT: C 1137 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8545 (pm20) REVERT: C 1220 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8999 (tt0) REVERT: C 1233 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9263 (mt) REVERT: D 160 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9071 (pp) REVERT: D 179 LYS cc_start: 0.9282 (OUTLIER) cc_final: 0.8842 (mppt) REVERT: D 255 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8459 (mm) REVERT: D 701 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9062 (tt) REVERT: D 747 MET cc_start: 0.8543 (pmm) cc_final: 0.8311 (pmm) REVERT: D 901 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7845 (ptp-170) REVERT: D 1222 ARG cc_start: 0.9546 (OUTLIER) cc_final: 0.8841 (ttm-80) REVERT: D 1330 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8915 (tmm-80) REVERT: E 8 ASP cc_start: 0.9052 (m-30) cc_final: 0.8840 (m-30) REVERT: E 42 GLU cc_start: 0.9155 (OUTLIER) cc_final: 0.8421 (mp0) outliers start: 96 outliers final: 43 residues processed: 208 average time/residue: 0.5605 time to fit residues: 140.4654 Evaluate side-chains 182 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 121 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 230 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 314 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 243 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 354 optimal weight: 30.0000 chunk 150 optimal weight: 30.0000 chunk 198 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 50.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN D 430 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.067182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.042396 restraints weight = 107303.242| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.29 r_work: 0.2693 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29802 Z= 0.120 Angle : 0.553 11.778 40905 Z= 0.289 Chirality : 0.042 0.362 4851 Planarity : 0.004 0.058 5004 Dihedral : 16.227 179.485 5097 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.90 % Favored : 94.07 % Rotamer: Outliers : 3.29 % Allowed : 23.93 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3643 helix: 1.71 (0.15), residues: 1360 sheet: 0.51 (0.27), residues: 384 loop : -1.16 (0.14), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 678 TYR 0.021 0.001 TYR M 361 PHE 0.007 0.001 PHE D1325 TRP 0.009 0.001 TRP M 126 HIS 0.005 0.001 HIS M 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (29798) covalent geometry : angle 0.55303 / 0.29 (40905) hydrogen bonds : bond 0.03590 / 2.47 ( 1263) hydrogen bonds : angle 3.87963 / 2.67 ( 3481) metal coordination : bond 0.01342 / 0.67 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 120 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: B 76 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: B 93 GLN cc_start: 0.9199 (tp40) cc_final: 0.8538 (mm110) REVERT: B 215 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8304 (tm-30) REVERT: C 105 TYR cc_start: 0.8471 (m-10) cc_final: 0.7797 (m-80) REVERT: C 240 GLU cc_start: 0.9017 (OUTLIER) cc_final: 0.8802 (mp0) REVERT: C 246 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9528 (pp) REVERT: C 370 MET cc_start: 0.8534 (tmm) cc_final: 0.8314 (ppp) REVERT: C 459 MET cc_start: 0.9113 (OUTLIER) cc_final: 0.8872 (mtp) REVERT: C 470 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8816 (mtt-85) REVERT: C 492 MET cc_start: 0.8024 (mmp) cc_final: 0.7779 (mmm) REVERT: C 548 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.7564 (mtp85) REVERT: C 1069 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.8247 (ptt-90) REVERT: C 1137 GLU cc_start: 0.8736 (OUTLIER) cc_final: 0.8521 (pm20) REVERT: C 1220 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.9008 (tt0) REVERT: C 1233 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9254 (mt) REVERT: D 160 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9071 (pp) REVERT: D 179 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.8833 (mppt) REVERT: D 255 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8485 (mm) REVERT: D 832 LYS cc_start: 0.9553 (OUTLIER) cc_final: 0.8969 (mptp) REVERT: D 901 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.7775 (ptp-170) REVERT: D 1330 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8906 (tmm-80) REVERT: E 42 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8490 (mp0) outliers start: 89 outliers final: 42 residues processed: 198 average time/residue: 0.5723 time to fit residues: 136.0612 Evaluate side-chains 180 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 119 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 47 optimal weight: 0.0020 chunk 12 optimal weight: 10.0000 chunk 217 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 340 optimal weight: 50.0000 chunk 181 optimal weight: 10.0000 chunk 311 optimal weight: 20.0000 chunk 76 optimal weight: 40.0000 chunk 21 optimal weight: 10.0000 chunk 369 optimal weight: 70.0000 overall best weight: 5.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN D 430 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.066373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.041264 restraints weight = 108142.325| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.32 r_work: 0.2659 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 29802 Z= 0.185 Angle : 0.582 12.078 40905 Z= 0.304 Chirality : 0.042 0.251 4851 Planarity : 0.004 0.058 5004 Dihedral : 16.264 179.895 5095 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.20 % Favored : 93.77 % Rotamer: Outliers : 3.55 % Allowed : 23.67 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.14), residues: 3643 helix: 1.73 (0.15), residues: 1363 sheet: 0.52 (0.27), residues: 382 loop : -1.16 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 678 TYR 0.033 0.001 TYR M 361 PHE 0.011 0.001 PHE D 49 TRP 0.009 0.001 TRP M 126 HIS 0.005 0.001 HIS M 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (29798) covalent geometry : angle 0.58234 / 0.30 (40905) hydrogen bonds : bond 0.03937 / 2.69 ( 1263) hydrogen bonds : angle 3.89442 / 2.68 ( 3481) metal coordination : bond 0.00975 / 0.49 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 120 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: B 76 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8125 (mt-10) REVERT: B 93 GLN cc_start: 0.9207 (tp40) cc_final: 0.8599 (mm110) REVERT: B 215 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8326 (tm-30) REVERT: C 105 TYR cc_start: 0.8568 (m-10) cc_final: 0.7884 (m-80) REVERT: C 246 LEU cc_start: 0.9753 (OUTLIER) cc_final: 0.9537 (pp) REVERT: C 459 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8910 (mtt) REVERT: C 470 ARG cc_start: 0.9095 (OUTLIER) cc_final: 0.8851 (mtt-85) REVERT: C 492 MET cc_start: 0.8146 (mmp) cc_final: 0.7894 (mmm) REVERT: C 548 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.7528 (mtp85) REVERT: C 611 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8649 (tt0) REVERT: C 1069 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8280 (ptt-90) REVERT: C 1220 GLN cc_start: 0.9305 (OUTLIER) cc_final: 0.9003 (tt0) REVERT: C 1233 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9278 (mt) REVERT: D 160 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9060 (pp) REVERT: D 179 LYS cc_start: 0.9298 (OUTLIER) cc_final: 0.8862 (mppt) REVERT: D 330 MET cc_start: 0.9398 (OUTLIER) cc_final: 0.9182 (mpp) REVERT: D 701 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9065 (tt) REVERT: D 832 LYS cc_start: 0.9558 (OUTLIER) cc_final: 0.9028 (mmtt) REVERT: D 901 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.7741 (ptp-170) REVERT: D 1316 THR cc_start: 0.9402 (OUTLIER) cc_final: 0.9153 (p) REVERT: D 1330 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8932 (tmm-80) REVERT: E 8 ASP cc_start: 0.8939 (m-30) cc_final: 0.8656 (m-30) REVERT: E 42 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8411 (mp0) outliers start: 96 outliers final: 47 residues processed: 205 average time/residue: 0.5779 time to fit residues: 141.7224 Evaluate side-chains 186 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 119 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 63 optimal weight: 7.9990 chunk 350 optimal weight: 40.0000 chunk 272 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 192 optimal weight: 6.9990 chunk 4 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 chunk 155 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN D 430 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.066271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.041343 restraints weight = 107381.460| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.32 r_work: 0.2662 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29802 Z= 0.172 Angle : 0.582 12.269 40905 Z= 0.303 Chirality : 0.042 0.251 4851 Planarity : 0.004 0.058 5004 Dihedral : 16.258 179.492 5095 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 3.03 % Allowed : 23.93 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.14), residues: 3643 helix: 1.77 (0.15), residues: 1355 sheet: 0.42 (0.27), residues: 392 loop : -1.17 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 678 TYR 0.018 0.001 TYR M 361 PHE 0.009 0.001 PHE D 49 TRP 0.009 0.001 TRP M 126 HIS 0.004 0.001 HIS M 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (29798) covalent geometry : angle 0.58240 / 0.30 (40905) hydrogen bonds : bond 0.03868 / 2.65 ( 1263) hydrogen bonds : angle 3.89096 / 2.68 ( 3481) metal coordination : bond 0.01129 / 0.57 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 122 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8403 (tt0) REVERT: B 76 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: B 93 GLN cc_start: 0.9220 (tp40) cc_final: 0.8608 (mm110) REVERT: B 95 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8789 (mtmt) REVERT: B 215 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8292 (tm-30) REVERT: C 105 TYR cc_start: 0.8582 (m-10) cc_final: 0.7886 (m-80) REVERT: C 124 MET cc_start: 0.8953 (ptp) cc_final: 0.8711 (pmm) REVERT: C 240 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8852 (mp0) REVERT: C 246 LEU cc_start: 0.9748 (OUTLIER) cc_final: 0.9536 (pp) REVERT: C 459 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8879 (mtt) REVERT: C 492 MET cc_start: 0.8126 (mmp) cc_final: 0.7871 (mmm) REVERT: C 548 ARG cc_start: 0.9302 (OUTLIER) cc_final: 0.7525 (mtp85) REVERT: C 611 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8651 (tt0) REVERT: C 741 MET cc_start: 0.8653 (ttt) cc_final: 0.8365 (ttm) REVERT: C 1069 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8300 (ptt-90) REVERT: C 1137 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8529 (pm20) REVERT: C 1220 GLN cc_start: 0.9297 (OUTLIER) cc_final: 0.9001 (tt0) REVERT: C 1233 LEU cc_start: 0.9519 (OUTLIER) cc_final: 0.9266 (mt) REVERT: D 160 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9047 (pp) REVERT: D 179 LYS cc_start: 0.9293 (OUTLIER) cc_final: 0.8854 (mppt) REVERT: D 701 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9072 (tt) REVERT: D 832 LYS cc_start: 0.9555 (OUTLIER) cc_final: 0.9029 (mmtt) REVERT: D 901 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.7803 (ptp-170) REVERT: D 1316 THR cc_start: 0.9407 (OUTLIER) cc_final: 0.9160 (p) REVERT: D 1330 ARG cc_start: 0.9202 (OUTLIER) cc_final: 0.8924 (tmm-80) REVERT: E 42 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8445 (mp0) outliers start: 82 outliers final: 47 residues processed: 195 average time/residue: 0.5922 time to fit residues: 138.4905 Evaluate side-chains 187 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 120 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 103 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 127 optimal weight: 0.5980 chunk 286 optimal weight: 50.0000 chunk 117 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 281 optimal weight: 40.0000 chunk 326 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 346 optimal weight: 20.0000 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN D 430 HIS M 377 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.066428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.041397 restraints weight = 107195.058| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.34 r_work: 0.2668 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29802 Z= 0.156 Angle : 0.581 13.876 40905 Z= 0.302 Chirality : 0.042 0.253 4851 Planarity : 0.004 0.058 5004 Dihedral : 16.247 178.986 5095 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 2.92 % Allowed : 24.04 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.14), residues: 3643 helix: 1.78 (0.15), residues: 1354 sheet: 0.45 (0.27), residues: 392 loop : -1.15 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 69 TYR 0.019 0.001 TYR M 361 PHE 0.009 0.001 PHE D1325 TRP 0.009 0.001 TRP M 126 HIS 0.004 0.001 HIS M 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (29798) covalent geometry : angle 0.58096 / 0.30 (40905) hydrogen bonds : bond 0.03760 / 2.57 ( 1263) hydrogen bonds : angle 3.86311 / 2.66 ( 3481) metal coordination : bond 0.01177 / 0.59 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 122 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8286 (pm20) cc_final: 0.8075 (pm20) REVERT: A 206 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: B 76 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8099 (mt-10) REVERT: B 93 GLN cc_start: 0.9207 (tp40) cc_final: 0.8580 (mm110) REVERT: B 215 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: C 105 TYR cc_start: 0.8598 (m-10) cc_final: 0.7896 (m-80) REVERT: C 124 MET cc_start: 0.8907 (ptp) cc_final: 0.8604 (pmm) REVERT: C 246 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9533 (pp) REVERT: C 459 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8865 (mtt) REVERT: C 470 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8842 (mtt-85) REVERT: C 492 MET cc_start: 0.8069 (mmp) cc_final: 0.7827 (mmm) REVERT: C 548 ARG cc_start: 0.9305 (OUTLIER) cc_final: 0.7527 (mtp85) REVERT: C 611 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8652 (tt0) REVERT: C 741 MET cc_start: 0.8654 (ttt) cc_final: 0.8339 (ttm) REVERT: C 1069 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8298 (ptt-90) REVERT: C 1137 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8510 (pm20) REVERT: C 1220 GLN cc_start: 0.9295 (OUTLIER) cc_final: 0.9005 (tt0) REVERT: C 1233 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9260 (mt) REVERT: C 1315 MET cc_start: 0.9245 (ttm) cc_final: 0.9036 (ttp) REVERT: D 160 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9009 (pp) REVERT: D 179 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8850 (mppt) REVERT: D 466 MET cc_start: 0.9401 (mtm) cc_final: 0.9200 (mtm) REVERT: D 701 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9072 (tt) REVERT: D 832 LYS cc_start: 0.9554 (OUTLIER) cc_final: 0.9030 (mmtt) REVERT: D 901 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7797 (ptp-170) REVERT: D 1222 ARG cc_start: 0.9515 (OUTLIER) cc_final: 0.8922 (ttm-80) REVERT: D 1316 THR cc_start: 0.9413 (OUTLIER) cc_final: 0.9167 (p) REVERT: D 1330 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8898 (tmm-80) REVERT: E 42 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8365 (mp0) outliers start: 79 outliers final: 47 residues processed: 194 average time/residue: 0.6001 time to fit residues: 139.0390 Evaluate side-chains 188 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 120 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 436 ARG Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 470 ARG Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 611 GLU Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 701 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 857 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 104 optimal weight: 0.8980 chunk 79 optimal weight: 50.0000 chunk 115 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 260 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 199 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 207 optimal weight: 0.0170 chunk 103 optimal weight: 7.9990 overall best weight: 3.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 GLN D 430 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.066304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.041289 restraints weight = 109211.982| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.31 r_work: 0.2663 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29802 Z= 0.157 Angle : 0.583 13.193 40905 Z= 0.303 Chirality : 0.042 0.254 4851 Planarity : 0.004 0.057 5004 Dihedral : 16.243 178.575 5095 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.12 % Favored : 93.85 % Rotamer: Outliers : 2.70 % Allowed : 24.30 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.14), residues: 3643 helix: 1.83 (0.15), residues: 1347 sheet: 0.45 (0.27), residues: 392 loop : -1.11 (0.14), residues: 1904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 12 TYR 0.018 0.001 TYR M 361 PHE 0.009 0.001 PHE D1325 TRP 0.009 0.001 TRP M 126 HIS 0.005 0.001 HIS M 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (29798) covalent geometry : angle 0.58298 / 0.30 (40905) hydrogen bonds : bond 0.03742 / 2.56 ( 1263) hydrogen bonds : angle 3.84674 / 2.65 ( 3481) metal coordination : bond 0.01161 / 0.59 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9525.36 seconds wall clock time: 162 minutes 37.19 seconds (9757.19 seconds total)