Starting phenix.real_space_refine on Mon May 26 22:41:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8re4_19079/05_2025/8re4_19079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8re4_19079/05_2025/8re4_19079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8re4_19079/05_2025/8re4_19079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8re4_19079/05_2025/8re4_19079.map" model { file = "/net/cci-nas-00/data/ceres_data/8re4_19079/05_2025/8re4_19079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8re4_19079/05_2025/8re4_19079.cif" } resolution = 2.8 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 102 5.49 5 Mg 1 5.21 5 S 102 5.16 5 C 17981 2.51 5 N 5167 2.21 5 O 5810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.29s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29165 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2365 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1733 Classifications: {'peptide': 234} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 224} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 4, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 70 Chain: "C" Number of atoms: 10080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10080 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, '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: 9685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 9685 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PTRANS': 53, 'TRANS': 1276} Chain breaks: 5 Unresolved non-hydrogen bonds: 688 Unresolved non-hydrogen angles: 836 Unresolved non-hydrogen dihedrals: 583 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 9, 'GLU:plan': 31, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 441 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 2657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2657 Classifications: {'peptide': 380} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 16, 'TRANS': 363} Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 436 Unresolved non-hydrogen dihedrals: 270 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 8, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 12, 'ASP:plan': 14} Unresolved non-hydrogen planarities: 217 Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 960 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain breaks: 1 Chain: "R" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 106 Classifications: {'RNA': 5} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Chain breaks: 1 Chain: "T" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1030 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14701 SG CYS D 70 103.972 112.746 93.290 1.00 58.66 S ATOM 14715 SG CYS D 72 102.253 116.852 95.537 1.00 47.22 S ATOM 14830 SG CYS D 88 102.041 113.314 96.978 1.00 51.38 S ATOM 20946 SG CYS D 898 93.575 45.025 89.115 1.00 44.84 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.58 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.58 Time building chain proxies: 15.30, per 1000 atoms: 0.52 Number of scatterers: 29165 At special positions: 0 Unit cell: (140.8, 169.4, 166.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 102 16.00 P 102 15.00 Mg 1 11.99 O 5810 8.00 N 5167 7.00 C 17981 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.25 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6802 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 45 sheets defined 41.4% alpha, 14.0% beta 38 base pairs and 78 stacking pairs defined. Time for finding SS restraints: 9.90 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.842A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.760A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.363A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 273 removed outlier: 3.573A pdb=" N ALA A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.985A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 296 through 310 removed outlier: 3.526A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.721A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.515A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 164 through 171 Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.695A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.752A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 48 through 57 removed outlier: 4.079A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.712A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 288 through 295 Processing helix chain 'C' and resid 318 through 329 removed outlier: 3.771A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.612A pdb=" N GLU C 386 " --> pdb=" O GLU C 382 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.844A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 436 " --> pdb=" O LEU C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.681A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 491 Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.340A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.743A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 614 removed outlier: 3.602A pdb=" N TYR C 614 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.547A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 858 through 863 removed outlier: 3.528A pdb=" N SER C 863 " --> pdb=" O ALA C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.554A pdb=" N LEU C 946 " --> pdb=" O ASP C 942 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.658A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 1000 removed outlier: 3.834A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.626A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 3.563A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.298A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.638A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.765A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1239 through 1241 No H-bonds generated for 'chain 'C' and resid 1239 through 1241' Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.846A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.768A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 13 removed outlier: 3.747A pdb=" N THR D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 removed outlier: 4.003A pdb=" N LYS D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 100 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.984A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 removed outlier: 4.442A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.647A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 327 through 331 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 540 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.737A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 removed outlier: 3.515A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 612 removed outlier: 3.922A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.651A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.672A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 671 removed outlier: 3.538A pdb=" N GLY D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.067A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 742 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.857A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.591A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 3.556A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.507A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.757A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.157A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1295 through 1299 removed outlier: 3.561A pdb=" N GLY D1299 " --> pdb=" O GLY D1296 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1314 Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.728A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1354 removed outlier: 3.563A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1376 Processing helix chain 'E' and resid 6 through 13 removed outlier: 3.792A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.623A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 119 through 130 Processing helix chain 'M' and resid 134 through 147 removed outlier: 3.732A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 171 through 184 removed outlier: 3.597A pdb=" N ALA M 177 " --> pdb=" O GLU M 173 " (cutoff:3.500A) Processing helix chain 'M' and resid 194 through 205 removed outlier: 3.903A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 218 removed outlier: 4.348A pdb=" N LEU M 218 " --> pdb=" O GLU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 230 Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 242 through 256 removed outlier: 3.544A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 311 removed outlier: 3.883A pdb=" N GLY M 307 " --> pdb=" O TYR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 322 through 351 removed outlier: 3.658A pdb=" N ARG M 327 " --> pdb=" O LEU M 323 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TRP M 328 " --> pdb=" O GLN M 324 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 356 removed outlier: 3.628A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.757A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 removed outlier: 3.550A pdb=" N ILE M 381 " --> pdb=" O HIS M 377 " (cutoff:3.500A) Processing helix chain 'M' and resid 399 through 404 removed outlier: 3.710A pdb=" N SER M 404 " --> pdb=" O TYR M 401 " (cutoff:3.500A) Processing helix chain 'M' and resid 416 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 466 removed outlier: 3.526A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 8.794A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.534A pdb=" N VAL A 98 " --> pdb=" O VAL A 146 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.729A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.386A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 61 removed outlier: 7.133A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.224A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.779A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.779A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.663A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.102A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.213A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.606A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 723 through 727 removed outlier: 6.685A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC4, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.222A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.713A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 841 removed outlier: 3.713A pdb=" N THR C 830 " --> pdb=" O ARG C1058 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AC8, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.798A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1243 through 1246 Processing sheet with id=AD1, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.731A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD3, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.760A pdb=" N LYS D 50 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 104 through 111 removed outlier: 10.330A pdb=" N LEU D 107 " --> pdb=" O PRO D 243 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N SER D 109 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL D 241 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.774A pdb=" N VAL D 145 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD7, first strand: chain 'D' and resid 526 through 527 removed outlier: 7.097A pdb=" N LEU D 527 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 9.347A pdb=" N THR D 553 " --> pdb=" O LEU D 527 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR D 572 " --> pdb=" O VAL D 548 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS D 570 " --> pdb=" O VAL D 550 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 706 through 708 Processing sheet with id=AD9, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE1, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE2, first strand: chain 'D' and resid 825 through 827 removed outlier: 6.654A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 848 through 849 removed outlier: 7.181A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 958 Processing sheet with id=AE5, first strand: chain 'D' and resid 974 through 975 removed outlier: 4.071A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1059 through 1060 removed outlier: 3.801A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1174 through 1177 removed outlier: 4.306A pdb=" N VAL D1176 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU D1188 " --> pdb=" O VAL D1176 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE9, first strand: chain 'M' and resid 277 through 278 removed outlier: 7.023A pdb=" N LEU M 277 " --> pdb=" O HIS M 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 1181 hydrogen bonds defined for protein. 3285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 196 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 78 stacking parallelities Total time for adding SS restraints: 14.28 Time building geometry restraints manager: 8.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8484 1.34 - 1.46: 4728 1.46 - 1.58: 16210 1.58 - 1.70: 199 1.70 - 1.82: 177 Bond restraints: 29798 Sorted by residual: bond pdb=" N GLU C1316 " pdb=" CA GLU C1316 " ideal model delta sigma weight residual 1.458 1.491 -0.033 7.40e-03 1.83e+04 2.05e+01 bond pdb=" N GLY D 742 " pdb=" CA GLY D 742 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.99e+01 bond pdb=" CE1 HIS C1237 " pdb=" NE2 HIS C1237 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.77e+01 bond pdb=" CE1 HIS C 628 " pdb=" NE2 HIS C 628 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.77e+01 bond pdb=" CE1 HIS D 430 " pdb=" NE2 HIS D 430 " ideal model delta sigma weight residual 1.321 1.363 -0.042 1.00e-02 1.00e+04 1.76e+01 ... (remaining 29793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 40367 2.88 - 5.75: 505 5.75 - 8.63: 26 8.63 - 11.51: 5 11.51 - 14.38: 2 Bond angle restraints: 40905 Sorted by residual: angle pdb=" C3' DT N 2 " pdb=" O3' DT N 2 " pdb=" P DA N 3 " ideal model delta sigma weight residual 120.20 108.30 11.90 1.50e+00 4.44e-01 6.29e+01 angle pdb=" C3' DA N 3 " pdb=" O3' DA N 3 " pdb=" P DG N 4 " ideal model delta sigma weight residual 120.20 111.82 8.38 1.50e+00 4.44e-01 3.12e+01 angle pdb=" CA GLY C 48 " pdb=" C GLY C 48 " pdb=" O GLY C 48 " ideal model delta sigma weight residual 122.29 118.08 4.21 8.10e-01 1.52e+00 2.71e+01 angle pdb=" C ARG A 235 " pdb=" CA ARG A 235 " pdb=" CB ARG A 235 " ideal model delta sigma weight residual 116.54 110.77 5.77 1.15e+00 7.56e-01 2.52e+01 angle pdb=" CA GLY D 103 " pdb=" C GLY D 103 " pdb=" O GLY D 103 " ideal model delta sigma weight residual 122.24 117.98 4.26 8.70e-01 1.32e+00 2.40e+01 ... (remaining 40900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.30: 16902 34.30 - 68.60: 977 68.60 - 102.90: 36 102.90 - 137.20: 0 137.20 - 171.50: 3 Dihedral angle restraints: 17918 sinusoidal: 7374 harmonic: 10544 Sorted by residual: dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 137.49 42.51 0 5.00e+00 4.00e-02 7.23e+01 dihedral pdb=" CD ARG A 235 " pdb=" NE ARG A 235 " pdb=" CZ ARG A 235 " pdb=" NH1 ARG A 235 " ideal model delta sinusoidal sigma weight residual 0.00 -57.78 57.78 1 1.00e+01 1.00e-02 4.48e+01 dihedral pdb=" CA PHE C 15 " pdb=" C PHE C 15 " pdb=" N GLY C 16 " pdb=" CA GLY C 16 " ideal model delta harmonic sigma weight residual 180.00 154.39 25.61 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 17915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4338 0.096 - 0.193: 500 0.193 - 0.289: 11 0.289 - 0.386: 0 0.386 - 0.482: 2 Chirality restraints: 4851 Sorted by residual: chirality pdb=" P DT N 2 " pdb=" OP1 DT N 2 " pdb=" OP2 DT N 2 " pdb=" O5' DT N 2 " both_signs ideal model delta sigma weight residual True 2.35 -2.83 -0.48 2.00e-01 2.50e+01 5.81e+00 chirality pdb=" P DA N 3 " pdb=" OP1 DA N 3 " pdb=" OP2 DA N 3 " pdb=" O5' DA N 3 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" CA ILE D 856 " pdb=" N ILE D 856 " pdb=" C ILE D 856 " pdb=" CB ILE D 856 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 4848 not shown) Planarity restraints: 5004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 235 " -0.920 9.50e-02 1.11e+02 4.13e-01 1.03e+02 pdb=" NE ARG A 235 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG A 235 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 235 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 235 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1330 " 0.544 9.50e-02 1.11e+02 2.44e-01 3.64e+01 pdb=" NE ARG D1330 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG D1330 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D1330 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D1330 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 535 " -0.420 9.50e-02 1.11e+02 1.88e-01 2.17e+01 pdb=" NE ARG D 535 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 535 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 535 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 535 " -0.014 2.00e-02 2.50e+03 ... (remaining 5001 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 113 2.52 - 3.12: 22072 3.12 - 3.71: 46098 3.71 - 4.31: 62752 4.31 - 4.90: 103319 Nonbonded interactions: 234354 Sorted by model distance: nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 1.931 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.088 2.170 nonbonded pdb=" OG1 THR D 980 " pdb=" O VAL D 997 " model vdw 2.188 3.040 nonbonded pdb=" OH TYR C 179 " pdb=" OE2 GLU C 458 " model vdw 2.202 3.040 nonbonded pdb=" O TYR C 810 " pdb=" OG SER C1077 " model vdw 2.206 3.040 ... (remaining 234349 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 0.020 Extract box with map and model: 1.050 Check model and map are aligned: 0.210 Set scattering table: 0.240 Process input model: 74.480 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.684 29802 Z= 0.462 Angle : 0.838 14.383 40905 Z= 0.573 Chirality : 0.057 0.482 4851 Planarity : 0.010 0.413 5004 Dihedral : 18.842 171.503 11116 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.09 % Favored : 93.66 % Rotamer: Outliers : 1.66 % Allowed : 24.96 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (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: -0.49 (0.14), residues: 3643 helix: 0.92 (0.15), residues: 1323 sheet: 0.30 (0.27), residues: 396 loop : -1.39 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 115 HIS 0.005 0.001 HIS C1116 PHE 0.023 0.001 PHE M 354 TYR 0.021 0.001 TYR A 177 ARG 0.010 0.001 ARG M 279 Details of bonding type rmsd hydrogen bonds : bond 0.18451 ( 1263) hydrogen bonds : angle 6.50588 ( 3481) metal coordination : bond 0.40579 ( 4) covalent geometry : bond 0.00611 (29798) covalent geometry : angle 0.83823 (40905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 186 time to evaluate : 3.301 Fit side-chains revert: symmetry clash REVERT: C 1240 ASP cc_start: 0.6790 (OUTLIER) cc_final: 0.6552 (m-30) outliers start: 45 outliers final: 12 residues processed: 220 average time/residue: 1.3603 time to fit residues: 354.2429 Evaluate side-chains 135 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 3.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 194 GLN Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1240 ASP Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 315 optimal weight: 6.9990 chunk 283 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 191 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 293 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 218 optimal weight: 20.0000 chunk 339 optimal weight: 30.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 294 ASN B 18 GLN C 518 ASN D 300 GLN D 430 HIS D 450 HIS D1249 ASN D1259 GLN ** M 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 406 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.066973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.041879 restraints weight = 107611.273| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.33 r_work: 0.2666 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 29802 Z= 0.275 Angle : 0.669 9.934 40905 Z= 0.351 Chirality : 0.045 0.176 4851 Planarity : 0.005 0.065 5004 Dihedral : 16.410 169.511 5113 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.24 % Rotamer: Outliers : 4.76 % Allowed : 22.27 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.35 (0.14), residues: 3643 helix: 1.07 (0.14), residues: 1371 sheet: 0.45 (0.27), residues: 370 loop : -1.41 (0.13), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 115 HIS 0.008 0.001 HIS C 832 PHE 0.017 0.002 PHE A 231 TYR 0.018 0.002 TYR D 631 ARG 0.006 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04879 ( 1263) hydrogen bonds : angle 4.53506 ( 3481) metal coordination : bond 0.00940 ( 4) covalent geometry : bond 0.00640 (29798) covalent geometry : angle 0.66907 (40905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 128 time to evaluate : 3.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8560 (mmmm) REVERT: A 93 GLN cc_start: 0.7716 (mp10) cc_final: 0.7360 (mp-120) REVERT: A 206 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: B 4 SER cc_start: 0.8861 (OUTLIER) cc_final: 0.8332 (t) REVERT: B 215 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8471 (tm-30) REVERT: C 246 LEU cc_start: 0.9752 (OUTLIER) cc_final: 0.9521 (pp) REVERT: C 289 VAL cc_start: 0.8149 (OUTLIER) cc_final: 0.7922 (t) REVERT: C 370 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8264 (ppp) REVERT: C 1069 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8655 (ptt-90) REVERT: D 115 TRP cc_start: 0.8632 (OUTLIER) cc_final: 0.6772 (m-90) REVERT: D 160 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9102 (pp) REVERT: D 1222 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.8737 (ttm-80) REVERT: E 8 ASP cc_start: 0.9098 (m-30) cc_final: 0.8840 (m-30) REVERT: E 69 ARG cc_start: 0.8748 (mmm160) cc_final: 0.8187 (tpm-80) outliers start: 129 outliers final: 36 residues processed: 245 average time/residue: 1.1673 time to fit residues: 347.6887 Evaluate side-chains 169 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 2.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 4 SER Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 896 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 115 TRP Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 790 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 99 optimal weight: 8.9990 chunk 262 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 361 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 chunk 84 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 76 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN D 430 HIS M 290 ASN ** M 406 HIS ** 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 = 0.3577 r_free = 0.3577 target = 0.066609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.041743 restraints weight = 107430.458| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.28 r_work: 0.2666 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2661 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2661 r_free = 0.2661 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2661 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 29802 Z= 0.197 Angle : 0.585 9.335 40905 Z= 0.307 Chirality : 0.042 0.156 4851 Planarity : 0.004 0.064 5004 Dihedral : 16.235 172.707 5104 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.71 % Favored : 94.26 % Rotamer: Outliers : 4.14 % Allowed : 22.45 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 3643 helix: 1.46 (0.15), residues: 1359 sheet: 0.27 (0.26), residues: 395 loop : -1.27 (0.14), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 115 HIS 0.004 0.001 HIS C 832 PHE 0.011 0.001 PHE D 49 TYR 0.015 0.001 TYR D 140 ARG 0.006 0.001 ARG C 678 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 1263) hydrogen bonds : angle 4.23601 ( 3481) metal coordination : bond 0.01644 ( 4) covalent geometry : bond 0.00456 (29798) covalent geometry : angle 0.58536 (40905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 124 time to evaluate : 3.070 Fit side-chains REVERT: A 25 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8522 (mmmm) REVERT: B 93 GLN cc_start: 0.9134 (tp40) cc_final: 0.8454 (mm110) REVERT: B 215 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8391 (tm-30) REVERT: C 105 TYR cc_start: 0.8480 (m-10) cc_final: 0.7850 (m-80) REVERT: C 492 MET cc_start: 0.8384 (mmm) cc_final: 0.8019 (mpm) REVERT: C 1069 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8306 (ptt-90) REVERT: C 1220 GLN cc_start: 0.9293 (OUTLIER) cc_final: 0.8981 (tt0) REVERT: D 160 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9095 (pp) REVERT: D 179 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8863 (mppt) REVERT: D 255 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8476 (mm) REVERT: D 747 MET cc_start: 0.8616 (pmm) cc_final: 0.8353 (pmm) REVERT: D 1222 ARG cc_start: 0.9514 (OUTLIER) cc_final: 0.8860 (ttm-80) REVERT: D 1289 ASN cc_start: 0.9476 (OUTLIER) cc_final: 0.9246 (p0) REVERT: D 1330 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8920 (tmm-80) REVERT: E 42 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8463 (mp0) REVERT: M 361 TYR cc_start: 0.9167 (m-80) cc_final: 0.8661 (m-10) outliers start: 112 outliers final: 39 residues processed: 221 average time/residue: 1.2705 time to fit residues: 336.2704 Evaluate side-chains 167 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 117 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 124 MET Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1289 ASN Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 356 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 364 optimal weight: 9.9990 chunk 141 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 372 optimal weight: 20.0000 chunk 143 optimal weight: 0.9990 chunk 220 optimal weight: 10.0000 chunk 326 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 228 optimal weight: 8.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN D 430 HIS M 391 HIS ** M 406 HIS ** 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 = 0.3563 r_free = 0.3563 target = 0.065933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.040952 restraints weight = 108612.806| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.31 r_work: 0.2648 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2640 r_free = 0.2640 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 29802 Z= 0.216 Angle : 0.592 9.020 40905 Z= 0.308 Chirality : 0.042 0.178 4851 Planarity : 0.004 0.060 5004 Dihedral : 16.208 173.747 5102 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.29 % Favored : 93.69 % Rotamer: Outliers : 4.32 % Allowed : 23.04 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 3643 helix: 1.46 (0.14), residues: 1372 sheet: 0.18 (0.27), residues: 394 loop : -1.29 (0.14), residues: 1877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 126 HIS 0.006 0.001 HIS M 377 PHE 0.012 0.001 PHE D 49 TYR 0.014 0.001 TYR D 631 ARG 0.005 0.000 ARG C 678 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 1263) hydrogen bonds : angle 4.10592 ( 3481) metal coordination : bond 0.01032 ( 4) covalent geometry : bond 0.00502 (29798) covalent geometry : angle 0.59165 (40905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 123 time to evaluate : 2.996 Fit side-chains revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8543 (mmmm) REVERT: A 206 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8295 (tt0) REVERT: B 18 GLN cc_start: 0.7465 (tm130) cc_final: 0.7252 (tm-30) REVERT: B 51 MET cc_start: 0.9170 (OUTLIER) cc_final: 0.8728 (mmm) REVERT: B 93 GLN cc_start: 0.9132 (tp40) cc_final: 0.8452 (mm110) REVERT: B 215 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: C 105 TYR cc_start: 0.8512 (m-10) cc_final: 0.7828 (m-80) REVERT: C 240 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.8774 (mp0) REVERT: C 246 LEU cc_start: 0.9749 (OUTLIER) cc_final: 0.9520 (pp) REVERT: C 370 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8341 (ppp) REVERT: C 492 MET cc_start: 0.8365 (mmm) cc_final: 0.8001 (mpm) REVERT: C 548 ARG cc_start: 0.9325 (OUTLIER) cc_final: 0.7583 (mtp85) REVERT: C 1069 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8350 (ptt-90) REVERT: C 1233 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9284 (mt) REVERT: D 160 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9019 (pp) REVERT: D 179 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.8857 (mppt) REVERT: D 747 MET cc_start: 0.8692 (pmm) cc_final: 0.8393 (pmm) REVERT: D 901 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7830 (ptp-170) REVERT: D 1222 ARG cc_start: 0.9576 (OUTLIER) cc_final: 0.8861 (ttm-80) REVERT: D 1316 THR cc_start: 0.9435 (OUTLIER) cc_final: 0.9193 (p) REVERT: E 42 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: M 361 TYR cc_start: 0.9144 (m-80) cc_final: 0.8691 (m-10) outliers start: 117 outliers final: 42 residues processed: 224 average time/residue: 1.2317 time to fit residues: 331.4660 Evaluate side-chains 181 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 123 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 370 MET Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 364 optimal weight: 5.9990 chunk 357 optimal weight: 5.9990 chunk 253 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 306 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 265 optimal weight: 10.0000 chunk 315 optimal weight: 5.9990 chunk 23 optimal weight: 0.0050 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 430 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.066030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.040869 restraints weight = 107511.746| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.34 r_work: 0.2653 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29802 Z= 0.186 Angle : 0.573 9.434 40905 Z= 0.298 Chirality : 0.042 0.227 4851 Planarity : 0.004 0.059 5004 Dihedral : 16.164 175.054 5101 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.96 % Favored : 94.02 % Rotamer: Outliers : 4.51 % Allowed : 22.97 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 3643 helix: 1.60 (0.14), residues: 1364 sheet: 0.33 (0.27), residues: 383 loop : -1.27 (0.14), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 212 HIS 0.005 0.001 HIS M 377 PHE 0.010 0.001 PHE D 49 TYR 0.013 0.001 TYR D 140 ARG 0.005 0.000 ARG C 678 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 1263) hydrogen bonds : angle 4.00045 ( 3481) metal coordination : bond 0.01172 ( 4) covalent geometry : bond 0.00429 (29798) covalent geometry : angle 0.57289 (40905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 125 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8538 (mmmm) REVERT: A 206 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8285 (tt0) REVERT: B 18 GLN cc_start: 0.7555 (tm130) cc_final: 0.7348 (tm-30) REVERT: B 76 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8140 (mt-10) REVERT: B 93 GLN cc_start: 0.9195 (tp40) cc_final: 0.8529 (mm110) REVERT: B 215 GLU cc_start: 0.9008 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: C 124 MET cc_start: 0.9070 (ptp) cc_final: 0.8858 (pmm) REVERT: C 246 LEU cc_start: 0.9754 (OUTLIER) cc_final: 0.9535 (pp) REVERT: C 492 MET cc_start: 0.8399 (mmm) cc_final: 0.8024 (mpm) REVERT: C 548 ARG cc_start: 0.9340 (OUTLIER) cc_final: 0.7540 (mtp85) REVERT: C 1069 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8299 (ptt-90) REVERT: C 1137 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8530 (pm20) REVERT: C 1220 GLN cc_start: 0.9302 (OUTLIER) cc_final: 0.9040 (tt0) REVERT: C 1233 LEU cc_start: 0.9532 (OUTLIER) cc_final: 0.9293 (mt) REVERT: D 29 MET cc_start: 0.8881 (tpp) cc_final: 0.8535 (tpp) REVERT: D 160 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9072 (pp) REVERT: D 179 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8856 (mppt) REVERT: D 744 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.8366 (ttt90) REVERT: D 901 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.7800 (ptp-170) REVERT: D 1222 ARG cc_start: 0.9589 (OUTLIER) cc_final: 0.8833 (ttm-80) REVERT: D 1316 THR cc_start: 0.9440 (OUTLIER) cc_final: 0.9201 (p) REVERT: D 1330 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8916 (tmm-80) REVERT: E 42 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8485 (mp0) REVERT: M 361 TYR cc_start: 0.9138 (m-80) cc_final: 0.8864 (m-10) outliers start: 122 outliers final: 53 residues processed: 229 average time/residue: 1.2330 time to fit residues: 340.6030 Evaluate side-chains 192 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 121 time to evaluate : 2.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 25 LYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 142 MET Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 805 MET Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 400 MET Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 991 THR Chi-restraints excluded: chain D residue 1222 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 11 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 147 optimal weight: 10.0000 chunk 154 optimal weight: 40.0000 chunk 13 optimal weight: 0.8980 chunk 194 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 337 optimal weight: 6.9990 chunk 242 optimal weight: 0.0970 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1288 GLN D 430 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.066325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.041476 restraints weight = 107477.367| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.37 r_work: 0.2665 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29802 Z= 0.144 Angle : 0.557 9.676 40905 Z= 0.288 Chirality : 0.041 0.211 4851 Planarity : 0.004 0.058 5004 Dihedral : 16.118 175.750 5101 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.26 % Favored : 93.71 % Rotamer: Outliers : 3.88 % Allowed : 24.00 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.15 (0.14), residues: 3643 helix: 1.72 (0.15), residues: 1359 sheet: 0.34 (0.27), residues: 386 loop : -1.21 (0.14), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 212 HIS 0.004 0.001 HIS A 66 PHE 0.008 0.001 PHE D 116 TYR 0.013 0.001 TYR M 401 ARG 0.007 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 1263) hydrogen bonds : angle 3.88226 ( 3481) metal coordination : bond 0.01232 ( 4) covalent geometry : bond 0.00329 (29798) covalent geometry : angle 0.55708 (40905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 123 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: B 18 GLN cc_start: 0.7544 (tm130) cc_final: 0.7308 (tm-30) REVERT: B 76 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8145 (mt-10) REVERT: B 93 GLN cc_start: 0.9228 (tp40) cc_final: 0.8563 (mm110) REVERT: B 215 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: C 240 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8865 (mp0) REVERT: C 246 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9529 (pp) REVERT: C 459 MET cc_start: 0.9143 (OUTLIER) cc_final: 0.8894 (mtt) REVERT: C 492 MET cc_start: 0.8315 (mmm) cc_final: 0.7961 (mpm) REVERT: C 548 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.7554 (mtp85) REVERT: C 888 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8541 (p) REVERT: C 1069 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8286 (ptt-90) REVERT: C 1137 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8512 (pm20) REVERT: C 1220 GLN cc_start: 0.9298 (OUTLIER) cc_final: 0.8995 (tt0) REVERT: C 1233 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.9288 (mt) REVERT: D 29 MET cc_start: 0.8923 (tpp) cc_final: 0.8624 (tpp) REVERT: D 160 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9080 (pp) REVERT: D 179 LYS cc_start: 0.9287 (OUTLIER) cc_final: 0.8846 (mppt) REVERT: D 832 LYS cc_start: 0.9555 (OUTLIER) cc_final: 0.9195 (mttp) REVERT: D 901 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.7801 (ptp-170) REVERT: D 1330 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8891 (tmm-80) REVERT: E 8 ASP cc_start: 0.8934 (m-30) cc_final: 0.8722 (m-30) REVERT: E 42 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8469 (mp0) REVERT: M 365 MET cc_start: 0.8113 (ptm) cc_final: 0.7608 (ppp) outliers start: 105 outliers final: 45 residues processed: 216 average time/residue: 1.1894 time to fit residues: 310.3975 Evaluate side-chains 184 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 121 time to evaluate : 2.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 157 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 38 optimal weight: 9.9990 chunk 347 optimal weight: 50.0000 chunk 48 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 225 optimal weight: 4.9990 chunk 365 optimal weight: 30.0000 chunk 35 optimal weight: 7.9990 chunk 168 optimal weight: 10.0000 chunk 199 optimal weight: 9.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 430 HIS ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.064894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.039741 restraints weight = 108378.678| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.32 r_work: 0.2614 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2610 r_free = 0.2610 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 29802 Z= 0.278 Angle : 0.636 9.384 40905 Z= 0.330 Chirality : 0.044 0.295 4851 Planarity : 0.004 0.060 5004 Dihedral : 16.229 176.523 5099 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.75 % Favored : 93.22 % Rotamer: Outliers : 3.91 % Allowed : 24.15 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.03 (0.14), residues: 3643 helix: 1.58 (0.14), residues: 1375 sheet: 0.26 (0.27), residues: 392 loop : -1.28 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 126 HIS 0.004 0.001 HIS M 406 PHE 0.016 0.001 PHE D 49 TYR 0.017 0.001 TYR D 631 ARG 0.005 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.04549 ( 1263) hydrogen bonds : angle 4.03788 ( 3481) metal coordination : bond 0.01546 ( 4) covalent geometry : bond 0.00647 (29798) covalent geometry : angle 0.63586 (40905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 119 time to evaluate : 2.909 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8387 (tt0) REVERT: A 295 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8397 (tm) REVERT: B 18 GLN cc_start: 0.7551 (tm130) cc_final: 0.7313 (tm-30) REVERT: B 51 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8740 (mmm) REVERT: B 76 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: B 93 GLN cc_start: 0.9228 (tp40) cc_final: 0.8605 (mm110) REVERT: B 215 GLU cc_start: 0.9026 (OUTLIER) cc_final: 0.8343 (tm-30) REVERT: C 105 TYR cc_start: 0.8650 (m-10) cc_final: 0.7939 (m-80) REVERT: C 124 MET cc_start: 0.9203 (ptp) cc_final: 0.8898 (pmm) REVERT: C 240 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8872 (mp0) REVERT: C 246 LEU cc_start: 0.9761 (OUTLIER) cc_final: 0.9508 (pp) REVERT: C 492 MET cc_start: 0.8415 (mmm) cc_final: 0.8071 (mpm) REVERT: C 548 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.7570 (mtp85) REVERT: C 741 MET cc_start: 0.8594 (ttt) cc_final: 0.8338 (ttm) REVERT: C 888 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8522 (p) REVERT: C 1069 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8365 (ptt-90) REVERT: C 1220 GLN cc_start: 0.9278 (OUTLIER) cc_final: 0.8988 (tt0) REVERT: C 1233 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9258 (mt) REVERT: D 29 MET cc_start: 0.9011 (tpp) cc_final: 0.8667 (tpp) REVERT: D 160 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9005 (pp) REVERT: D 179 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8884 (mppt) REVERT: D 744 ARG cc_start: 0.9391 (OUTLIER) cc_final: 0.8317 (ttt90) REVERT: D 747 MET cc_start: 0.8707 (pmm) cc_final: 0.8347 (pmm) REVERT: D 832 LYS cc_start: 0.9541 (OUTLIER) cc_final: 0.8973 (mmtt) REVERT: D 901 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.7832 (ptp-170) REVERT: D 1316 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9231 (p) REVERT: D 1330 ARG cc_start: 0.9203 (OUTLIER) cc_final: 0.8939 (tmm-80) REVERT: E 42 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: M 156 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8294 (mp) REVERT: M 365 MET cc_start: 0.8229 (ptm) cc_final: 0.7591 (ppp) outliers start: 106 outliers final: 49 residues processed: 212 average time/residue: 1.2536 time to fit residues: 317.9415 Evaluate side-chains 188 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 118 time to evaluate : 2.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 558 VAL Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 744 ARG Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 224 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 153 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 285 optimal weight: 6.9990 chunk 350 optimal weight: 0.1980 chunk 150 optimal weight: 40.0000 chunk 36 optimal weight: 20.0000 chunk 255 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 156 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 430 HIS ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.066025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.041243 restraints weight = 107738.249| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.29 r_work: 0.2658 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2657 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29802 Z= 0.138 Angle : 0.571 11.144 40905 Z= 0.294 Chirality : 0.041 0.206 4851 Planarity : 0.004 0.060 5004 Dihedral : 16.145 177.316 5098 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.87 % Favored : 94.10 % Rotamer: Outliers : 3.06 % Allowed : 25.00 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.19 (0.14), residues: 3643 helix: 1.73 (0.14), residues: 1366 sheet: 0.38 (0.27), residues: 386 loop : -1.19 (0.14), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 212 HIS 0.004 0.001 HIS M 406 PHE 0.008 0.001 PHE M 403 TYR 0.015 0.001 TYR M 401 ARG 0.006 0.000 ARG A 12 Details of bonding type rmsd hydrogen bonds : bond 0.03636 ( 1263) hydrogen bonds : angle 3.86513 ( 3481) metal coordination : bond 0.01190 ( 4) covalent geometry : bond 0.00314 (29798) covalent geometry : angle 0.57141 (40905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 119 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: B 18 GLN cc_start: 0.7567 (tm130) cc_final: 0.7309 (tm-30) REVERT: B 76 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: B 93 GLN cc_start: 0.9237 (tp40) cc_final: 0.8641 (mm110) REVERT: B 215 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8287 (tm-30) REVERT: C 124 MET cc_start: 0.9121 (ptp) cc_final: 0.8914 (pmm) REVERT: C 240 GLU cc_start: 0.9106 (OUTLIER) cc_final: 0.8846 (mp0) REVERT: C 246 LEU cc_start: 0.9764 (OUTLIER) cc_final: 0.9528 (pp) REVERT: C 492 MET cc_start: 0.8250 (mmm) cc_final: 0.7918 (mpm) REVERT: C 548 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.7610 (mtp85) REVERT: C 741 MET cc_start: 0.8546 (ttt) cc_final: 0.8319 (ttm) REVERT: C 888 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8557 (p) REVERT: C 1069 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.8308 (ptt-90) REVERT: C 1137 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8469 (pm20) REVERT: C 1220 GLN cc_start: 0.9306 (OUTLIER) cc_final: 0.8996 (tt0) REVERT: D 29 MET cc_start: 0.8941 (tpp) cc_final: 0.8566 (tpp) REVERT: D 160 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9072 (pp) REVERT: D 179 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8817 (mppt) REVERT: D 747 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8328 (pmm) REVERT: D 832 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.9177 (mttp) REVERT: D 1330 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8879 (tmm-80) REVERT: E 42 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8481 (mp0) REVERT: M 156 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8147 (mp) REVERT: M 365 MET cc_start: 0.8128 (ptm) cc_final: 0.7617 (ppp) outliers start: 83 outliers final: 45 residues processed: 194 average time/residue: 1.4002 time to fit residues: 325.7619 Evaluate side-chains 181 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 119 time to evaluate : 3.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 132 HIS Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 12 LYS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 73 optimal weight: 8.9990 chunk 317 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 357 optimal weight: 7.9990 chunk 282 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 372 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 430 HIS ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.065726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.040926 restraints weight = 107277.545| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.32 r_work: 0.2648 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2644 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2644 r_free = 0.2644 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2644 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29802 Z= 0.172 Angle : 0.582 13.009 40905 Z= 0.300 Chirality : 0.042 0.212 4851 Planarity : 0.004 0.058 5004 Dihedral : 16.145 177.574 5098 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.34 % Favored : 93.63 % Rotamer: Outliers : 2.70 % Allowed : 25.52 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.23 (0.14), residues: 3643 helix: 1.76 (0.14), residues: 1363 sheet: 0.46 (0.27), residues: 378 loop : -1.16 (0.14), residues: 1902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 126 HIS 0.004 0.001 HIS M 406 PHE 0.009 0.001 PHE D 49 TYR 0.015 0.001 TYR M 401 ARG 0.007 0.000 ARG M 196 Details of bonding type rmsd hydrogen bonds : bond 0.03796 ( 1263) hydrogen bonds : angle 3.86130 ( 3481) metal coordination : bond 0.01159 ( 4) covalent geometry : bond 0.00399 (29798) covalent geometry : angle 0.58185 (40905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 123 time to evaluate : 2.959 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: A 295 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8454 (tm) REVERT: B 18 GLN cc_start: 0.7606 (tm130) cc_final: 0.7376 (tm-30) REVERT: B 76 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: B 93 GLN cc_start: 0.9227 (tp40) cc_final: 0.8643 (mm110) REVERT: B 215 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8286 (tm-30) REVERT: C 105 TYR cc_start: 0.8632 (m-10) cc_final: 0.7878 (m-80) REVERT: C 240 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8854 (mp0) REVERT: C 246 LEU cc_start: 0.9771 (OUTLIER) cc_final: 0.9540 (pp) REVERT: C 492 MET cc_start: 0.8306 (mmm) cc_final: 0.7962 (mpm) REVERT: C 548 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.7613 (mtp85) REVERT: C 741 MET cc_start: 0.8591 (ttt) cc_final: 0.8359 (ttm) REVERT: C 888 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8584 (p) REVERT: C 1069 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.8335 (ptt-90) REVERT: C 1137 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8466 (pm20) REVERT: C 1220 GLN cc_start: 0.9303 (OUTLIER) cc_final: 0.8993 (tt0) REVERT: C 1233 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9265 (mt) REVERT: D 29 MET cc_start: 0.8970 (tpp) cc_final: 0.8598 (tpp) REVERT: D 160 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9064 (pp) REVERT: D 179 LYS cc_start: 0.9264 (OUTLIER) cc_final: 0.8812 (mppt) REVERT: D 192 MET cc_start: 0.9578 (ttm) cc_final: 0.9352 (ptm) REVERT: D 832 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.9169 (mttp) REVERT: D 1316 THR cc_start: 0.9441 (OUTLIER) cc_final: 0.9201 (p) REVERT: D 1330 ARG cc_start: 0.9195 (OUTLIER) cc_final: 0.8901 (tmm-80) REVERT: E 42 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8432 (mp0) REVERT: M 156 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8186 (mp) REVERT: M 365 MET cc_start: 0.8203 (ptm) cc_final: 0.7744 (ppp) outliers start: 73 outliers final: 44 residues processed: 188 average time/residue: 1.2315 time to fit residues: 278.7058 Evaluate side-chains 183 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 120 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 240 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Chi-restraints excluded: chain M residue 380 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 300 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 274 optimal weight: 0.5980 chunk 371 optimal weight: 10.0000 chunk 36 optimal weight: 20.0000 chunk 229 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 430 HIS ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.065817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.040892 restraints weight = 108926.209| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.32 r_work: 0.2654 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2652 r_free = 0.2652 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 29802 Z= 0.157 Angle : 0.579 13.067 40905 Z= 0.297 Chirality : 0.041 0.193 4851 Planarity : 0.004 0.059 5004 Dihedral : 16.148 178.144 5098 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.93 % Rotamer: Outliers : 2.55 % Allowed : 25.55 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: 0.25 (0.14), residues: 3643 helix: 1.78 (0.14), residues: 1363 sheet: 0.39 (0.27), residues: 386 loop : -1.15 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 212 HIS 0.005 0.001 HIS M 406 PHE 0.011 0.001 PHE M 403 TYR 0.019 0.001 TYR M 401 ARG 0.007 0.000 ARG D 388 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 1263) hydrogen bonds : angle 3.82829 ( 3481) metal coordination : bond 0.01206 ( 4) covalent geometry : bond 0.00363 (29798) covalent geometry : angle 0.57873 (40905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7286 Ramachandran restraints generated. 3643 Oldfield, 0 Emsley, 3643 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 121 time to evaluate : 3.484 Fit side-chains revert: symmetry clash REVERT: A 206 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8395 (tt0) REVERT: B 18 GLN cc_start: 0.7604 (tm130) cc_final: 0.7370 (tm-30) REVERT: B 76 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: B 93 GLN cc_start: 0.9227 (tp40) cc_final: 0.8605 (mm110) REVERT: B 215 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8274 (tm-30) REVERT: C 105 TYR cc_start: 0.8611 (m-10) cc_final: 0.7868 (m-80) REVERT: C 246 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9540 (pp) REVERT: C 459 MET cc_start: 0.9078 (mtp) cc_final: 0.8839 (mtt) REVERT: C 492 MET cc_start: 0.8289 (mmm) cc_final: 0.7977 (mpm) REVERT: C 548 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.7621 (mtp85) REVERT: C 741 MET cc_start: 0.8509 (ttt) cc_final: 0.8230 (ttm) REVERT: C 888 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8583 (p) REVERT: C 1069 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.8307 (ptt-90) REVERT: C 1137 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8449 (pm20) REVERT: C 1220 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.9006 (tt0) REVERT: C 1232 MET cc_start: 0.9520 (mtp) cc_final: 0.9310 (mmm) REVERT: C 1233 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9290 (mt) REVERT: D 29 MET cc_start: 0.8958 (tpp) cc_final: 0.8579 (tpp) REVERT: D 160 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9061 (pp) REVERT: D 179 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8826 (mppt) REVERT: D 192 MET cc_start: 0.9576 (ttm) cc_final: 0.9365 (ptm) REVERT: D 747 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8299 (pmm) REVERT: D 832 LYS cc_start: 0.9544 (OUTLIER) cc_final: 0.9183 (mttp) REVERT: D 1316 THR cc_start: 0.9433 (OUTLIER) cc_final: 0.9190 (p) REVERT: D 1330 ARG cc_start: 0.9191 (OUTLIER) cc_final: 0.8892 (tmm-80) REVERT: E 42 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8447 (mp0) REVERT: M 365 MET cc_start: 0.8110 (ptm) cc_final: 0.7607 (ppp) outliers start: 69 outliers final: 46 residues processed: 182 average time/residue: 1.2707 time to fit residues: 278.8545 Evaluate side-chains 183 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 120 time to evaluate : 3.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 206 GLU Chi-restraints excluded: chain A residue 249 PHE Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain B residue 51 MET Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain C residue 62 TYR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 548 ARG Chi-restraints excluded: chain C residue 599 VAL Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 723 VAL Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 895 LEU Chi-restraints excluded: chain C residue 1037 THR Chi-restraints excluded: chain C residue 1069 ARG Chi-restraints excluded: chain C residue 1137 GLU Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1220 GLN Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 179 LYS Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 697 MET Chi-restraints excluded: chain D residue 747 MET Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 822 MET Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 832 LYS Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 863 LEU Chi-restraints excluded: chain D residue 932 MET Chi-restraints excluded: chain D residue 1163 VAL Chi-restraints excluded: chain D residue 1316 THR Chi-restraints excluded: chain D residue 1330 ARG Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain M residue 93 THR Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 287 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 348 optimal weight: 10.0000 chunk 79 optimal weight: 50.0000 chunk 217 optimal weight: 10.0000 chunk 293 optimal weight: 0.0470 chunk 279 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 153 optimal weight: 40.0000 chunk 172 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 430 HIS ** M 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.065311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.040426 restraints weight = 107693.206| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.33 r_work: 0.2636 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2631 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2631 r_free = 0.2631 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2631 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 29802 Z= 0.199 Angle : 0.599 12.347 40905 Z= 0.308 Chirality : 0.042 0.196 4851 Planarity : 0.004 0.059 5004 Dihedral : 16.215 178.493 5097 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.48 % Favored : 93.49 % Rotamer: Outliers : 2.77 % Allowed : 25.37 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.33 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (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: 0.25 (0.14), residues: 3643 helix: 1.78 (0.14), residues: 1360 sheet: 0.47 (0.27), residues: 378 loop : -1.16 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 212 HIS 0.004 0.001 HIS M 406 PHE 0.013 0.001 PHE M 403 TYR 0.021 0.001 TYR M 401 ARG 0.007 0.000 ARG D 388 Details of bonding type rmsd hydrogen bonds : bond 0.03945 ( 1263) hydrogen bonds : angle 3.87121 ( 3481) metal coordination : bond 0.01088 ( 4) covalent geometry : bond 0.00462 (29798) covalent geometry : angle 0.59857 (40905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20666.56 seconds wall clock time: 355 minutes 44.90 seconds (21344.90 seconds total)