Starting phenix.real_space_refine on Sat Aug 8 14:03:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8red_19083/08_2026/8red_19083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8red_19083/08_2026/8red_19083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8red_19083/08_2026/8red_19083.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8red_19083/08_2026/8red_19083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8red_19083/08_2026/8red_19083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8red_19083/08_2026/8red_19083.map" model { file = "/net/cci-nas-00/data/ceres_data/8red_19083/08_2026/8red_19083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8red_19083/08_2026/8red_19083.cif" } resolution = 3.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 105 5.49 5 Mg 1 5.21 5 S 101 5.16 5 C 17785 2.51 5 N 5115 2.21 5 O 5769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28878 Number of models: 1 Model: "" Number of chains: 10 Chain: "N" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 936 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "R" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 171 Classifications: {'RNAv2': 8} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 6} Chain: "T" Number of atoms: 1051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1051 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain breaks: 1 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: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1735 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 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': 5} Unresolved non-hydrogen planarities: 75 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: 9654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 9654 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 53, 'TRANS': 1276} Chain breaks: 5 Unresolved non-hydrogen bonds: 721 Unresolved non-hydrogen angles: 878 Unresolved non-hydrogen dihedrals: 612 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 15, 'ASN:plan1': 6, 'TYR:plan': 4, 'ARG:plan': 19, 'PHE:plan': 10, 'ASP:plan': 18, 'GLU:plan': 31, 'HIS:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 462 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: 2337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2337 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 191 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'ASN:plan1': 6, 'ASP:plan': 10, 'GLU:plan': 11, 'HIS:plan': 2, 'PHE:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 135 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 16833 SG CYS D 70 106.207 113.798 91.476 1.00 46.98 S ATOM 16962 SG CYS D 88 105.029 115.022 94.292 1.00 36.36 S ATOM 23075 SG CYS D 898 100.706 46.830 88.144 1.00 20.87 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.29 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.29 Time building chain proxies: 5.64, per 1000 atoms: 0.20 Number of scatterers: 28878 At special positions: 0 Unit cell: (142.576, 170.448, 168.304, 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 101 16.00 P 105 15.00 Mg 1 11.99 O 5769 8.00 N 5115 7.00 C 17785 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: 2.31 Conformation dependent library (CDL) restraints added in 1.5 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 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6706 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 43 sheets defined 39.8% alpha, 14.2% beta 41 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.740A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.841A 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 232 removed outlier: 4.118A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.647A pdb=" N ASN A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.881A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.681A pdb=" N LEU A 289 " --> pdb=" O THR A 285 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 285 through 290' Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.669A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.810A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.649A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.757A pdb=" N ILE B 115 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.721A 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 10 removed outlier: 3.805A pdb=" N ARG C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.659A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.518A 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: 3.536A pdb=" N GLY C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 163' Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.734A pdb=" N LEU C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.633A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 removed outlier: 4.084A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 294' Processing helix chain 'C' and resid 318 through 329 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: 3.572A 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: 3.917A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.572A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.489A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.519A pdb=" N SER C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 612 Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.980A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 686 Processing helix chain 'C' and resid 687 through 689 No H-bonds generated for 'chain 'C' and resid 687 through 689' 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 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.607A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.661A pdb=" N ASP C 990 " --> pdb=" O ALA C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1000 removed outlier: 3.744A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.000A 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 Processing helix chain 'C' and resid 1099 through 1101 No H-bonds generated for 'chain 'C' and resid 1099 through 1101' Processing helix chain 'C' and resid 1102 through 1107 removed outlier: 3.927A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.975A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.605A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (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 1271 through 1282 Processing helix chain 'C' and resid 1284 through 1292 Processing helix chain 'C' and resid 1299 through 1311 Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.769A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 14 removed outlier: 4.115A pdb=" N THR D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 122 through 128 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 192 removed outlier: 4.098A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.902A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.245A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (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: 4.101A 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 removed outlier: 3.573A pdb=" N ILE D 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.786A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) 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 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 539 Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.590A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 671 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.833A 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 741 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.796A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.598A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.713A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1147 Processing helix chain 'D' and resid 1216 through 1225 removed outlier: 3.722A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY D1225 " --> pdb=" O LEU D1221 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.621A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.145A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1295 through 1299 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.555A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.677A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 4.314A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG D1372 " --> pdb=" O ASP D1368 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.636A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.865A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 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 146 Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 171 through 183 Processing helix chain 'M' and resid 194 through 205 removed outlier: 4.172A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 218 removed outlier: 4.171A 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 232 through 240 removed outlier: 3.853A pdb=" N MET M 236 " --> pdb=" O PHE M 232 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARG M 237 " --> pdb=" O ARG M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 256 removed outlier: 3.671A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU M 256 " --> pdb=" O LEU M 252 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 351 removed outlier: 4.187A pdb=" N ASP M 338 " --> pdb=" O GLU M 334 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 356 Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.729A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 removed outlier: 4.046A pdb=" N ILE M 381 " --> pdb=" O HIS M 377 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR M 385 " --> pdb=" O ILE M 381 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 429 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 466 removed outlier: 3.843A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 4.213A 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 18 removed outlier: 9.049A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N HIS A 23 " --> pdb=" O THR A 207 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR A 207 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N LYS A 25 " --> pdb=" O MET A 205 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N MET A 205 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N THR A 27 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE A 203 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLU A 29 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LEU A 201 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 111 removed outlier: 3.668A pdb=" N GLY A 106 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N ALA A 138 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 8.864A pdb=" N GLY A 108 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 9.607A pdb=" N GLU A 136 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 11.798A pdb=" N VAL A 110 " --> pdb=" O THR A 134 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N THR A 134 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (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 'B' and resid 15 through 19 removed outlier: 6.535A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 61 removed outlier: 3.534A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.565A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.815A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.709A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.709A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.514A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB5, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB6, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.089A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.782A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB9, first strand: chain 'C' and resid 633 through 636 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.862A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N MET C 768 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 723 through 727 removed outlier: 6.715A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.808A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.477A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LYS C1057 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N SER C 925 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 830 through 841 Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.983A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AD1, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 6.157A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (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: 3.612A 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 106 Processing sheet with id=AD5, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.958A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 4.080A 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 525 through 527 removed outlier: 6.600A pdb=" N MET D 525 " --> pdb=" O LYS D 549 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ARG D 551 " --> pdb=" O MET D 525 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.889A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AD9, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE1, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.776A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 957 through 958 Processing sheet with id=AE3, first strand: chain 'D' and resid 966 through 967 removed outlier: 3.533A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D1003 " --> pdb=" O LEU D 973 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1059 through 1062 removed outlier: 3.793A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1174 through 1177 removed outlier: 4.552A pdb=" N VAL D1176 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU D1188 " --> pdb=" O VAL D1176 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE7, first strand: chain 'M' and resid 287 through 289 1127 hydrogen bonds defined for protein. 3192 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 106 hydrogen bonds 212 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 9.95 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8823 1.33 - 1.45: 4467 1.45 - 1.58: 15832 1.58 - 1.70: 211 1.70 - 1.82: 175 Bond restraints: 29508 Sorted by residual: bond pdb=" CG PRO C 567 " pdb=" CD PRO C 567 " ideal model delta sigma weight residual 1.503 1.362 0.141 3.40e-02 8.65e+02 1.71e+01 bond pdb=" C3' DA T 16 " pdb=" C2' DA T 16 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.32e+01 bond pdb=" CB PRO A 251 " pdb=" CG PRO A 251 " ideal model delta sigma weight residual 1.492 1.662 -0.170 5.00e-02 4.00e+02 1.16e+01 bond pdb=" C3' DT N 4 " pdb=" C2' DT N 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DA T 18 " pdb=" C2' DA T 18 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.96e+00 ... (remaining 29503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.58: 40421 4.58 - 9.17: 84 9.17 - 13.75: 9 13.75 - 18.33: 3 18.33 - 22.92: 1 Bond angle restraints: 40518 Sorted by residual: angle pdb=" CA PRO C 567 " pdb=" N PRO C 567 " pdb=" CD PRO C 567 " ideal model delta sigma weight residual 112.00 94.88 17.12 1.40e+00 5.10e-01 1.50e+02 angle pdb=" CA PRO D1139 " pdb=" N PRO D1139 " pdb=" CD PRO D1139 " ideal model delta sigma weight residual 112.00 96.40 15.60 1.40e+00 5.10e-01 1.24e+02 angle pdb=" CA PRO A 251 " pdb=" N PRO A 251 " pdb=" CD PRO A 251 " ideal model delta sigma weight residual 112.00 97.20 14.80 1.40e+00 5.10e-01 1.12e+02 angle pdb=" CA PRO C 375 " pdb=" N PRO C 375 " pdb=" CD PRO C 375 " ideal model delta sigma weight residual 112.00 101.42 10.58 1.40e+00 5.10e-01 5.71e+01 angle pdb=" N PRO C 567 " pdb=" CD PRO C 567 " pdb=" CG PRO C 567 " ideal model delta sigma weight residual 103.20 93.56 9.64 1.50e+00 4.44e-01 4.13e+01 ... (remaining 40513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.55: 16718 35.55 - 71.09: 959 71.09 - 106.64: 51 106.64 - 142.18: 1 142.18 - 177.73: 3 Dihedral angle restraints: 17732 sinusoidal: 7338 harmonic: 10394 Sorted by residual: dihedral pdb=" C4' G R -1 " pdb=" C3' G R -1 " pdb=" C2' G R -1 " pdb=" C1' G R -1 " ideal model delta sinusoidal sigma weight residual 36.34 -32.67 69.01 1 3.10e+00 1.04e-01 6.41e+02 dihedral pdb=" O4' G R -1 " pdb=" C4' G R -1 " pdb=" C3' G R -1 " pdb=" C2' G R -1 " ideal model delta sinusoidal sigma weight residual -35.15 22.54 -57.69 1 4.00e+00 6.25e-02 2.79e+02 dihedral pdb=" O4' G R -1 " pdb=" C2' G R -1 " pdb=" C1' G R -1 " pdb=" C3' G R -1 " ideal model delta sinusoidal sigma weight residual 25.59 -32.22 57.82 3 3.80e+00 6.93e-02 1.47e+02 ... (remaining 17729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 4436 0.085 - 0.169: 362 0.169 - 0.254: 8 0.254 - 0.339: 1 0.339 - 0.423: 1 Chirality restraints: 4808 Sorted by residual: chirality pdb=" P C R 0 " pdb=" OP1 C R 0 " pdb=" OP2 C R 0 " pdb=" O5' C R 0 " both_signs ideal model delta sigma weight residual True 2.17 -2.60 -0.42 2.00e-01 2.50e+01 4.48e+00 chirality pdb=" C2' G R -1 " pdb=" C3' G R -1 " pdb=" O2' G R -1 " pdb=" C1' G R -1 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" P C R 1 " pdb=" OP1 C R 1 " pdb=" OP2 C R 1 " pdb=" O5' C R 1 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 4805 not shown) Planarity restraints: 4943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D1138 " 0.162 5.00e-02 4.00e+02 2.25e-01 8.07e+01 pdb=" N PRO D1139 " -0.386 5.00e-02 4.00e+02 pdb=" CA PRO D1139 " 0.137 5.00e-02 4.00e+02 pdb=" CD PRO D1139 " 0.087 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 566 " -0.145 5.00e-02 4.00e+02 2.01e-01 6.49e+01 pdb=" N PRO C 567 " 0.347 5.00e-02 4.00e+02 pdb=" CA PRO C 567 " -0.112 5.00e-02 4.00e+02 pdb=" CD PRO C 567 " -0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 250 " -0.100 5.00e-02 4.00e+02 1.40e-01 3.12e+01 pdb=" N PRO A 251 " 0.241 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " -0.069 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " -0.072 5.00e-02 4.00e+02 ... (remaining 4940 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 425 2.65 - 3.21: 26847 3.21 - 3.78: 44241 3.78 - 4.34: 56958 4.34 - 4.90: 93924 Nonbonded interactions: 222395 Sorted by model distance: nonbonded pdb=" O LEU D 71 " pdb="ZN ZN D1502 " model vdw 2.088 2.230 nonbonded pdb=" O PRO B 179 " pdb=" OG1 THR B 207 " model vdw 2.176 3.040 nonbonded pdb=" O LEU D 363 " pdb=" OG SER D 486 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASP C 654 " pdb=" NE2 GLN C 659 " model vdw 2.186 3.120 nonbonded pdb=" NH2 ARG C 528 " pdb=" O SER C 576 " model vdw 2.191 3.120 ... (remaining 222390 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.850 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 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 : 0.005 0.170 29511 Z= 0.265 Angle : 0.710 22.919 40518 Z= 0.423 Chirality : 0.045 0.423 4808 Planarity : 0.007 0.225 4943 Dihedral : 19.801 177.728 11026 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.44 % Favored : 93.54 % Rotamer: Outliers : 0.41 % Allowed : 29.69 % Favored : 69.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.58 (0.14), residues: 3589 helix: 0.90 (0.15), residues: 1282 sheet: 0.49 (0.26), residues: 377 loop : -1.52 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG D1149 TYR 0.012 0.001 TYR D 631 PHE 0.018 0.001 PHE D 7 TRP 0.033 0.002 TRP M 212 HIS 0.005 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.26 (29508) covalent geometry : angle 0.71016 / 0.42 (40518) hydrogen bonds : bond 0.16399 / 16.46 ( 1213) hydrogen bonds : angle 5.83389 / 7.39 ( 3404) metal coordination : bond 0.00205 / 0.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 270 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 MET cc_start: 0.7391 (ttp) cc_final: 0.7148 (ttt) REVERT: M 193 LYS cc_start: 0.8159 (mmmt) cc_final: 0.7917 (mttt) REVERT: M 280 LYS cc_start: 0.6541 (pttm) cc_final: 0.5493 (tppt) REVERT: M 346 CYS cc_start: 0.8325 (m) cc_final: 0.7868 (p) REVERT: M 354 PHE cc_start: 0.7567 (t80) cc_final: 0.7201 (t80) REVERT: M 365 MET cc_start: 0.3420 (tmm) cc_final: 0.3079 (tpt) REVERT: M 406 HIS cc_start: 0.6298 (m90) cc_final: 0.5596 (m-70) REVERT: M 426 LYS cc_start: 0.7437 (pttm) cc_final: 0.7159 (ptpt) outliers start: 11 outliers final: 1 residues processed: 278 average time/residue: 0.1766 time to fit residues: 78.8702 Evaluate side-chains 184 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 183 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 304 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.0970 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 148 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN D 450 HIS D 477 GLN D 504 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 ASN E 62 GLN M 262 GLN M 351 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.077910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.052998 restraints weight = 126578.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.054432 restraints weight = 67644.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.055355 restraints weight = 45055.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.055942 restraints weight = 35087.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.056257 restraints weight = 30262.048| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 29511 Z= 0.153 Angle : 0.655 11.252 40518 Z= 0.335 Chirality : 0.046 0.993 4808 Planarity : 0.006 0.141 4943 Dihedral : 16.585 178.312 5071 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 3.51 % Allowed : 27.60 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.42 (0.14), residues: 3589 helix: 0.98 (0.15), residues: 1328 sheet: 0.62 (0.26), residues: 389 loop : -1.47 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 317 TYR 0.016 0.001 TYR D 631 PHE 0.015 0.001 PHE C1270 TRP 0.012 0.001 TRP M 126 HIS 0.003 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (29508) covalent geometry : angle 0.65511 / 0.33 (40518) hydrogen bonds : bond 0.04330 / 4.48 ( 1213) hydrogen bonds : angle 4.63748 / 5.96 ( 3404) metal coordination : bond 0.00328 / 0.20 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 202 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8889 (mp) cc_final: 0.8586 (tp) REVERT: A 277 TYR cc_start: 0.7839 (m-80) cc_final: 0.7635 (m-80) REVERT: B 25 LYS cc_start: 0.9124 (ttmm) cc_final: 0.8850 (ttmm) REVERT: B 27 THR cc_start: 0.9571 (OUTLIER) cc_final: 0.9211 (p) REVERT: C 62 TYR cc_start: 0.7699 (p90) cc_final: 0.7326 (p90) REVERT: C 685 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8832 (mtm) REVERT: C 826 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8109 (t0) REVERT: C 903 ARG cc_start: 0.8569 (mtt180) cc_final: 0.8223 (mmt180) REVERT: C 908 GLU cc_start: 0.8866 (mp0) cc_final: 0.8463 (tp30) REVERT: C 1085 MET cc_start: 0.9254 (mmm) cc_final: 0.8921 (mmm) REVERT: C 1304 MET cc_start: 0.9503 (tpt) cc_final: 0.9127 (tpp) REVERT: D 29 MET cc_start: 0.8947 (mmm) cc_final: 0.8078 (tmm) REVERT: D 743 MET cc_start: 0.8511 (ttp) cc_final: 0.8306 (ttm) REVERT: D 821 MET cc_start: 0.9063 (tpp) cc_final: 0.8715 (tpp) REVERT: D 1366 HIS cc_start: 0.9273 (OUTLIER) cc_final: 0.8864 (m-70) REVERT: M 262 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7997 (pp30) REVERT: M 280 LYS cc_start: 0.7212 (pttm) cc_final: 0.6434 (tppt) REVERT: M 346 CYS cc_start: 0.8633 (m) cc_final: 0.8112 (p) REVERT: M 365 MET cc_start: 0.4192 (mmm) cc_final: 0.3729 (mmm) REVERT: M 406 HIS cc_start: 0.7000 (m90) cc_final: 0.6270 (m-70) REVERT: M 425 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8442 (mmtt) outliers start: 94 outliers final: 45 residues processed: 284 average time/residue: 0.1606 time to fit residues: 75.2638 Evaluate side-chains 232 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 182 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 316 MET Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 781 ASP Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 705 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1219 ASP Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 262 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 126 optimal weight: 0.0870 chunk 235 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 59 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 142 optimal weight: 7.9990 chunk 197 optimal weight: 0.6980 chunk 328 optimal weight: 6.9990 overall best weight: 3.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN 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 = 0.078171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.053148 restraints weight = 127432.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.054568 restraints weight = 68097.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.055466 restraints weight = 46059.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.056004 restraints weight = 36329.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.056355 restraints weight = 31732.927| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 29511 Z= 0.146 Angle : 0.599 10.173 40518 Z= 0.310 Chirality : 0.043 0.661 4808 Planarity : 0.005 0.109 4943 Dihedral : 16.576 178.709 5067 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.55 % Allowed : 27.45 % Favored : 69.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.28 (0.14), residues: 3589 helix: 1.18 (0.15), residues: 1333 sheet: 0.58 (0.26), residues: 389 loop : -1.44 (0.14), residues: 1867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 317 TYR 0.019 0.001 TYR D1232 PHE 0.013 0.001 PHE M 355 TRP 0.015 0.001 TRP M 212 HIS 0.003 0.001 HIS D 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (29508) covalent geometry : angle 0.59889 / 0.31 (40518) hydrogen bonds : bond 0.03813 / 3.89 ( 1213) hydrogen bonds : angle 4.34629 / 5.58 ( 3404) metal coordination : bond 0.00186 / 0.15 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 192 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 VAL cc_start: 0.9651 (t) cc_final: 0.9415 (p) REVERT: A 253 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8529 (tp) REVERT: A 277 TYR cc_start: 0.7774 (m-80) cc_final: 0.7544 (m-80) REVERT: B 25 LYS cc_start: 0.9100 (ttmm) cc_final: 0.8827 (ttmm) REVERT: B 27 THR cc_start: 0.9556 (OUTLIER) cc_final: 0.9192 (p) REVERT: B 86 LYS cc_start: 0.9350 (ttmm) cc_final: 0.8980 (ttmm) REVERT: C 62 TYR cc_start: 0.7714 (p90) cc_final: 0.7301 (p90) REVERT: C 488 MET cc_start: 0.7865 (mmt) cc_final: 0.7391 (mtp) REVERT: C 685 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8736 (mtm) REVERT: C 826 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8139 (t0) REVERT: C 853 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7137 (p0) REVERT: C 903 ARG cc_start: 0.8580 (mtt180) cc_final: 0.8296 (mmt180) REVERT: C 951 MET cc_start: 0.9115 (tmm) cc_final: 0.8821 (tmm) REVERT: C 1029 LEU cc_start: 0.9499 (tp) cc_final: 0.8858 (pp) REVERT: C 1085 MET cc_start: 0.9314 (mmm) cc_final: 0.9001 (mmm) REVERT: C 1131 MET cc_start: 0.8919 (tpp) cc_final: 0.8696 (tpp) REVERT: C 1304 MET cc_start: 0.9445 (tpt) cc_final: 0.9117 (tpp) REVERT: D 248 ASP cc_start: 0.8956 (t0) cc_final: 0.8701 (t0) REVERT: D 698 MET cc_start: 0.9186 (tpp) cc_final: 0.8880 (mmm) REVERT: D 725 MET cc_start: 0.9203 (mtm) cc_final: 0.8757 (mtm) REVERT: D 1366 HIS cc_start: 0.9310 (OUTLIER) cc_final: 0.8933 (m-70) REVERT: M 125 MET cc_start: 0.9052 (mmt) cc_final: 0.8799 (mmm) REVERT: M 280 LYS cc_start: 0.7349 (pttm) cc_final: 0.6632 (tppt) REVERT: M 346 CYS cc_start: 0.8621 (m) cc_final: 0.8102 (p) REVERT: M 406 HIS cc_start: 0.6893 (m90) cc_final: 0.6143 (m-70) REVERT: M 425 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8500 (mmtt) outliers start: 95 outliers final: 54 residues processed: 274 average time/residue: 0.1467 time to fit residues: 68.5988 Evaluate side-chains 237 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 177 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 304 ASP Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 286 VAL Chi-restraints excluded: chain M residue 426 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 189 optimal weight: 7.9990 chunk 98 optimal weight: 20.0000 chunk 321 optimal weight: 7.9990 chunk 136 optimal weight: 30.0000 chunk 290 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 155 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 246 optimal weight: 0.9990 chunk 146 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 357 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.077966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.053032 restraints weight = 127970.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.054402 restraints weight = 69549.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.055289 restraints weight = 47377.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055824 restraints weight = 37636.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.056129 restraints weight = 33042.040| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29511 Z= 0.142 Angle : 0.587 9.273 40518 Z= 0.304 Chirality : 0.043 0.506 4808 Planarity : 0.004 0.089 4943 Dihedral : 16.593 178.778 5067 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.85 % Allowed : 27.33 % Favored : 68.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 3589 helix: 1.25 (0.15), residues: 1337 sheet: 0.55 (0.26), residues: 389 loop : -1.42 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 101 TYR 0.020 0.001 TYR D1232 PHE 0.015 0.001 PHE D 116 TRP 0.016 0.001 TRP A 321 HIS 0.002 0.001 HIS M 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (29508) covalent geometry : angle 0.58700 / 0.30 (40518) hydrogen bonds : bond 0.03535 / 3.63 ( 1213) hydrogen bonds : angle 4.21378 / 5.45 ( 3404) metal coordination : bond 0.00200 / 0.17 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 182 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 VAL cc_start: 0.9637 (t) cc_final: 0.9404 (p) REVERT: B 25 LYS cc_start: 0.9088 (ttmm) cc_final: 0.8845 (ttmm) REVERT: B 27 THR cc_start: 0.9572 (OUTLIER) cc_final: 0.9213 (p) REVERT: B 86 LYS cc_start: 0.9347 (ttmm) cc_final: 0.8973 (ttmm) REVERT: C 62 TYR cc_start: 0.7729 (p90) cc_final: 0.7291 (p90) REVERT: C 239 MET cc_start: 0.6880 (mmm) cc_final: 0.6109 (mmm) REVERT: C 685 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8750 (mtm) REVERT: C 826 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8113 (t0) REVERT: C 853 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7121 (p0) REVERT: C 903 ARG cc_start: 0.8586 (mtt180) cc_final: 0.8228 (mtt-85) REVERT: C 951 MET cc_start: 0.9059 (tmm) cc_final: 0.8721 (tmm) REVERT: C 1085 MET cc_start: 0.9287 (mmm) cc_final: 0.8999 (mmm) REVERT: C 1239 VAL cc_start: 0.9066 (OUTLIER) cc_final: 0.8826 (p) REVERT: C 1304 MET cc_start: 0.9429 (tpt) cc_final: 0.9128 (tpp) REVERT: D 29 MET cc_start: 0.8909 (mmm) cc_final: 0.8095 (tmm) REVERT: D 248 ASP cc_start: 0.8965 (t0) cc_final: 0.8736 (t0) REVERT: D 698 MET cc_start: 0.9129 (tpp) cc_final: 0.8595 (mmm) REVERT: D 725 MET cc_start: 0.9147 (mtm) cc_final: 0.8681 (mtm) REVERT: D 821 MET cc_start: 0.9156 (tpp) cc_final: 0.8873 (tpp) REVERT: D 1366 HIS cc_start: 0.9331 (OUTLIER) cc_final: 0.9002 (m-70) REVERT: M 125 MET cc_start: 0.9063 (mmt) cc_final: 0.8811 (mmm) REVERT: M 280 LYS cc_start: 0.7292 (pttm) cc_final: 0.6568 (tppt) REVERT: M 346 CYS cc_start: 0.8611 (m) cc_final: 0.8105 (p) REVERT: M 406 HIS cc_start: 0.6902 (m90) cc_final: 0.6155 (m-70) REVERT: M 425 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8429 (mmtt) outliers start: 103 outliers final: 58 residues processed: 270 average time/residue: 0.1463 time to fit residues: 67.1183 Evaluate side-chains 242 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 178 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 220 ILE Chi-restraints excluded: chain M residue 286 VAL Chi-restraints excluded: chain M residue 426 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 118 optimal weight: 0.8980 chunk 359 optimal weight: 8.9990 chunk 242 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 347 optimal weight: 40.0000 chunk 291 optimal weight: 0.0050 chunk 176 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 5 optimal weight: 50.0000 chunk 3 optimal weight: 40.0000 chunk 318 optimal weight: 8.9990 overall best weight: 3.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 276 HIS ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.077690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.052701 restraints weight = 128149.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.054085 restraints weight = 69787.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.054964 restraints weight = 47591.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.055476 restraints weight = 37840.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.055805 restraints weight = 33315.249| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29511 Z= 0.132 Angle : 0.579 9.611 40518 Z= 0.297 Chirality : 0.042 0.427 4808 Planarity : 0.004 0.077 4943 Dihedral : 16.595 178.626 5067 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 3.29 % Allowed : 28.53 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.18 (0.14), residues: 3589 helix: 1.29 (0.15), residues: 1338 sheet: 0.57 (0.26), residues: 379 loop : -1.38 (0.14), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 317 TYR 0.020 0.001 TYR D1232 PHE 0.008 0.001 PHE C 405 TRP 0.012 0.001 TRP M 212 HIS 0.002 0.001 HIS M 391 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (29508) covalent geometry : angle 0.57854 / 0.30 (40518) hydrogen bonds : bond 0.03440 / 3.52 ( 1213) hydrogen bonds : angle 4.11054 / 5.32 ( 3404) metal coordination : bond 0.00217 / 0.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 186 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8871 (ttmm) REVERT: B 27 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9208 (p) REVERT: B 86 LYS cc_start: 0.9337 (ttmm) cc_final: 0.8944 (ttmm) REVERT: C 239 MET cc_start: 0.7245 (mmm) cc_final: 0.6422 (mmm) REVERT: C 488 MET cc_start: 0.7858 (mmt) cc_final: 0.7385 (mtp) REVERT: C 685 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8733 (mtm) REVERT: C 826 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.8113 (t0) REVERT: C 853 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7131 (p0) REVERT: C 951 MET cc_start: 0.9058 (tmm) cc_final: 0.8735 (tmm) REVERT: C 1085 MET cc_start: 0.9278 (mmm) cc_final: 0.8995 (mmm) REVERT: C 1230 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8495 (ttp) REVERT: C 1239 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8811 (p) REVERT: C 1265 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.8103 (t80) REVERT: C 1304 MET cc_start: 0.9413 (tpt) cc_final: 0.9138 (tpp) REVERT: C 1319 MET cc_start: 0.8916 (tmm) cc_final: 0.8643 (tmm) REVERT: C 1333 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9128 (mp) REVERT: D 29 MET cc_start: 0.8866 (mmm) cc_final: 0.7941 (tmm) REVERT: D 248 ASP cc_start: 0.8990 (t0) cc_final: 0.8752 (t0) REVERT: D 698 MET cc_start: 0.9213 (tpp) cc_final: 0.8714 (mmm) REVERT: D 822 MET cc_start: 0.8061 (ttp) cc_final: 0.7837 (ttt) REVERT: D 1366 HIS cc_start: 0.9335 (OUTLIER) cc_final: 0.9008 (m-70) REVERT: M 115 GLU cc_start: 0.8303 (tp30) cc_final: 0.7995 (mp0) REVERT: M 125 MET cc_start: 0.9016 (mmt) cc_final: 0.8750 (mmm) REVERT: M 130 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8863 (mm) REVERT: M 280 LYS cc_start: 0.7290 (pttm) cc_final: 0.6565 (tppt) REVERT: M 346 CYS cc_start: 0.8606 (m) cc_final: 0.8103 (p) REVERT: M 406 HIS cc_start: 0.6889 (m90) cc_final: 0.6211 (m-70) REVERT: M 425 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8421 (mmtt) outliers start: 88 outliers final: 56 residues processed: 262 average time/residue: 0.1596 time to fit residues: 70.6176 Evaluate side-chains 242 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 176 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 877 VAL Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 220 ILE Chi-restraints excluded: chain M residue 286 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 131 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 302 optimal weight: 40.0000 chunk 361 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 357 optimal weight: 10.0000 chunk 337 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 285 optimal weight: 20.0000 chunk 154 optimal weight: 0.0170 chunk 270 optimal weight: 20.0000 overall best weight: 6.6030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 314 ASN C 437 ASN D 158 GLN D 504 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 357 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.076033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.051436 restraints weight = 128308.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.052759 restraints weight = 69852.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.053617 restraints weight = 47698.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.054133 restraints weight = 37802.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.054450 restraints weight = 33088.237| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 29511 Z= 0.215 Angle : 0.622 12.107 40518 Z= 0.320 Chirality : 0.043 0.350 4808 Planarity : 0.004 0.070 4943 Dihedral : 16.647 179.197 5067 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 4.29 % Allowed : 27.82 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.19 (0.14), residues: 3589 helix: 1.29 (0.15), residues: 1338 sheet: 0.55 (0.26), residues: 394 loop : -1.40 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 317 TYR 0.020 0.001 TYR D1232 PHE 0.013 0.001 PHE D1325 TRP 0.011 0.001 TRP M 126 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.22 (29508) covalent geometry : angle 0.62181 / 0.32 (40518) hydrogen bonds : bond 0.03781 / 3.88 ( 1213) hydrogen bonds : angle 4.20194 / 5.42 ( 3404) metal coordination : bond 0.00418 / 0.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 171 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8850 (ttmm) REVERT: B 27 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9189 (p) REVERT: B 86 LYS cc_start: 0.9343 (ttmm) cc_final: 0.8918 (ttmm) REVERT: B 211 ILE cc_start: 0.9249 (OUTLIER) cc_final: 0.8982 (mm) REVERT: C 62 TYR cc_start: 0.7796 (OUTLIER) cc_final: 0.7395 (p90) REVERT: C 239 MET cc_start: 0.7564 (mmm) cc_final: 0.6550 (mmm) REVERT: C 853 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7173 (p0) REVERT: C 951 MET cc_start: 0.9099 (tmm) cc_final: 0.8789 (tmm) REVERT: C 1085 MET cc_start: 0.9283 (mmm) cc_final: 0.8986 (mmm) REVERT: C 1131 MET cc_start: 0.8714 (tpp) cc_final: 0.8511 (tpp) REVERT: C 1304 MET cc_start: 0.9461 (tpt) cc_final: 0.9182 (tpp) REVERT: C 1319 MET cc_start: 0.8979 (tmm) cc_final: 0.8692 (tmm) REVERT: C 1333 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9133 (mp) REVERT: D 29 MET cc_start: 0.8889 (mmm) cc_final: 0.7926 (tmm) REVERT: D 698 MET cc_start: 0.9245 (tpp) cc_final: 0.8778 (mmm) REVERT: D 747 MET cc_start: 0.8262 (ppp) cc_final: 0.7914 (ppp) REVERT: D 1366 HIS cc_start: 0.9320 (OUTLIER) cc_final: 0.9011 (m-70) REVERT: E 30 MET cc_start: 0.8701 (mtp) cc_final: 0.8383 (mtt) REVERT: M 115 GLU cc_start: 0.8375 (tp30) cc_final: 0.8022 (tp30) REVERT: M 130 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8856 (mm) REVERT: M 280 LYS cc_start: 0.7299 (pttm) cc_final: 0.6581 (tppt) REVERT: M 346 CYS cc_start: 0.8618 (m) cc_final: 0.8108 (p) REVERT: M 425 LYS cc_start: 0.8767 (mmtt) cc_final: 0.8410 (mmtt) outliers start: 115 outliers final: 75 residues processed: 271 average time/residue: 0.1467 time to fit residues: 66.9584 Evaluate side-chains 250 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 168 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1066 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 507 VAL Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 220 ILE Chi-restraints excluded: chain M residue 286 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 78 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 296 optimal weight: 20.0000 chunk 251 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 191 optimal weight: 7.9990 chunk 158 optimal weight: 2.9990 chunk 279 optimal weight: 8.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN C1136 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.075967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.051243 restraints weight = 128092.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.052579 restraints weight = 70020.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.053417 restraints weight = 47759.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.053955 restraints weight = 37905.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.054258 restraints weight = 33205.256| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2944 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2944 r_free = 0.2944 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2944 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29511 Z= 0.174 Angle : 0.597 10.160 40518 Z= 0.308 Chirality : 0.043 0.316 4808 Planarity : 0.004 0.064 4943 Dihedral : 16.640 179.390 5067 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.92 % Allowed : 28.16 % Favored : 67.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3589 helix: 1.31 (0.15), residues: 1338 sheet: 0.59 (0.26), residues: 393 loop : -1.39 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 780 TYR 0.020 0.001 TYR D1232 PHE 0.014 0.001 PHE M 355 TRP 0.009 0.001 TRP M 126 HIS 0.003 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (29508) covalent geometry : angle 0.59661 / 0.31 (40518) hydrogen bonds : bond 0.03628 / 3.73 ( 1213) hydrogen bonds : angle 4.14975 / 5.34 ( 3404) metal coordination : bond 0.00392 / 0.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 172 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8832 (ttmm) REVERT: B 27 THR cc_start: 0.9559 (OUTLIER) cc_final: 0.9186 (p) REVERT: B 211 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8976 (mm) REVERT: C 62 TYR cc_start: 0.7811 (OUTLIER) cc_final: 0.7403 (p90) REVERT: C 239 MET cc_start: 0.7631 (mmm) cc_final: 0.6905 (mmm) REVERT: C 488 MET cc_start: 0.7946 (mmt) cc_final: 0.7416 (mtp) REVERT: C 685 MET cc_start: 0.8948 (mtm) cc_final: 0.8498 (mtm) REVERT: C 853 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7103 (p0) REVERT: C 951 MET cc_start: 0.9090 (tmm) cc_final: 0.8776 (tmm) REVERT: C 1085 MET cc_start: 0.9258 (mmm) cc_final: 0.8971 (mmm) REVERT: C 1131 MET cc_start: 0.8752 (tpp) cc_final: 0.8527 (tpp) REVERT: C 1274 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8601 (mp0) REVERT: C 1304 MET cc_start: 0.9434 (tpt) cc_final: 0.9200 (tpp) REVERT: C 1319 MET cc_start: 0.9006 (tmm) cc_final: 0.8174 (tmm) REVERT: C 1333 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9061 (mp) REVERT: D 29 MET cc_start: 0.8913 (mmm) cc_final: 0.7951 (tmm) REVERT: D 115 TRP cc_start: 0.8544 (OUTLIER) cc_final: 0.7251 (m-90) REVERT: D 133 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8632 (ttm-80) REVERT: D 698 MET cc_start: 0.9244 (tpp) cc_final: 0.8737 (mmm) REVERT: D 747 MET cc_start: 0.8259 (ppp) cc_final: 0.7894 (ppp) REVERT: D 821 MET cc_start: 0.9195 (tpp) cc_final: 0.8907 (tpp) REVERT: D 1366 HIS cc_start: 0.9324 (OUTLIER) cc_final: 0.9038 (m-70) REVERT: E 30 MET cc_start: 0.8680 (mtp) cc_final: 0.8351 (mtt) REVERT: M 115 GLU cc_start: 0.8317 (tp30) cc_final: 0.8077 (tp30) REVERT: M 125 MET cc_start: 0.9080 (mmt) cc_final: 0.8824 (mmm) REVERT: M 130 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8855 (mm) REVERT: M 280 LYS cc_start: 0.7315 (pttm) cc_final: 0.6611 (tppt) REVERT: M 346 CYS cc_start: 0.8612 (m) cc_final: 0.8106 (p) REVERT: M 425 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8430 (mmtt) outliers start: 105 outliers final: 70 residues processed: 265 average time/residue: 0.1536 time to fit residues: 68.5799 Evaluate side-chains 247 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 167 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 220 ILE Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 286 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 51 optimal weight: 6.9990 chunk 167 optimal weight: 6.9990 chunk 300 optimal weight: 40.0000 chunk 134 optimal weight: 0.8980 chunk 308 optimal weight: 50.0000 chunk 230 optimal weight: 10.0000 chunk 303 optimal weight: 5.9990 chunk 273 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 196 optimal weight: 0.1980 chunk 221 optimal weight: 10.0000 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN D 504 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 408 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.076022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.051238 restraints weight = 127709.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.052610 restraints weight = 68437.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.053503 restraints weight = 46268.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.054039 restraints weight = 36368.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.054341 restraints weight = 31720.850| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29511 Z= 0.152 Angle : 0.592 10.052 40518 Z= 0.304 Chirality : 0.043 0.309 4808 Planarity : 0.004 0.061 4943 Dihedral : 16.619 179.279 5067 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.66 % Allowed : 28.08 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.14 (0.14), residues: 3589 helix: 1.35 (0.15), residues: 1337 sheet: 0.56 (0.26), residues: 399 loop : -1.39 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 780 TYR 0.021 0.001 TYR D1232 PHE 0.015 0.001 PHE M 355 TRP 0.009 0.001 TRP M 126 HIS 0.003 0.001 HIS M 377 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (29508) covalent geometry : angle 0.59184 / 0.30 (40518) hydrogen bonds : bond 0.03471 / 3.57 ( 1213) hydrogen bonds : angle 4.08384 / 5.24 ( 3404) metal coordination : bond 0.00366 / 0.25 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 172 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8832 (ttmm) REVERT: B 27 THR cc_start: 0.9552 (OUTLIER) cc_final: 0.9182 (p) REVERT: B 211 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.8968 (mm) REVERT: C 62 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.7432 (p90) REVERT: C 239 MET cc_start: 0.7631 (mmm) cc_final: 0.7053 (mmm) REVERT: C 488 MET cc_start: 0.7875 (mmt) cc_final: 0.7429 (mtp) REVERT: C 685 MET cc_start: 0.8939 (mtm) cc_final: 0.8386 (mtm) REVERT: C 853 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.7216 (p0) REVERT: C 951 MET cc_start: 0.9057 (tmm) cc_final: 0.8801 (tmm) REVERT: C 1085 MET cc_start: 0.9241 (mmm) cc_final: 0.8968 (mmm) REVERT: C 1131 MET cc_start: 0.8698 (tpp) cc_final: 0.8455 (tpp) REVERT: C 1274 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8582 (mp0) REVERT: C 1304 MET cc_start: 0.9405 (tpt) cc_final: 0.9195 (tpp) REVERT: C 1319 MET cc_start: 0.8967 (tmm) cc_final: 0.8316 (tmm) REVERT: C 1333 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9064 (mp) REVERT: D 29 MET cc_start: 0.8889 (mmm) cc_final: 0.7879 (tmm) REVERT: D 115 TRP cc_start: 0.8533 (OUTLIER) cc_final: 0.7256 (m-90) REVERT: D 133 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8631 (ttm-80) REVERT: D 581 MET cc_start: 0.8823 (mtp) cc_final: 0.8612 (mtt) REVERT: D 698 MET cc_start: 0.9251 (tpp) cc_final: 0.8766 (mmm) REVERT: D 725 MET cc_start: 0.9176 (mtm) cc_final: 0.8499 (mtm) REVERT: D 747 MET cc_start: 0.8176 (ppp) cc_final: 0.7864 (ppp) REVERT: D 785 ASP cc_start: 0.8371 (t0) cc_final: 0.8076 (t0) REVERT: D 821 MET cc_start: 0.9170 (tpp) cc_final: 0.8909 (tpp) REVERT: D 1366 HIS cc_start: 0.9324 (OUTLIER) cc_final: 0.9043 (m-70) REVERT: E 30 MET cc_start: 0.8657 (mtp) cc_final: 0.8336 (mtt) REVERT: M 125 MET cc_start: 0.9072 (mmt) cc_final: 0.8797 (mmm) REVERT: M 130 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8831 (mm) REVERT: M 201 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8210 (tp) REVERT: M 280 LYS cc_start: 0.7319 (pttm) cc_final: 0.6607 (tppt) REVERT: M 346 CYS cc_start: 0.8617 (m) cc_final: 0.8104 (p) REVERT: M 425 LYS cc_start: 0.8758 (mmtt) cc_final: 0.8453 (mmtt) outliers start: 98 outliers final: 74 residues processed: 258 average time/residue: 0.1547 time to fit residues: 67.0670 Evaluate side-chains 252 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 167 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 513 GLN Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 220 ILE Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 286 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 63 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 352 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 358 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 186 optimal weight: 5.9990 chunk 8 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 chunk 136 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.075438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.050736 restraints weight = 128374.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.052059 restraints weight = 70436.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.052905 restraints weight = 48127.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.053443 restraints weight = 38238.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.053715 restraints weight = 33398.933| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29511 Z= 0.184 Angle : 0.610 9.525 40518 Z= 0.314 Chirality : 0.042 0.307 4808 Planarity : 0.004 0.059 4943 Dihedral : 16.632 179.507 5067 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 3.73 % Allowed : 28.38 % Favored : 67.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.17 (0.14), residues: 3589 helix: 1.32 (0.15), residues: 1345 sheet: 0.53 (0.26), residues: 399 loop : -1.41 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 780 TYR 0.021 0.001 TYR D1232 PHE 0.017 0.001 PHE M 355 TRP 0.010 0.001 TRP A 321 HIS 0.002 0.001 HIS D 430 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.18 (29508) covalent geometry : angle 0.61024 / 0.31 (40518) hydrogen bonds : bond 0.03627 / 3.72 ( 1213) hydrogen bonds : angle 4.12887 / 5.31 ( 3404) metal coordination : bond 0.00423 / 0.29 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 163 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LYS cc_start: 0.9066 (ttmm) cc_final: 0.8821 (ttmm) REVERT: B 27 THR cc_start: 0.9561 (OUTLIER) cc_final: 0.9189 (p) REVERT: B 211 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.8968 (mm) REVERT: C 62 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7449 (p90) REVERT: C 239 MET cc_start: 0.7640 (mmm) cc_final: 0.7146 (mmm) REVERT: C 685 MET cc_start: 0.8969 (mtm) cc_final: 0.8414 (mtm) REVERT: C 853 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7204 (p0) REVERT: C 951 MET cc_start: 0.9068 (tmm) cc_final: 0.8805 (tmm) REVERT: C 1085 MET cc_start: 0.9251 (mmm) cc_final: 0.8963 (mmm) REVERT: C 1131 MET cc_start: 0.8711 (tpp) cc_final: 0.8455 (tpp) REVERT: C 1274 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8607 (mp0) REVERT: C 1304 MET cc_start: 0.9416 (tpt) cc_final: 0.9206 (tpp) REVERT: C 1319 MET cc_start: 0.8980 (tmm) cc_final: 0.8369 (tmm) REVERT: C 1333 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9055 (mp) REVERT: D 29 MET cc_start: 0.8894 (mmm) cc_final: 0.7882 (tmm) REVERT: D 115 TRP cc_start: 0.8579 (OUTLIER) cc_final: 0.7258 (m-90) REVERT: D 133 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8634 (ttm-80) REVERT: D 698 MET cc_start: 0.9245 (tpp) cc_final: 0.8785 (mmm) REVERT: D 747 MET cc_start: 0.8192 (ppp) cc_final: 0.7879 (ppp) REVERT: D 785 ASP cc_start: 0.8337 (t0) cc_final: 0.8049 (t0) REVERT: D 821 MET cc_start: 0.9129 (tpp) cc_final: 0.8890 (tpp) REVERT: D 1366 HIS cc_start: 0.9336 (OUTLIER) cc_final: 0.9051 (m-70) REVERT: E 30 MET cc_start: 0.8657 (mtp) cc_final: 0.8322 (mtt) REVERT: M 125 MET cc_start: 0.9064 (mmt) cc_final: 0.8766 (mmm) REVERT: M 130 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8840 (mm) REVERT: M 280 LYS cc_start: 0.7277 (pttm) cc_final: 0.6582 (tppt) REVERT: M 346 CYS cc_start: 0.8609 (m) cc_final: 0.8102 (p) REVERT: M 425 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8440 (mmtt) outliers start: 100 outliers final: 81 residues processed: 253 average time/residue: 0.1474 time to fit residues: 63.6623 Evaluate side-chains 252 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 161 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 649 GLN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 220 ILE Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 133 optimal weight: 3.9990 chunk 361 optimal weight: 8.9990 chunk 329 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 7 optimal weight: 50.0000 chunk 68 optimal weight: 30.0000 chunk 330 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN M 408 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.075107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050183 restraints weight = 128969.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.051513 restraints weight = 70904.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.052380 restraints weight = 48680.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.052897 restraints weight = 38633.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.053152 restraints weight = 33985.106| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 29511 Z= 0.195 Angle : 0.628 9.656 40518 Z= 0.323 Chirality : 0.043 0.309 4808 Planarity : 0.004 0.059 4943 Dihedral : 16.652 179.892 5067 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.62 % Allowed : 28.38 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: 3589 helix: 1.31 (0.15), residues: 1345 sheet: 0.50 (0.26), residues: 399 loop : -1.45 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 780 TYR 0.021 0.001 TYR D1232 PHE 0.020 0.001 PHE M 355 TRP 0.012 0.001 TRP A 321 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (29508) covalent geometry : angle 0.62812 / 0.32 (40518) hydrogen bonds : bond 0.03724 / 3.83 ( 1213) hydrogen bonds : angle 4.16870 / 5.35 ( 3404) metal coordination : bond 0.00471 / 0.33 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7178 Ramachandran restraints generated. 3589 Oldfield, 0 Emsley, 3589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 162 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8783 (ttmm) REVERT: B 27 THR cc_start: 0.9565 (OUTLIER) cc_final: 0.9188 (p) REVERT: B 211 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8989 (mm) REVERT: C 62 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.7435 (p90) REVERT: C 239 MET cc_start: 0.7665 (mmm) cc_final: 0.7237 (mmm) REVERT: C 488 MET cc_start: 0.7901 (mmt) cc_final: 0.7546 (mtp) REVERT: C 685 MET cc_start: 0.8988 (mtm) cc_final: 0.8393 (mtm) REVERT: C 853 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7113 (p0) REVERT: C 951 MET cc_start: 0.9069 (tmm) cc_final: 0.8824 (tmm) REVERT: C 1085 MET cc_start: 0.9237 (mmm) cc_final: 0.8943 (mmm) REVERT: C 1131 MET cc_start: 0.8719 (tpp) cc_final: 0.8447 (tpp) REVERT: C 1274 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8623 (mp0) REVERT: C 1304 MET cc_start: 0.9412 (tpt) cc_final: 0.9206 (tpp) REVERT: C 1319 MET cc_start: 0.9017 (tmm) cc_final: 0.8443 (tmm) REVERT: C 1333 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.9061 (mp) REVERT: D 29 MET cc_start: 0.8894 (mmm) cc_final: 0.7825 (tmm) REVERT: D 115 TRP cc_start: 0.8617 (OUTLIER) cc_final: 0.7244 (m-90) REVERT: D 133 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8635 (ttm-80) REVERT: D 698 MET cc_start: 0.9239 (tpp) cc_final: 0.8770 (mmm) REVERT: D 725 MET cc_start: 0.9186 (mtm) cc_final: 0.8446 (mtm) REVERT: D 747 MET cc_start: 0.8162 (ppp) cc_final: 0.7857 (ppp) REVERT: D 785 ASP cc_start: 0.8358 (t0) cc_final: 0.8071 (t0) REVERT: D 1366 HIS cc_start: 0.9318 (OUTLIER) cc_final: 0.9017 (m-70) REVERT: E 30 MET cc_start: 0.8697 (mtp) cc_final: 0.8332 (mtt) REVERT: M 125 MET cc_start: 0.9020 (mmt) cc_final: 0.8704 (mmm) REVERT: M 130 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8816 (mm) REVERT: M 262 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8122 (pp30) REVERT: M 280 LYS cc_start: 0.7332 (pttm) cc_final: 0.6701 (tppt) REVERT: M 346 CYS cc_start: 0.8597 (m) cc_final: 0.8100 (p) REVERT: M 425 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8474 (mmtt) outliers start: 97 outliers final: 79 residues processed: 249 average time/residue: 0.1476 time to fit residues: 62.2769 Evaluate side-chains 249 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 159 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 49 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 LYS Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 510 GLN Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 700 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 853 ASP Chi-restraints excluded: chain C residue 870 ILE Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 902 LEU Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 942 ASP Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1274 GLU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1333 LEU Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 133 ARG Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 661 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 823 THR Chi-restraints excluded: chain D residue 881 LYS Chi-restraints excluded: chain D residue 954 ASN Chi-restraints excluded: chain D residue 997 VAL Chi-restraints excluded: chain D residue 1046 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain M residue 130 LEU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 220 ILE Chi-restraints excluded: chain M residue 245 VAL Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 154 optimal weight: 0.0020 chunk 284 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 163 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 59 optimal weight: 10.0000 chunk 292 optimal weight: 0.9980 chunk 304 optimal weight: 0.3980 chunk 11 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 overall best weight: 2.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.075021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.050362 restraints weight = 128964.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.051695 restraints weight = 70652.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.052533 restraints weight = 48186.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.053071 restraints weight = 38283.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.053368 restraints weight = 33420.739| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 29511 Z= 0.196 Angle : 0.735 59.189 40518 Z= 0.406 Chirality : 0.044 0.753 4808 Planarity : 0.004 0.058 4943 Dihedral : 16.656 179.880 5067 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.62 % Allowed : 28.53 % Favored : 67.85 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.20 (0.14), residues: 3589 helix: 1.33 (0.15), residues: 1343 sheet: 0.50 (0.26), residues: 399 loop : -1.45 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.060 0.002 TYR M 389 PHE 0.018 0.001 PHE M 355 TRP 0.011 0.001 TRP A 321 HIS 0.004 0.001 HIS M 406 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 (29508) covalent geometry : angle 0.73540 / 0.41 (40518) hydrogen bonds : bond 0.03707 / 3.81 ( 1213) hydrogen bonds : angle 4.16681 / 5.35 ( 3404) metal coordination : bond 0.00355 / 0.23 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4568.72 seconds wall clock time: 79 minutes 25.33 seconds (4765.33 seconds total)