Starting phenix.real_space_refine on Mon May 26 19:00:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8red_19083/05_2025/8red_19083.cif Found real_map, /net/cci-nas-00/data/ceres_data/8red_19083/05_2025/8red_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8red_19083/05_2025/8red_19083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8red_19083/05_2025/8red_19083.map" model { file = "/net/cci-nas-00/data/ceres_data/8red_19083/05_2025/8red_19083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8red_19083/05_2025/8red_19083.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'RNA': 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: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 2} 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, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 18} 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, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 10, 'GLU:plan': 31, 'ARG:plan': 19} 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: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} 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: {'GLN:plan1': 3, 'ASP:plan': 10, 'ASN:plan1': 6, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 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: 17.86, per 1000 atoms: 0.62 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: 7.54 Conformation dependent library (CDL) restraints added in 3.6 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: 10.44 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: 14.20 Time building geometry restraints manager: 8.73 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=" 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=" CB PRO C 567 " pdb=" CG PRO C 567 " ideal model delta sigma weight residual 1.492 1.648 -0.156 5.00e-02 4.00e+02 9.76e+00 bond pdb=" N PRO C 567 " pdb=" CA PRO C 567 " ideal model delta sigma weight residual 1.473 1.433 0.040 1.32e-02 5.74e+03 9.10e+00 bond pdb=" C GLU M 268 " pdb=" N PRO M 269 " ideal model delta sigma weight residual 1.333 1.363 -0.029 1.01e-02 9.80e+03 8.33e+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: 16729 35.55 - 71.09: 952 71.09 - 106.64: 51 106.64 - 142.18: 1 142.18 - 177.73: 3 Dihedral angle restraints: 17736 sinusoidal: 7342 harmonic: 10394 Sorted by residual: dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 143.03 36.97 0 5.00e+00 4.00e-02 5.47e+01 dihedral pdb=" CA ILE D 416 " pdb=" C ILE D 416 " pdb=" N ARG D 417 " pdb=" CA ARG D 417 " ideal model delta harmonic sigma weight residual 180.00 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA SER C1295 " pdb=" C SER C1295 " pdb=" N ASP C1296 " pdb=" CA ASP C1296 " ideal model delta harmonic sigma weight residual -180.00 -158.53 -21.47 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 17733 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 3621 0.044 - 0.088: 904 0.088 - 0.133: 267 0.133 - 0.177: 14 0.177 - 0.221: 2 Chirality restraints: 4808 Sorted by residual: chirality pdb=" CG LEU D 166 " pdb=" CB LEU D 166 " pdb=" CD1 LEU D 166 " pdb=" CD2 LEU D 166 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 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 2.41 -2.60 -0.19 2.00e-01 2.50e+01 8.68e-01 chirality pdb=" CA PRO C1062 " pdb=" N PRO C1062 " pdb=" C PRO C1062 " pdb=" CB PRO C1062 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.16 2.00e-01 2.50e+01 6.72e-01 ... (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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.260 Check model and map are aligned: 0.240 Set scattering table: 0.300 Process input model: 80.060 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 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= 0.186 Angle : 0.682 22.919 40518 Z= 0.358 Chirality : 0.042 0.221 4808 Planarity : 0.007 0.225 4943 Dihedral : 19.760 177.728 11030 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.002 TRP M 212 HIS 0.005 0.001 HIS D 430 PHE 0.018 0.001 PHE D 7 TYR 0.012 0.001 TYR D 631 ARG 0.016 0.000 ARG D1149 Details of bonding type rmsd hydrogen bonds : bond 0.16399 ( 1213) hydrogen bonds : angle 5.83389 ( 3404) metal coordination : bond 0.00205 ( 3) covalent geometry : bond 0.00468 (29508) covalent geometry : angle 0.68165 (40518) *********************** 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 : 3.486 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: 0.7149 (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: 0.4011 time to fit residues: 177.1380 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 : 2.995 ------------------------------------------------------------------------------- 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 310 optimal weight: 0.0060 chunk 278 optimal weight: 0.3980 chunk 154 optimal weight: 4.9990 chunk 95 optimal weight: 0.0020 chunk 188 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 chunk 288 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 175 optimal weight: 0.0570 chunk 214 optimal weight: 4.9990 chunk 334 optimal weight: 5.9990 overall best weight: 1.0924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 276 ASN D 450 HIS ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.079194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.054138 restraints weight = 126209.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.055592 restraints weight = 67236.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.056548 restraints weight = 44900.974| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29511 Z= 0.117 Angle : 0.595 10.921 40518 Z= 0.305 Chirality : 0.041 0.182 4808 Planarity : 0.005 0.144 4943 Dihedral : 16.410 178.295 5075 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.47 % Allowed : 27.48 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3589 helix: 1.00 (0.15), residues: 1335 sheet: 0.68 (0.26), residues: 389 loop : -1.45 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 126 HIS 0.002 0.001 HIS C1116 PHE 0.015 0.001 PHE M 355 TYR 0.016 0.001 TYR A 277 ARG 0.010 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 1213) hydrogen bonds : angle 4.41017 ( 3404) metal coordination : bond 0.00203 ( 3) covalent geometry : bond 0.00258 (29508) covalent geometry : angle 0.59510 (40518) *********************** 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 302 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 209 time to evaluate : 3.531 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: A 253 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8584 (tp) REVERT: A 277 TYR cc_start: 0.7867 (m-80) cc_final: 0.7638 (m-80) REVERT: B 25 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8881 (ttmm) REVERT: B 27 THR cc_start: 0.9575 (OUTLIER) cc_final: 0.9185 (p) REVERT: B 174 ASP cc_start: 0.8037 (OUTLIER) cc_final: 0.7659 (t70) REVERT: C 62 TYR cc_start: 0.7696 (p90) cc_final: 0.7318 (p90) REVERT: C 685 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8815 (mtm) REVERT: C 813 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7342 (mm-30) REVERT: C 826 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8099 (t0) REVERT: C 853 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7187 (p0) REVERT: C 903 ARG cc_start: 0.8629 (mtt180) cc_final: 0.8327 (mmt-90) REVERT: C 908 GLU cc_start: 0.8855 (mp0) cc_final: 0.8519 (tp30) REVERT: C 1029 LEU cc_start: 0.9471 (tp) cc_final: 0.8856 (pp) REVERT: C 1085 MET cc_start: 0.9270 (mmm) cc_final: 0.8997 (mmm) REVERT: C 1131 MET cc_start: 0.8910 (tpp) cc_final: 0.8708 (tpp) REVERT: D 29 MET cc_start: 0.8851 (mmm) cc_final: 0.8045 (tmm) REVERT: D 698 MET cc_start: 0.9252 (mmm) cc_final: 0.8960 (mmt) REVERT: D 725 MET cc_start: 0.9213 (mtm) cc_final: 0.8675 (mtm) REVERT: D 821 MET cc_start: 0.9132 (tpp) cc_final: 0.8784 (tpp) REVERT: D 1366 HIS cc_start: 0.9339 (OUTLIER) cc_final: 0.8960 (m-70) REVERT: M 262 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7958 (pp30) REVERT: M 280 LYS cc_start: 0.7355 (pttm) cc_final: 0.6693 (tppt) REVERT: M 346 CYS cc_start: 0.8609 (m) cc_final: 0.8093 (p) REVERT: M 391 HIS cc_start: 0.7300 (t70) cc_final: 0.7063 (t70) REVERT: M 406 HIS cc_start: 0.6945 (m90) cc_final: 0.6222 (m-70) REVERT: M 425 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8384 (mmtt) outliers start: 93 outliers final: 33 residues processed: 291 average time/residue: 0.3910 time to fit residues: 187.7783 Evaluate side-chains 225 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 4.070 ------------------------------------------------------------------------------- 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 98 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 160 HIS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 298 LYS Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 174 ASP 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 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 1056 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1275 VAL 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 304 ASP Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN 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 151 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 268 optimal weight: 10.0000 chunk 168 optimal weight: 8.9990 chunk 276 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 180 optimal weight: 0.0020 chunk 133 optimal weight: 9.9990 chunk 146 optimal weight: 0.0070 chunk 23 optimal weight: 20.0000 chunk 348 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 overall best weight: 2.1410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 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 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.079034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.054099 restraints weight = 126789.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.055537 restraints weight = 67661.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.056451 restraints weight = 45597.844| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1524 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= 0.115 Angle : 0.556 8.205 40518 Z= 0.285 Chirality : 0.041 0.190 4808 Planarity : 0.004 0.115 4943 Dihedral : 16.367 177.890 5071 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.06 % Allowed : 27.45 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3589 helix: 1.21 (0.15), residues: 1339 sheet: 0.64 (0.26), residues: 391 loop : -1.39 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP M 285 HIS 0.002 0.000 HIS C1116 PHE 0.015 0.001 PHE M 355 TYR 0.019 0.001 TYR D1232 ARG 0.009 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03307 ( 1213) hydrogen bonds : angle 4.12984 ( 3404) metal coordination : bond 0.00127 ( 3) covalent geometry : bond 0.00258 (29508) covalent geometry : angle 0.55598 (40518) *********************** 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 275 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 193 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 VAL cc_start: 0.9567 (t) cc_final: 0.9363 (p) REVERT: A 253 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8588 (tp) REVERT: A 277 TYR cc_start: 0.7811 (m-80) cc_final: 0.7560 (m-80) REVERT: B 27 THR cc_start: 0.9563 (OUTLIER) cc_final: 0.9185 (p) REVERT: B 200 LYS cc_start: 0.9054 (tttt) cc_final: 0.8776 (ttpp) REVERT: C 62 TYR cc_start: 0.7746 (p90) cc_final: 0.7313 (p90) REVERT: C 239 MET cc_start: 0.7065 (mmm) cc_final: 0.6599 (mmm) REVERT: C 523 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8383 (mt-10) REVERT: C 685 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8697 (mtm) REVERT: C 813 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7341 (mm-30) REVERT: C 826 ASP cc_start: 0.8453 (OUTLIER) cc_final: 0.8083 (t0) REVERT: C 903 ARG cc_start: 0.8634 (mtt180) cc_final: 0.8231 (mmt180) REVERT: C 908 GLU cc_start: 0.8822 (mp0) cc_final: 0.8621 (tp30) REVERT: C 951 MET cc_start: 0.9078 (tmm) cc_final: 0.8731 (tmm) REVERT: C 1085 MET cc_start: 0.9304 (mmm) cc_final: 0.8967 (mmm) REVERT: C 1131 MET cc_start: 0.8915 (tpp) cc_final: 0.8715 (tpp) REVERT: C 1230 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8453 (ttp) REVERT: C 1304 MET cc_start: 0.9470 (tpt) cc_final: 0.9076 (tpp) REVERT: D 29 MET cc_start: 0.8842 (mmm) cc_final: 0.7878 (tmm) REVERT: D 248 ASP cc_start: 0.8846 (t0) cc_final: 0.8624 (t0) REVERT: D 725 MET cc_start: 0.9194 (mtm) cc_final: 0.8787 (mtm) REVERT: D 747 MET cc_start: 0.8223 (ppp) cc_final: 0.7968 (ppp) REVERT: D 1366 HIS cc_start: 0.9357 (OUTLIER) cc_final: 0.9019 (m-70) REVERT: E 30 MET cc_start: 0.8724 (mtp) cc_final: 0.8359 (mtt) REVERT: M 125 MET cc_start: 0.9050 (mmt) cc_final: 0.8817 (mmm) REVERT: M 130 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8849 (mm) REVERT: M 280 LYS cc_start: 0.7337 (pttm) cc_final: 0.6707 (tppt) REVERT: M 346 CYS cc_start: 0.8626 (m) cc_final: 0.8137 (p) REVERT: M 365 MET cc_start: 0.3526 (mmm) cc_final: 0.2968 (mmm) REVERT: M 425 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8510 (mmtt) outliers start: 82 outliers final: 37 residues processed: 264 average time/residue: 0.3648 time to fit residues: 161.4454 Evaluate side-chains 223 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 3.068 ------------------------------------------------------------------------------- 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 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 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 516 ASP 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 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 C residue 1230 MET 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 504 GLN Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 877 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 286 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 172 optimal weight: 8.9990 chunk 223 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 39 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 146 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1157 GLN D 158 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1367 GLN M 391 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.075735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.050844 restraints weight = 129790.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.052188 restraints weight = 70988.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.053009 restraints weight = 48440.928| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 29511 Z= 0.237 Angle : 0.631 8.745 40518 Z= 0.329 Chirality : 0.042 0.183 4808 Planarity : 0.005 0.104 4943 Dihedral : 16.432 179.867 5071 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.41 % Allowed : 26.85 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.14), residues: 3589 helix: 1.21 (0.15), residues: 1340 sheet: 0.53 (0.26), residues: 399 loop : -1.44 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 126 HIS 0.004 0.001 HIS A 276 PHE 0.014 0.001 PHE C1270 TYR 0.019 0.002 TYR D1232 ARG 0.009 0.001 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04067 ( 1213) hydrogen bonds : angle 4.28558 ( 3404) metal coordination : bond 0.00494 ( 3) covalent geometry : bond 0.00522 (29508) covalent geometry : angle 0.63146 (40518) *********************** 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 299 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 181 time to evaluate : 3.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8928 (mp) cc_final: 0.8648 (tp) REVERT: A 277 TYR cc_start: 0.7770 (m-80) cc_final: 0.7461 (m-80) REVERT: B 27 THR cc_start: 0.9571 (OUTLIER) cc_final: 0.9183 (p) REVERT: C 62 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7457 (p90) REVERT: C 239 MET cc_start: 0.7494 (mmm) cc_final: 0.6548 (mmm) REVERT: C 685 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8866 (mtm) REVERT: C 853 ASP cc_start: 0.8089 (OUTLIER) cc_final: 0.7110 (p0) REVERT: C 951 MET cc_start: 0.9121 (tmm) cc_final: 0.8861 (tmm) REVERT: C 1085 MET cc_start: 0.9303 (mmm) cc_final: 0.9026 (mmm) REVERT: C 1304 MET cc_start: 0.9464 (tpt) cc_final: 0.9150 (tpp) REVERT: C 1319 MET cc_start: 0.8905 (tpt) cc_final: 0.8540 (tpp) REVERT: C 1333 LEU cc_start: 0.9473 (OUTLIER) cc_final: 0.9192 (mp) REVERT: D 8 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7960 (pp) REVERT: D 29 MET cc_start: 0.8933 (mmm) cc_final: 0.7947 (tmm) REVERT: D 785 ASP cc_start: 0.8352 (t0) cc_final: 0.8061 (t0) REVERT: D 821 MET cc_start: 0.9173 (tpp) cc_final: 0.8882 (tpp) REVERT: D 1263 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7983 (tmtt) REVERT: D 1366 HIS cc_start: 0.9336 (OUTLIER) cc_final: 0.9039 (m-70) REVERT: E 30 MET cc_start: 0.8742 (mtp) cc_final: 0.8424 (mtt) REVERT: M 280 LYS cc_start: 0.7385 (pttm) cc_final: 0.6756 (tppt) REVERT: M 346 CYS cc_start: 0.8611 (m) cc_final: 0.8133 (p) REVERT: M 425 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8453 (mmtt) outliers start: 118 outliers final: 64 residues processed: 283 average time/residue: 0.3668 time to fit residues: 173.0094 Evaluate side-chains 241 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 169 time to evaluate : 3.230 ------------------------------------------------------------------------------- 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 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 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 246 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 400 VAL 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 553 THR 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 845 LEU 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 1206 THR Chi-restraints excluded: chain C residue 1243 MET Chi-restraints excluded: chain C residue 1265 PHE 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 429 LEU 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 697 MET Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 803 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 1263 LYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 261 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 324 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 245 optimal weight: 0.1980 chunk 109 optimal weight: 8.9990 chunk 239 optimal weight: 0.0570 chunk 76 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 overall best weight: 1.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** 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 = 0.3568 r_free = 0.3568 target = 0.077412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.052659 restraints weight = 127799.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.054046 restraints weight = 69158.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.054934 restraints weight = 46924.511| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 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 = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29511 Z= 0.111 Angle : 0.557 9.864 40518 Z= 0.286 Chirality : 0.041 0.187 4808 Planarity : 0.004 0.086 4943 Dihedral : 16.356 178.320 5071 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.95 % Allowed : 28.42 % Favored : 68.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3589 helix: 1.38 (0.15), residues: 1337 sheet: 0.75 (0.26), residues: 381 loop : -1.33 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 126 HIS 0.002 0.000 HIS D 777 PHE 0.011 0.001 PHE C1323 TYR 0.021 0.001 TYR D1232 ARG 0.007 0.000 ARG C 101 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 1213) hydrogen bonds : angle 4.02316 ( 3404) metal coordination : bond 0.00257 ( 3) covalent geometry : bond 0.00243 (29508) covalent geometry : angle 0.55699 (40518) *********************** 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 263 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 184 time to evaluate : 3.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 253 LEU cc_start: 0.8873 (mp) cc_final: 0.8529 (tp) REVERT: A 277 TYR cc_start: 0.7824 (m-80) cc_final: 0.7571 (m-80) REVERT: B 27 THR cc_start: 0.9566 (OUTLIER) cc_final: 0.9181 (p) REVERT: B 205 MET cc_start: 0.8382 (tpp) cc_final: 0.8153 (tpp) REVERT: B 211 ILE cc_start: 0.9206 (OUTLIER) cc_final: 0.8936 (mm) REVERT: C 62 TYR cc_start: 0.7833 (p90) cc_final: 0.7380 (p90) REVERT: C 239 MET cc_start: 0.7489 (mmm) cc_final: 0.6942 (mmm) REVERT: C 488 MET cc_start: 0.7895 (mmt) cc_final: 0.7421 (mtp) REVERT: C 685 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8847 (mtm) REVERT: C 813 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7386 (mm-30) REVERT: C 853 ASP cc_start: 0.8160 (OUTLIER) cc_final: 0.7314 (p0) REVERT: C 903 ARG cc_start: 0.8455 (mtt180) cc_final: 0.8159 (mtt180) REVERT: C 951 MET cc_start: 0.9080 (tmm) cc_final: 0.8788 (tmm) REVERT: C 1085 MET cc_start: 0.9262 (mmm) cc_final: 0.8962 (mmm) REVERT: C 1265 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8022 (t80) REVERT: C 1304 MET cc_start: 0.9406 (tpt) cc_final: 0.9190 (tpp) REVERT: C 1319 MET cc_start: 0.8952 (tpt) cc_final: 0.8554 (tpp) REVERT: D 8 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7935 (pp) REVERT: D 29 MET cc_start: 0.8884 (mmm) cc_final: 0.7997 (mmm) REVERT: D 747 MET cc_start: 0.8158 (ppp) cc_final: 0.7817 (ppp) REVERT: D 821 MET cc_start: 0.9126 (tpp) cc_final: 0.8851 (tpp) REVERT: D 1263 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7979 (tmtt) REVERT: D 1366 HIS cc_start: 0.9358 (OUTLIER) cc_final: 0.9062 (m-70) REVERT: M 125 MET cc_start: 0.9056 (mmt) cc_final: 0.8793 (mmm) REVERT: M 280 LYS cc_start: 0.7291 (pttm) cc_final: 0.6661 (tppt) REVERT: M 346 CYS cc_start: 0.8612 (m) cc_final: 0.8139 (p) REVERT: M 406 HIS cc_start: 0.7021 (m90) cc_final: 0.5936 (m-70) REVERT: M 425 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8504 (mmtt) outliers start: 79 outliers final: 54 residues processed: 253 average time/residue: 0.3616 time to fit residues: 154.0604 Evaluate side-chains 236 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 174 time to evaluate : 3.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 HIS 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 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 71 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 246 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 516 ASP Chi-restraints excluded: chain C residue 553 THR 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 723 VAL Chi-restraints excluded: chain C residue 845 LEU 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 953 LEU 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 1248 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1339 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 472 LEU Chi-restraints excluded: chain D residue 672 LEU 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 1046 ILE Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1263 LYS 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 286 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 128 optimal weight: 4.9990 chunk 364 optimal weight: 8.9990 chunk 309 optimal weight: 30.0000 chunk 175 optimal weight: 8.9990 chunk 246 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 271 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 408 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.076334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.051498 restraints weight = 129215.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.052860 restraints weight = 70416.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.053716 restraints weight = 48037.328| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2920 r_free = 0.2920 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 = 0.2920 r_free = 0.2920 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29511 Z= 0.152 Angle : 0.565 9.061 40518 Z= 0.292 Chirality : 0.041 0.159 4808 Planarity : 0.004 0.083 4943 Dihedral : 16.338 178.978 5071 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.77 % Allowed : 27.74 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.14), residues: 3589 helix: 1.43 (0.15), residues: 1339 sheet: 0.66 (0.26), residues: 387 loop : -1.33 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 126 HIS 0.002 0.001 HIS A 276 PHE 0.014 0.001 PHE M 355 TYR 0.020 0.001 TYR D1232 ARG 0.006 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 1213) hydrogen bonds : angle 4.01455 ( 3404) metal coordination : bond 0.00366 ( 3) covalent geometry : bond 0.00340 (29508) covalent geometry : angle 0.56458 (40518) *********************** 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 277 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 176 time to evaluate : 3.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 TYR cc_start: 0.7855 (m-80) cc_final: 0.7564 (m-80) REVERT: B 27 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9127 (p) REVERT: B 205 MET cc_start: 0.8389 (tpp) cc_final: 0.8151 (tpp) REVERT: B 211 ILE cc_start: 0.9230 (OUTLIER) cc_final: 0.8953 (mm) REVERT: C 62 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7490 (p90) REVERT: C 239 MET cc_start: 0.7524 (mmm) cc_final: 0.7070 (mmm) REVERT: C 488 MET cc_start: 0.7850 (mmt) cc_final: 0.7326 (mtp) REVERT: C 523 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8433 (mt-10) REVERT: C 813 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7728 (mm-30) REVERT: C 853 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7163 (p0) REVERT: C 903 ARG cc_start: 0.8347 (mtt180) cc_final: 0.8086 (mtt-85) REVERT: C 951 MET cc_start: 0.9115 (tmm) cc_final: 0.8852 (tmm) REVERT: C 1085 MET cc_start: 0.9275 (mmm) cc_final: 0.9050 (mmm) REVERT: C 1319 MET cc_start: 0.8978 (tpt) cc_final: 0.8577 (tpp) REVERT: D 8 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7952 (pp) REVERT: D 29 MET cc_start: 0.8911 (mmm) cc_final: 0.7983 (mmm) REVERT: D 133 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8617 (ttm-80) REVERT: D 581 MET cc_start: 0.8982 (mmm) cc_final: 0.8620 (mtt) REVERT: D 716 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7934 (pt0) REVERT: D 747 MET cc_start: 0.8134 (ppp) cc_final: 0.7820 (ppp) REVERT: D 785 ASP cc_start: 0.8411 (t0) cc_final: 0.8104 (t0) REVERT: D 1366 HIS cc_start: 0.9338 (OUTLIER) cc_final: 0.9028 (m-70) REVERT: E 30 MET cc_start: 0.8665 (mtp) cc_final: 0.8341 (mtt) REVERT: M 125 MET cc_start: 0.9110 (mmt) cc_final: 0.8808 (mmm) REVERT: M 280 LYS cc_start: 0.7328 (pttm) cc_final: 0.6693 (tppt) REVERT: M 406 HIS cc_start: 0.7160 (m90) cc_final: 0.6015 (m-70) REVERT: M 425 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8459 (mmtt) outliers start: 101 outliers final: 66 residues processed: 264 average time/residue: 0.3777 time to fit residues: 167.2568 Evaluate side-chains 243 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 168 time to evaluate : 3.209 ------------------------------------------------------------------------------- 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 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 129 VAL Chi-restraints excluded: chain B residue 146 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 246 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 523 GLU Chi-restraints excluded: chain C residue 553 THR 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 845 LEU 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 1248 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 95 THR 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 387 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 716 GLN 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 1177 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 32 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 186 optimal weight: 0.6980 chunk 203 optimal weight: 30.0000 chunk 343 optimal weight: 6.9990 chunk 365 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 345 optimal weight: 0.9990 chunk 208 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C1136 GLN ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3555 r_free = 0.3555 target = 0.076591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.051810 restraints weight = 128685.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.053179 restraints weight = 69961.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.054055 restraints weight = 47662.743| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 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 = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2458 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= 0.130 Angle : 0.566 13.582 40518 Z= 0.288 Chirality : 0.041 0.166 4808 Planarity : 0.004 0.071 4943 Dihedral : 16.309 178.463 5071 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.81 % Allowed : 28.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.14), residues: 3589 helix: 1.46 (0.15), residues: 1338 sheet: 0.60 (0.26), residues: 394 loop : -1.31 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 126 HIS 0.002 0.000 HIS D 430 PHE 0.015 0.001 PHE M 355 TYR 0.021 0.001 TYR D1232 ARG 0.006 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.03163 ( 1213) hydrogen bonds : angle 3.95549 ( 3404) metal coordination : bond 0.00345 ( 3) covalent geometry : bond 0.00290 (29508) covalent geometry : angle 0.56565 (40518) *********************** 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: 102 poor density : 175 time to evaluate : 3.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 TYR cc_start: 0.7882 (m-80) cc_final: 0.7585 (m-80) REVERT: B 27 THR cc_start: 0.9548 (OUTLIER) cc_final: 0.9149 (p) REVERT: B 86 LYS cc_start: 0.9299 (ttmm) cc_final: 0.8937 (ttmm) REVERT: B 205 MET cc_start: 0.8387 (tpp) cc_final: 0.8147 (tpp) REVERT: B 211 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8938 (mm) REVERT: C 62 TYR cc_start: 0.7927 (OUTLIER) cc_final: 0.7550 (p90) REVERT: C 239 MET cc_start: 0.7619 (mmm) cc_final: 0.7238 (mmm) REVERT: C 488 MET cc_start: 0.7736 (mmt) cc_final: 0.7365 (mtp) REVERT: C 523 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8399 (mt-10) REVERT: C 685 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8263 (mtm) REVERT: C 813 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7715 (mm-30) REVERT: C 853 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7101 (p0) REVERT: C 903 ARG cc_start: 0.8474 (mtt180) cc_final: 0.8233 (mmt180) REVERT: C 951 MET cc_start: 0.9116 (tmm) cc_final: 0.8852 (tmm) REVERT: C 1085 MET cc_start: 0.9251 (mmm) cc_final: 0.8984 (mmm) REVERT: C 1131 MET cc_start: 0.8781 (tpp) cc_final: 0.8561 (tpp) REVERT: C 1265 PHE cc_start: 0.8536 (OUTLIER) cc_final: 0.8003 (t80) REVERT: C 1319 MET cc_start: 0.8963 (tpt) cc_final: 0.8554 (tpp) REVERT: D 8 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7922 (pp) REVERT: D 29 MET cc_start: 0.8899 (mmm) cc_final: 0.8036 (mmm) REVERT: D 130 MET cc_start: 0.8318 (mmm) cc_final: 0.7986 (mmt) REVERT: D 133 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8582 (ttm-80) REVERT: D 716 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7997 (pt0) REVERT: D 747 MET cc_start: 0.8162 (ppp) cc_final: 0.7839 (ppp) REVERT: D 785 ASP cc_start: 0.8407 (t0) cc_final: 0.8073 (t0) REVERT: D 821 MET cc_start: 0.9057 (tpp) cc_final: 0.8828 (tpp) REVERT: D 881 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.9112 (tptp) REVERT: D 1366 HIS cc_start: 0.9383 (OUTLIER) cc_final: 0.9096 (m-70) REVERT: M 125 MET cc_start: 0.9029 (mmt) cc_final: 0.8701 (mmm) REVERT: M 201 ILE cc_start: 0.8448 (tp) cc_final: 0.8194 (tp) REVERT: M 280 LYS cc_start: 0.7406 (pttm) cc_final: 0.6794 (tppt) REVERT: M 425 LYS cc_start: 0.8773 (mmtt) cc_final: 0.8455 (mmtt) outliers start: 102 outliers final: 68 residues processed: 265 average time/residue: 0.3730 time to fit residues: 164.9276 Evaluate side-chains 249 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 169 time to evaluate : 3.343 ------------------------------------------------------------------------------- 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 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 B residue 27 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 93 GLN 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 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 246 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 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 553 THR 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 685 MET 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 845 LEU 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 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 1248 THR Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 95 THR 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 387 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 716 GLN Chi-restraints excluded: chain D residue 881 LYS 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 1197 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 277 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 225 optimal weight: 7.9990 chunk 300 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 344 optimal weight: 10.0000 chunk 351 optimal weight: 1.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.076158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.051349 restraints weight = 129877.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.052692 restraints weight = 70694.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.053580 restraints weight = 48317.788| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 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 = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29511 Z= 0.141 Angle : 0.570 11.203 40518 Z= 0.291 Chirality : 0.041 0.164 4808 Planarity : 0.004 0.108 4943 Dihedral : 16.300 178.657 5071 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.44 % Allowed : 28.16 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.14), residues: 3589 helix: 1.48 (0.15), residues: 1341 sheet: 0.56 (0.26), residues: 396 loop : -1.31 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 126 HIS 0.002 0.000 HIS D 865 PHE 0.015 0.001 PHE C1270 TYR 0.021 0.001 TYR D1232 ARG 0.008 0.000 ARG C 359 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 1213) hydrogen bonds : angle 3.94324 ( 3404) metal coordination : bond 0.00361 ( 3) covalent geometry : bond 0.00315 (29508) covalent geometry : angle 0.56988 (40518) *********************** 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 267 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 175 time to evaluate : 3.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 TYR cc_start: 0.7952 (m-80) cc_final: 0.7660 (m-80) REVERT: B 27 THR cc_start: 0.9533 (OUTLIER) cc_final: 0.9159 (p) REVERT: B 86 LYS cc_start: 0.9297 (ttmm) cc_final: 0.8927 (ttmm) REVERT: B 205 MET cc_start: 0.8376 (tpp) cc_final: 0.8121 (tpp) REVERT: B 211 ILE cc_start: 0.9219 (OUTLIER) cc_final: 0.8946 (mm) REVERT: C 62 TYR cc_start: 0.7975 (OUTLIER) cc_final: 0.7594 (p90) REVERT: C 239 MET cc_start: 0.7646 (mmm) cc_final: 0.7235 (mmm) REVERT: C 488 MET cc_start: 0.7783 (mmt) cc_final: 0.7428 (mtp) REVERT: C 523 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8414 (mt-10) REVERT: C 685 MET cc_start: 0.8959 (mtm) cc_final: 0.8279 (mtm) REVERT: C 853 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7093 (p0) REVERT: C 951 MET cc_start: 0.9112 (tmm) cc_final: 0.8860 (tmm) REVERT: C 1085 MET cc_start: 0.9237 (mmm) cc_final: 0.8978 (mmm) REVERT: C 1131 MET cc_start: 0.8728 (tpp) cc_final: 0.8505 (tpp) REVERT: C 1253 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8716 (mm) REVERT: C 1265 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.8009 (t80) REVERT: C 1319 MET cc_start: 0.8986 (tpt) cc_final: 0.8621 (tpp) REVERT: D 8 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7940 (pp) REVERT: D 29 MET cc_start: 0.8893 (mmm) cc_final: 0.8022 (mmm) REVERT: D 133 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8580 (ttm-80) REVERT: D 233 LYS cc_start: 0.9420 (OUTLIER) cc_final: 0.8985 (ttpp) REVERT: D 725 MET cc_start: 0.9200 (mtm) cc_final: 0.8515 (mtm) REVERT: D 785 ASP cc_start: 0.8410 (t0) cc_final: 0.8084 (t0) REVERT: D 821 MET cc_start: 0.9093 (tpp) cc_final: 0.8881 (tpp) REVERT: D 1366 HIS cc_start: 0.9364 (OUTLIER) cc_final: 0.9067 (m-70) REVERT: E 30 MET cc_start: 0.8654 (mtp) cc_final: 0.8307 (mtt) REVERT: M 201 ILE cc_start: 0.8456 (tp) cc_final: 0.8201 (tp) REVERT: M 280 LYS cc_start: 0.7411 (pttm) cc_final: 0.6781 (tppt) REVERT: M 425 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8467 (mmtt) outliers start: 92 outliers final: 72 residues processed: 255 average time/residue: 0.3574 time to fit residues: 152.9897 Evaluate side-chains 250 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 167 time to evaluate : 3.131 ------------------------------------------------------------------------------- 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 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 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 209 ILE Chi-restraints excluded: chain C residue 246 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 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 553 THR 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 845 LEU 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 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 1248 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 8 LEU Chi-restraints excluded: chain D residue 95 THR 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 233 LYS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN 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 1197 ASN Chi-restraints excluded: chain D residue 1233 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 159 optimal weight: 40.0000 chunk 217 optimal weight: 20.0000 chunk 136 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 347 optimal weight: 50.0000 chunk 19 optimal weight: 5.9990 chunk 231 optimal weight: 0.9980 chunk 274 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 345 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.074722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.049910 restraints weight = 129868.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.051243 restraints weight = 71357.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.052081 restraints weight = 48855.220| |-----------------------------------------------------------------------------| r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 29511 Z= 0.200 Angle : 0.625 10.216 40518 Z= 0.321 Chirality : 0.042 0.161 4808 Planarity : 0.004 0.066 4943 Dihedral : 16.345 177.772 5071 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.66 % Allowed : 27.82 % Favored : 68.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3589 helix: 1.40 (0.15), residues: 1338 sheet: 0.51 (0.26), residues: 393 loop : -1.37 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 126 HIS 0.004 0.001 HIS M 391 PHE 0.019 0.001 PHE C1270 TYR 0.022 0.002 TYR M 389 ARG 0.008 0.000 ARG C 359 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 1213) hydrogen bonds : angle 4.12631 ( 3404) metal coordination : bond 0.00495 ( 3) covalent geometry : bond 0.00443 (29508) covalent geometry : angle 0.62528 (40518) *********************** 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 264 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 166 time to evaluate : 3.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 277 TYR cc_start: 0.8006 (m-80) cc_final: 0.7698 (m-80) REVERT: B 27 THR cc_start: 0.9547 (OUTLIER) cc_final: 0.9136 (p) REVERT: B 205 MET cc_start: 0.8412 (tpp) cc_final: 0.8139 (tpp) REVERT: B 211 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8974 (mm) REVERT: C 62 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7645 (p90) REVERT: C 239 MET cc_start: 0.7657 (mmm) cc_final: 0.7157 (mmm) REVERT: C 488 MET cc_start: 0.7951 (mmt) cc_final: 0.7560 (mtp) REVERT: C 685 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8326 (mtm) REVERT: C 813 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7786 (mm-30) REVERT: C 853 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7022 (p0) REVERT: C 903 ARG cc_start: 0.8511 (mmt180) cc_final: 0.8307 (mmt180) REVERT: C 951 MET cc_start: 0.9113 (tmm) cc_final: 0.8884 (tmm) REVERT: C 1023 HIS cc_start: 0.8874 (t70) cc_final: 0.8590 (t70) REVERT: C 1085 MET cc_start: 0.9248 (mmm) cc_final: 0.8993 (mmm) REVERT: C 1107 MET cc_start: 0.8822 (mtt) cc_final: 0.8612 (mtp) REVERT: C 1131 MET cc_start: 0.8709 (tpp) cc_final: 0.8463 (tpp) REVERT: C 1253 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8736 (mm) REVERT: C 1319 MET cc_start: 0.9020 (tpt) cc_final: 0.8802 (tpp) REVERT: D 29 MET cc_start: 0.8924 (mmm) cc_final: 0.8037 (mmm) REVERT: D 133 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8609 (ttm-80) REVERT: D 233 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9168 (ttpp) REVERT: D 725 MET cc_start: 0.9195 (mtm) cc_final: 0.8406 (mtm) REVERT: D 785 ASP cc_start: 0.8393 (t0) cc_final: 0.8096 (t0) REVERT: D 821 MET cc_start: 0.9068 (tpp) cc_final: 0.8830 (tpp) REVERT: D 881 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9029 (tptt) REVERT: D 1366 HIS cc_start: 0.9340 (OUTLIER) cc_final: 0.9087 (m-70) REVERT: M 125 MET cc_start: 0.9063 (mmt) cc_final: 0.8794 (mmm) REVERT: M 280 LYS cc_start: 0.7485 (pttm) cc_final: 0.6888 (tppt) REVERT: M 346 CYS cc_start: 0.8613 (m) cc_final: 0.8190 (p) outliers start: 98 outliers final: 74 residues processed: 254 average time/residue: 0.3495 time to fit residues: 149.8535 Evaluate side-chains 244 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 160 time to evaluate : 3.141 ------------------------------------------------------------------------------- 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 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 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 246 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 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 553 THR 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 723 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 845 LEU 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 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 1094 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 95 THR 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 233 LYS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 881 LYS 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 1197 ASN Chi-restraints excluded: chain D residue 1233 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 348 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 217 optimal weight: 0.1980 chunk 334 optimal weight: 10.0000 chunk 338 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 347 optimal weight: 9.9990 overall best weight: 5.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 437 ASN D 504 GLN ** D 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.074560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.050120 restraints weight = 129030.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.051423 restraints weight = 70637.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.052277 restraints weight = 48340.836| |-----------------------------------------------------------------------------| r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 29511 Z= 0.191 Angle : 0.611 10.749 40518 Z= 0.313 Chirality : 0.041 0.164 4808 Planarity : 0.004 0.067 4943 Dihedral : 16.344 178.437 5071 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.44 % Allowed : 28.12 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.14), residues: 3589 helix: 1.45 (0.15), residues: 1323 sheet: 0.44 (0.26), residues: 395 loop : -1.37 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 212 HIS 0.003 0.001 HIS D 430 PHE 0.016 0.001 PHE C1270 TYR 0.021 0.001 TYR D1232 ARG 0.005 0.000 ARG C 542 Details of bonding type rmsd hydrogen bonds : bond 0.03569 ( 1213) hydrogen bonds : angle 4.11216 ( 3404) metal coordination : bond 0.00484 ( 3) covalent geometry : bond 0.00424 (29508) covalent geometry : angle 0.61101 (40518) ********************** 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 254 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 162 time to evaluate : 3.108 Fit side-chains revert: symmetry clash REVERT: A 277 TYR cc_start: 0.8048 (m-80) cc_final: 0.7750 (m-80) REVERT: B 27 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9143 (p) REVERT: B 205 MET cc_start: 0.8406 (tpp) cc_final: 0.8135 (tpp) REVERT: B 211 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8977 (mm) REVERT: C 62 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.7648 (p90) REVERT: C 239 MET cc_start: 0.7635 (mmm) cc_final: 0.7263 (mmm) REVERT: C 488 MET cc_start: 0.7901 (mmt) cc_final: 0.7584 (mtp) REVERT: C 685 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8312 (mtm) REVERT: C 853 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7089 (p0) REVERT: C 903 ARG cc_start: 0.8327 (mmt180) cc_final: 0.8100 (mmt180) REVERT: C 951 MET cc_start: 0.9108 (tmm) cc_final: 0.8869 (tmm) REVERT: C 1023 HIS cc_start: 0.8866 (t70) cc_final: 0.8503 (t-90) REVERT: C 1085 MET cc_start: 0.9244 (mmm) cc_final: 0.8977 (mmm) REVERT: C 1131 MET cc_start: 0.8691 (tpp) cc_final: 0.8462 (tpp) REVERT: C 1253 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8754 (mm) REVERT: C 1319 MET cc_start: 0.9012 (tpt) cc_final: 0.8776 (tmm) REVERT: D 29 MET cc_start: 0.8899 (mmm) cc_final: 0.8007 (mmm) REVERT: D 133 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8605 (ttm-80) REVERT: D 233 LYS cc_start: 0.9364 (OUTLIER) cc_final: 0.9154 (ttpp) REVERT: D 725 MET cc_start: 0.9213 (mtm) cc_final: 0.8451 (mtm) REVERT: D 785 ASP cc_start: 0.8418 (t0) cc_final: 0.8114 (t0) REVERT: D 821 MET cc_start: 0.9067 (tpp) cc_final: 0.8842 (tpp) REVERT: D 881 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9031 (tptt) REVERT: D 1366 HIS cc_start: 0.9332 (OUTLIER) cc_final: 0.9081 (m-70) REVERT: M 125 MET cc_start: 0.9089 (mmt) cc_final: 0.8788 (mmm) REVERT: M 280 LYS cc_start: 0.7521 (pttm) cc_final: 0.6896 (tppt) REVERT: M 346 CYS cc_start: 0.8648 (m) cc_final: 0.8202 (p) REVERT: M 397 PHE cc_start: 0.6820 (m-80) cc_final: 0.6480 (m-80) REVERT: M 402 PHE cc_start: 0.8571 (m-10) cc_final: 0.8283 (m-10) outliers start: 92 outliers final: 76 residues processed: 248 average time/residue: 0.3430 time to fit residues: 143.7345 Evaluate side-chains 245 residues out of total 3094 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 159 time to evaluate : 3.088 ------------------------------------------------------------------------------- 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 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 93 GLN 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 246 LEU Chi-restraints excluded: chain C residue 390 PHE Chi-restraints excluded: chain C residue 448 LEU Chi-restraints excluded: chain C residue 516 ASP Chi-restraints excluded: chain C residue 519 ASN Chi-restraints excluded: chain C residue 553 THR 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 723 VAL Chi-restraints excluded: chain C residue 750 ILE Chi-restraints excluded: chain C residue 845 LEU 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 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 1094 VAL Chi-restraints excluded: chain C residue 1206 THR Chi-restraints excluded: chain C residue 1248 THR Chi-restraints excluded: chain C residue 1253 LEU Chi-restraints excluded: chain C residue 1265 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1339 LEU Chi-restraints excluded: chain D residue 95 THR 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 233 LYS Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 392 THR Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 881 LYS 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 1197 ASN Chi-restraints excluded: chain D residue 1233 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 145 optimal weight: 5.9990 chunk 51 optimal weight: 0.0980 chunk 43 optimal weight: 9.9990 chunk 166 optimal weight: 20.0000 chunk 165 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 358 optimal weight: 30.0000 chunk 12 optimal weight: 8.9990 chunk 235 optimal weight: 0.4980 chunk 158 optimal weight: 9.9990 overall best weight: 4.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 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 = 0.3518 r_free = 0.3518 target = 0.074739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.050324 restraints weight = 128871.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.051650 restraints weight = 70355.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.052516 restraints weight = 47924.011| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29511 Z= 0.166 Angle : 0.600 10.585 40518 Z= 0.308 Chirality : 0.041 0.165 4808 Planarity : 0.004 0.064 4943 Dihedral : 16.326 178.370 5071 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.40 % Allowed : 28.19 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3589 helix: 1.46 (0.15), residues: 1323 sheet: 0.45 (0.26), residues: 395 loop : -1.36 (0.14), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 212 HIS 0.002 0.001 HIS D 430 PHE 0.015 0.001 PHE C1270 TYR 0.023 0.001 TYR M 361 ARG 0.008 0.000 ARG B 91 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 1213) hydrogen bonds : angle 4.07212 ( 3404) metal coordination : bond 0.00431 ( 3) covalent geometry : bond 0.00369 (29508) covalent geometry : angle 0.60049 (40518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9132.21 seconds wall clock time: 160 minutes 4.74 seconds (9604.74 seconds total)