Starting phenix.real_space_refine on Sun Jul 5 18:33:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pyk_13718/07_2026/7pyk_13718.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pyk_13718/07_2026/7pyk_13718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7pyk_13718/07_2026/7pyk_13718.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pyk_13718/07_2026/7pyk_13718.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pyk_13718/07_2026/7pyk_13718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pyk_13718/07_2026/7pyk_13718.map" model { file = "/net/cci-nas-00/data/ceres_data/7pyk_13718/07_2026/7pyk_13718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pyk_13718/07_2026/7pyk_13718.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.055 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 67 5.49 5 Mg 1 5.21 5 S 105 5.16 5 C 18081 2.51 5 N 5263 2.21 5 O 5823 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29342 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1775 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 9, 'TRANS': 219} Chain: "B" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2076 Classifications: {'peptide': 298} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 13, 'TRANS': 284} Chain breaks: 2 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 6, 'ARG:plan': 5, 'GLU:plan': 7, 'ASN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 111 Chain: "C" Number of atoms: 10577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10577 Classifications: {'peptide': 1341} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 56, 'TRANS': 1282} Chain: "D" Number of atoms: 10375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 10375 Classifications: {'peptide': 1334} Link IDs: {'PTRANS': 55, 'TRANS': 1278} Chain breaks: 2 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 709 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 2447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 2447 Classifications: {'peptide': 495} Incomplete info: {'truncation_to_alanine': 409} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 479} Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 1451 Unresolved non-hydrogen angles: 1853 Unresolved non-hydrogen dihedrals: 1145 Unresolved non-hydrogen chiralities: 145 Planarities with less than four sites: {'ASN:plan1': 19, 'GLU:plan': 56, 'ARG:plan': 33, 'PHE:plan': 14, 'TYR:plan': 6, 'GLN:plan1': 19, 'ASP:plan': 42, 'TRP:plan': 4, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 830 Chain: "N" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 554 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain breaks: 1 Chain: "T" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 611 Classifications: {'DNA': 30} Link IDs: {'rna3p': 29} Chain: "R" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 215 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 8} 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 14877 SG CYS D 70 107.767 126.019 80.965 1.00309.02 S ATOM 14891 SG CYS D 72 107.057 128.885 81.697 1.00300.42 S ATOM 20711 SG CYS D 814 118.669 64.937 110.080 1.00205.05 S ATOM 21327 SG CYS D 895 117.921 66.665 107.635 1.00198.23 S ATOM 21348 SG CYS D 898 115.751 63.769 108.194 1.00190.15 S Time building chain proxies: 5.84, per 1000 atoms: 0.20 Number of scatterers: 29342 At special positions: 0 Unit cell: (190.75, 152.6, 184.21, 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 105 16.00 P 67 15.00 Mg 1 11.99 O 5823 8.00 N 5263 7.00 C 18081 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 72 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 895 " 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7018 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 50 sheets defined 39.6% alpha, 13.5% beta 27 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 4.00 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 Processing helix chain 'A' and resid 77 through 87 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 154 through 161 removed outlier: 3.540A pdb=" N HIS A 160 " --> pdb=" O THR A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'B' and resid 34 through 51 removed outlier: 3.514A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET B 51 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 87 Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.768A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 Processing helix chain 'B' and resid 256 through 260 removed outlier: 3.989A pdb=" N ASP B 259 " --> pdb=" O PRO B 256 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 260 " --> pdb=" O VAL B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 260' Processing helix chain 'B' and resid 264 through 269 removed outlier: 4.476A pdb=" N ASN B 268 " --> pdb=" O ARG B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 296 through 309 removed outlier: 3.615A pdb=" N LYS B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 327 removed outlier: 3.994A pdb=" N ALA B 327 " --> pdb=" O ALA B 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 30 through 40 removed outlier: 3.737A pdb=" N GLN C 36 " --> pdb=" O LEU C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 57 removed outlier: 3.551A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.621A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.585A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.663A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 354 removed outlier: 3.707A pdb=" N GLU C 349 " --> pdb=" O PRO C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 377 through 389 removed outlier: 4.150A 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 437 removed outlier: 3.512A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 481 removed outlier: 4.036A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.674A 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 Processing helix chain 'C' and resid 607 through 612 removed outlier: 3.592A pdb=" N GLU C 611 " --> pdb=" O SER C 607 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY C 612 " --> pdb=" O ALA C 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 607 through 612' Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 657 through 661 removed outlier: 4.418A pdb=" N VAL C 660 " --> pdb=" O THR C 657 " (cutoff:3.500A) 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 688 removed outlier: 4.183A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 removed outlier: 3.679A pdb=" N GLU C 825 " --> pdb=" O ARG C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 860 through 864 removed outlier: 3.935A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 907 removed outlier: 4.333A pdb=" N ARG C 903 " --> pdb=" O GLU C 899 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA C 904 " --> pdb=" O LYS C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 981 Processing helix chain 'C' and resid 993 through 999 Processing helix chain 'C' and resid 1005 through 1038 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.326A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.577A pdb=" N ILE C1124 " --> pdb=" O ALA C1120 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.582A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C1144 " --> pdb=" O LYS C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 Processing helix chain 'C' and resid 1166 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.563A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) Processing helix chain 'C' and resid 1262 through 1266 removed outlier: 3.667A pdb=" N PHE C1265 " --> pdb=" O LYS C1262 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1281 removed outlier: 3.643A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1293 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.512A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1333 removed outlier: 3.588A pdb=" N LEU C1333 " --> pdb=" O GLU C1329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.543A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.760A pdb=" N LEU D 117 " --> pdb=" O HIS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 140 removed outlier: 4.161A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 173 through 176 Processing helix chain 'D' and resid 180 through 192 removed outlier: 3.738A pdb=" N ALA D 184 " --> pdb=" O MET D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 208 removed outlier: 4.141A pdb=" N GLU D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.988A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 256 through 258 No H-bonds generated for 'chain 'D' and resid 256 through 258' Processing helix chain 'D' and resid 263 through 286 removed outlier: 4.064A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.545A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.683A pdb=" N ILE D 331 " --> pdb=" O LEU D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 407 through 417 removed outlier: 3.795A pdb=" N ILE D 411 " --> pdb=" O VAL D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.581A pdb=" N CYS D 454 " --> pdb=" O HIS D 450 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.644A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 540 removed outlier: 3.892A pdb=" N ALA D 533 " --> pdb=" O GLY D 529 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.624A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.554A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 640 through 644 removed outlier: 3.561A pdb=" N MET D 644 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 removed outlier: 3.586A pdb=" N VAL D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.509A pdb=" N TYR D 772 " --> pdb=" O ASN D 768 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 794 " --> pdb=" O THR D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.914A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 876 Processing helix chain 'D' and resid 884 through 888 Processing helix chain 'D' and resid 895 through 900 Processing helix chain 'D' and resid 915 through 925 Processing helix chain 'D' and resid 926 through 929 Processing helix chain 'D' and resid 1138 through 1147 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1243 removed outlier: 3.531A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1260 removed outlier: 3.866A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET D1260 " --> pdb=" O ILE D1256 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1293 Processing helix chain 'D' and resid 1308 through 1315 Processing helix chain 'D' and resid 1318 through 1326 removed outlier: 3.507A pdb=" N ALA D1322 " --> pdb=" O SER D1318 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE D1325 " --> pdb=" O SER D1321 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN D1326 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.608A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1354 Processing helix chain 'D' and resid 1361 through 1373 removed outlier: 3.855A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG D1373 " --> pdb=" O ARG D1369 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 15 through 32 Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.663A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 90 removed outlier: 3.829A pdb=" N ARG E 90 " --> pdb=" O ILE E 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 21 through 39 removed outlier: 3.639A pdb=" N LEU F 27 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLU F 28 " --> pdb=" O PHE F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 74 removed outlier: 3.818A pdb=" N GLU F 74 " --> pdb=" O PRO F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 84 removed outlier: 5.884A pdb=" N ARG F 81 " --> pdb=" O GLU F 78 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP F 84 " --> pdb=" O ARG F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 131 removed outlier: 4.488A pdb=" N VAL F 115 " --> pdb=" O LYS F 111 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN F 116 " --> pdb=" O GLN F 112 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ARG F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 206 Processing helix chain 'F' and resid 207 through 211 Processing helix chain 'F' and resid 247 through 253 Processing helix chain 'F' and resid 281 through 287 Processing helix chain 'F' and resid 314 through 319 removed outlier: 4.015A pdb=" N ILE F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 333 removed outlier: 3.508A pdb=" N SER F 329 " --> pdb=" O VAL F 325 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER F 332 " --> pdb=" O ALA F 328 " (cutoff:3.500A) Processing helix chain 'F' and resid 348 through 353 removed outlier: 4.069A pdb=" N ALA F 352 " --> pdb=" O GLN F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 363 Processing helix chain 'F' and resid 391 through 395 removed outlier: 4.459A pdb=" N GLU F 394 " --> pdb=" O GLU F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 402 through 406 removed outlier: 3.576A pdb=" N ALA F 405 " --> pdb=" O THR F 402 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU F 406 " --> pdb=" O VAL F 403 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 402 through 406' Processing helix chain 'F' and resid 408 through 417 removed outlier: 3.821A pdb=" N ASN F 412 " --> pdb=" O GLU F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 441 through 447 Processing helix chain 'F' and resid 448 through 452 removed outlier: 4.037A pdb=" N ARG F 451 " --> pdb=" O LEU F 448 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLY F 452 " --> pdb=" O ALA F 449 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 448 through 452' Processing helix chain 'F' and resid 455 through 460 removed outlier: 3.549A pdb=" N LEU F 459 " --> pdb=" O THR F 455 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA F 460 " --> pdb=" O LEU F 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 455 through 460' Processing helix chain 'F' and resid 475 through 480 removed outlier: 4.377A pdb=" N ALA F 480 " --> pdb=" O GLU F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 482 through 487 Processing helix chain 'F' and resid 487 through 492 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 15 removed outlier: 7.286A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 104 removed outlier: 7.142A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 104 removed outlier: 3.918A pdb=" N VAL A 153 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.745A pdb=" N GLY A 108 " --> pdb=" O HIS A 132 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N HIS A 132 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 110 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 15 through 18 removed outlier: 3.691A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 52 through 58 removed outlier: 7.228A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.079A pdb=" N GLY B 108 " --> pdb=" O HIS B 132 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS B 132 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.522A pdb=" N ALA B 175 " --> pdb=" O VAL B 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 75 removed outlier: 5.144A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU C 102 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLU C 119 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE C 104 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N ILE C 117 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 453 Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 159 removed outlier: 3.917A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 180 through 181 Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 239 removed outlier: 4.190A pdb=" N GLN C 238 " --> pdb=" O GLU C 231 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU C 231 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 335 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE C 333 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 250 through 251 removed outlier: 4.032A pdb=" N ARG C 267 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 6.787A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.976A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC2, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC3, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.918A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 748 through 752 removed outlier: 3.500A pdb=" N TYR C 726 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS C 735 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VAL C 724 " --> pdb=" O LYS C 735 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC7, first strand: chain 'C' and resid 1065 through 1066 removed outlier: 7.746A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 846 through 847 removed outlier: 6.051A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N LYS C1057 " --> pdb=" O GLY C 926 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N GLY C 926 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.852A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.602A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.602A pdb=" N SER D 350 " --> pdb=" O ARG C1246 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD6, first strand: chain 'D' and resid 103 through 112 removed outlier: 4.223A pdb=" N GLY D 103 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 11.258A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.583A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 144 through 145 Processing sheet with id=AD8, first strand: chain 'D' and resid 252 through 254 removed outlier: 3.508A pdb=" N ALA D 261 " --> pdb=" O VAL D 253 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 547 through 549 Processing sheet with id=AE1, first strand: chain 'D' and resid 553 through 556 Processing sheet with id=AE2, first strand: chain 'D' and resid 706 through 709 Processing sheet with id=AE3, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 961 removed outlier: 4.159A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE6, first strand: chain 'D' and resid 1025 through 1028 removed outlier: 6.419A pdb=" N MET D1025 " --> pdb=" O ARG D1123 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ARG D1123 " --> pdb=" O MET D1025 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL D1027 " --> pdb=" O LEU D1121 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1098 through 1100 removed outlier: 3.615A pdb=" N THR D1038 " --> pdb=" O ALA D1077 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1046 through 1049 Processing sheet with id=AE9, first strand: chain 'D' and resid 1186 through 1190 removed outlier: 3.997A pdb=" N TYR D1186 " --> pdb=" O ILE D1177 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL D1176 " --> pdb=" O PHE D1165 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N PHE D1165 " --> pdb=" O VAL D1176 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N THR D1178 " --> pdb=" O VAL D1163 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL D1163 " --> pdb=" O THR D1178 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1278 through 1279 removed outlier: 5.364A pdb=" N ILE D1266 " --> pdb=" O SER D1303 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N SER D1303 " --> pdb=" O ILE D1266 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN D1268 " --> pdb=" O THR D1301 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 60 through 61 Processing sheet with id=AF3, first strand: chain 'F' and resid 138 through 141 Processing sheet with id=AF4, first strand: chain 'F' and resid 150 through 152 removed outlier: 6.450A pdb=" N GLU F 159 " --> pdb=" O LEU F 195 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 296 through 299 removed outlier: 3.749A pdb=" N ASP F 299 " --> pdb=" O THR F 304 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR F 304 " --> pdb=" O ASP F 299 " (cutoff:3.500A) 1109 hydrogen bonds defined for protein. 3039 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 126 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 7.94 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6728 1.33 - 1.45: 6018 1.45 - 1.57: 16809 1.57 - 1.70: 131 1.70 - 1.82: 182 Bond restraints: 29868 Sorted by residual: bond pdb=" C1' DC T 20 " pdb=" N1 DC T 20 " ideal model delta sigma weight residual 1.468 1.527 -0.059 1.40e-02 5.10e+03 1.78e+01 bond pdb=" C3' DC N 35 " pdb=" C2' DC N 35 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.24e+01 bond pdb=" C3' DC T 20 " pdb=" O3' DC T 20 " ideal model delta sigma weight residual 1.435 1.396 0.039 1.30e-02 5.92e+03 8.85e+00 bond pdb=" C3' DC T 3 " pdb=" O3' DC T 3 " ideal model delta sigma weight residual 1.435 1.473 -0.038 1.30e-02 5.92e+03 8.64e+00 bond pdb=" N1 DC T 11 " pdb=" C6 DC T 11 " ideal model delta sigma weight residual 1.367 1.350 0.017 6.00e-03 2.78e+04 7.88e+00 ... (remaining 29863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 40081 2.54 - 5.09: 601 5.09 - 7.63: 46 7.63 - 10.18: 18 10.18 - 12.72: 2 Bond angle restraints: 40748 Sorted by residual: angle pdb=" O4' DT T 10 " pdb=" C1' DT T 10 " pdb=" N1 DT T 10 " ideal model delta sigma weight residual 108.00 112.61 -4.61 7.00e-01 2.04e+00 4.34e+01 angle pdb=" N ILE D1210 " pdb=" CA ILE D1210 " pdb=" C ILE D1210 " ideal model delta sigma weight residual 112.12 107.32 4.80 8.40e-01 1.42e+00 3.27e+01 angle pdb=" O4' DG T 21 " pdb=" C4' DG T 21 " pdb=" C3' DG T 21 " ideal model delta sigma weight residual 106.00 102.59 3.41 6.00e-01 2.78e+00 3.24e+01 angle pdb=" O4' DT T 8 " pdb=" C1' DT T 8 " pdb=" N1 DT T 8 " ideal model delta sigma weight residual 108.00 111.55 -3.55 7.00e-01 2.04e+00 2.57e+01 angle pdb=" C ALA F 11 " pdb=" N VAL F 12 " pdb=" CA VAL F 12 " ideal model delta sigma weight residual 121.70 130.32 -8.62 1.80e+00 3.09e-01 2.29e+01 ... (remaining 40743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.55: 17300 29.55 - 59.10: 748 59.10 - 88.65: 52 88.65 - 118.21: 3 118.21 - 147.76: 5 Dihedral angle restraints: 18108 sinusoidal: 7228 harmonic: 10880 Sorted by residual: dihedral pdb=" CA GLY D 318 " pdb=" C GLY D 318 " pdb=" N SER D 319 " pdb=" CA SER D 319 " ideal model delta harmonic sigma weight residual 180.00 151.81 28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA ARG B 191 " pdb=" C ARG B 191 " pdb=" N VAL B 192 " pdb=" CA VAL B 192 " ideal model delta harmonic sigma weight residual 180.00 154.43 25.57 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLU B 319 " pdb=" C GLU B 319 " pdb=" N ASN B 320 " pdb=" CA ASN B 320 " ideal model delta harmonic sigma weight residual 180.00 154.95 25.05 0 5.00e+00 4.00e-02 2.51e+01 ... (remaining 18105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 3294 0.045 - 0.090: 1070 0.090 - 0.135: 348 0.135 - 0.180: 35 0.180 - 0.226: 5 Chirality restraints: 4752 Sorted by residual: chirality pdb=" CB ILE A 16 " pdb=" CA ILE A 16 " pdb=" CG1 ILE A 16 " pdb=" CG2 ILE A 16 " both_signs ideal model delta sigma weight residual False 2.64 2.87 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB THR D 48 " pdb=" CA THR D 48 " pdb=" OG1 THR D 48 " pdb=" CG2 THR D 48 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA GLU D1146 " pdb=" N GLU D1146 " pdb=" C GLU D1146 " pdb=" CB GLU D1146 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.68e-01 ... (remaining 4749 not shown) Planarity restraints: 5163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 686 " -0.021 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP D 686 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP D 686 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 686 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 686 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 686 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 686 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 686 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 686 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP D 686 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 563 " -0.041 5.00e-02 4.00e+02 6.25e-02 6.24e+00 pdb=" N PRO C 564 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 564 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 564 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C1184 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO C1185 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C1185 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C1185 " 0.034 5.00e-02 4.00e+02 ... (remaining 5160 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 12 2.19 - 2.87: 10739 2.87 - 3.54: 44486 3.54 - 4.22: 67574 4.22 - 4.90: 109903 Nonbonded interactions: 232714 Sorted by model distance: nonbonded pdb=" NH2 ARG D 883 " pdb=" SG CYS D 898 " model vdw 1.512 3.480 nonbonded pdb=" N CYS D 72 " pdb="ZN ZN D1502 " model vdw 2.027 2.310 nonbonded pdb=" N2 DG N 37 " pdb=" O2 DC T 3 " model vdw 2.086 2.496 nonbonded pdb=" OG1 THR D1169 " pdb=" O LYS D1172 " model vdw 2.136 3.040 nonbonded pdb=" NH2 ARG D 883 " pdb="ZN ZN D1503 " model vdw 2.140 2.310 ... (remaining 232709 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 35.340 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.417 29873 Z= 0.257 Angle : 0.783 12.723 40748 Z= 0.466 Chirality : 0.048 0.226 4752 Planarity : 0.005 0.062 5163 Dihedral : 15.432 147.756 11090 Min Nonbonded Distance : 1.512 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.04 % Allowed : 0.33 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.13), residues: 3767 helix: -0.30 (0.14), residues: 1255 sheet: -1.23 (0.25), residues: 423 loop : -1.71 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 191 TYR 0.023 0.001 TYR A 68 PHE 0.026 0.002 PHE C 186 TRP 0.056 0.004 TRP D 686 HIS 0.009 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.24 (29868) covalent geometry : angle 0.78274 / 0.47 (40748) hydrogen bonds : bond 0.21074 / 14.18 ( 1167) hydrogen bonds : angle 7.49770 / 5.24 ( 3165) metal coordination : bond 0.19209 / 14.42 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9438 (pmm) cc_final: 0.9054 (pmm) REVERT: A 177 TYR cc_start: 0.7630 (m-10) cc_final: 0.7295 (m-10) REVERT: B 214 GLU cc_start: 0.8687 (tt0) cc_final: 0.7825 (tp30) REVERT: C 403 MET cc_start: 0.9407 (tmm) cc_final: 0.9105 (tmm) REVERT: C 459 MET cc_start: 0.9555 (mmp) cc_final: 0.9320 (mmp) REVERT: C 515 MET cc_start: 0.7658 (ptm) cc_final: 0.7263 (ptp) REVERT: C 549 ASP cc_start: 0.9360 (t0) cc_final: 0.9048 (t0) REVERT: C 653 MET cc_start: 0.8806 (tpt) cc_final: 0.8540 (tpt) REVERT: C 681 MET cc_start: 0.9429 (mmp) cc_final: 0.9213 (mmp) REVERT: C 704 MET cc_start: 0.9453 (mmp) cc_final: 0.9230 (mmp) REVERT: C 764 CYS cc_start: 0.9461 (t) cc_final: 0.9252 (t) REVERT: C 805 MET cc_start: 0.8763 (ppp) cc_final: 0.8285 (ppp) REVERT: C 865 LEU cc_start: 0.9304 (mt) cc_final: 0.8966 (mt) REVERT: C 883 LEU cc_start: 0.8884 (mp) cc_final: 0.8636 (mp) REVERT: C 951 MET cc_start: 0.9233 (mmp) cc_final: 0.8966 (mmm) REVERT: C 1066 MET cc_start: 0.8857 (tpp) cc_final: 0.8571 (tpp) REVERT: C 1108 ASN cc_start: 0.9442 (m-40) cc_final: 0.8900 (t0) REVERT: C 1114 GLU cc_start: 0.9553 (tm-30) cc_final: 0.9233 (tm-30) REVERT: C 1232 MET cc_start: 0.9153 (mmm) cc_final: 0.8896 (mmm) REVERT: C 1273 MET cc_start: 0.9313 (mmp) cc_final: 0.8481 (mmm) REVERT: D 29 MET cc_start: 0.9374 (tmm) cc_final: 0.9134 (ppp) REVERT: D 245 LEU cc_start: 0.9337 (tp) cc_final: 0.9089 (tp) REVERT: D 265 LEU cc_start: 0.9856 (mp) cc_final: 0.9590 (pp) REVERT: D 329 ASP cc_start: 0.8980 (m-30) cc_final: 0.8714 (m-30) REVERT: D 330 MET cc_start: 0.9336 (tpt) cc_final: 0.8735 (tpp) REVERT: D 355 ILE cc_start: 0.9660 (tp) cc_final: 0.9458 (tp) REVERT: D 454 CYS cc_start: 0.9330 (m) cc_final: 0.9105 (m) REVERT: D 484 MET cc_start: 0.8725 (mpp) cc_final: 0.8466 (mpp) REVERT: D 485 MET cc_start: 0.9007 (mmp) cc_final: 0.7962 (mmm) REVERT: D 544 LEU cc_start: 0.8813 (tt) cc_final: 0.8410 (tp) REVERT: D 644 MET cc_start: 0.9394 (mpp) cc_final: 0.9078 (mpp) REVERT: D 698 MET cc_start: 0.9183 (tmm) cc_final: 0.8726 (tmm) REVERT: D 720 ASN cc_start: 0.9296 (t0) cc_final: 0.9034 (t0) REVERT: D 725 MET cc_start: 0.9524 (tpp) cc_final: 0.8775 (tpt) REVERT: D 982 LEU cc_start: 0.9742 (tp) cc_final: 0.9398 (pt) REVERT: D 1143 ASP cc_start: 0.9236 (p0) cc_final: 0.8918 (t0) REVERT: D 1186 TYR cc_start: 0.9038 (m-10) cc_final: 0.8696 (m-10) REVERT: E 18 ASP cc_start: 0.9473 (m-30) cc_final: 0.9225 (t70) REVERT: E 26 ARG cc_start: 0.9579 (tpm170) cc_final: 0.8993 (tpm170) REVERT: E 56 GLU cc_start: 0.9327 (mm-30) cc_final: 0.8973 (tm-30) outliers start: 1 outliers final: 0 residues processed: 248 average time/residue: 0.1723 time to fit residues: 73.7435 Evaluate side-chains 184 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.0370 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 8.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 604 HIS C 659 GLN C1237 HIS ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.056217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.036684 restraints weight = 195486.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.037977 restraints weight = 107981.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.038851 restraints weight = 71809.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.039491 restraints weight = 53446.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.039892 restraints weight = 43169.514| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.0847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29873 Z= 0.134 Angle : 0.632 9.662 40748 Z= 0.339 Chirality : 0.045 0.313 4752 Planarity : 0.005 0.060 5163 Dihedral : 14.323 150.834 4813 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.04 % Allowed : 5.13 % Favored : 94.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.13), residues: 3767 helix: -0.08 (0.14), residues: 1317 sheet: -1.23 (0.24), residues: 457 loop : -1.65 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 26 TYR 0.015 0.001 TYR D 165 PHE 0.017 0.001 PHE C1270 TRP 0.028 0.002 TRP D 686 HIS 0.005 0.001 HIS D 897 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (29868) covalent geometry : angle 0.63207 / 0.34 (40748) hydrogen bonds : bond 0.05807 / 4.06 ( 1167) hydrogen bonds : angle 5.80456 / 4.05 ( 3165) metal coordination : bond 0.02741 / 1.25 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9326 (pmm) cc_final: 0.8856 (pmm) REVERT: A 205 MET cc_start: 0.8485 (pmm) cc_final: 0.8252 (pmm) REVERT: B 205 MET cc_start: 0.8321 (tmm) cc_final: 0.8115 (tmm) REVERT: C 85 CYS cc_start: 0.9419 (m) cc_final: 0.9173 (m) REVERT: C 403 MET cc_start: 0.9318 (tmm) cc_final: 0.9007 (tmm) REVERT: C 459 MET cc_start: 0.9545 (mmp) cc_final: 0.9309 (mmm) REVERT: C 515 MET cc_start: 0.7796 (ptm) cc_final: 0.7263 (ptp) REVERT: C 549 ASP cc_start: 0.9320 (t0) cc_final: 0.8955 (t0) REVERT: C 653 MET cc_start: 0.8598 (tpt) cc_final: 0.8214 (tpt) REVERT: C 668 ILE cc_start: 0.9714 (mt) cc_final: 0.9513 (mm) REVERT: C 704 MET cc_start: 0.9474 (mmp) cc_final: 0.9226 (mmp) REVERT: C 805 MET cc_start: 0.8785 (ppp) cc_final: 0.8302 (ppp) REVERT: C 865 LEU cc_start: 0.9332 (mt) cc_final: 0.9084 (mt) REVERT: C 951 MET cc_start: 0.9264 (mmp) cc_final: 0.9014 (mmm) REVERT: C 1114 GLU cc_start: 0.9511 (tm-30) cc_final: 0.9151 (tm-30) REVERT: D 120 LEU cc_start: 0.9531 (mt) cc_final: 0.9135 (tp) REVERT: D 130 MET cc_start: 0.7564 (ppp) cc_final: 0.7251 (ppp) REVERT: D 180 MET cc_start: 0.7924 (ppp) cc_final: 0.7413 (ppp) REVERT: D 265 LEU cc_start: 0.9845 (mp) cc_final: 0.9609 (pp) REVERT: D 329 ASP cc_start: 0.9036 (m-30) cc_final: 0.8769 (m-30) REVERT: D 330 MET cc_start: 0.9272 (tpt) cc_final: 0.9031 (tpp) REVERT: D 355 ILE cc_start: 0.9631 (tp) cc_final: 0.9428 (tp) REVERT: D 454 CYS cc_start: 0.9267 (m) cc_final: 0.9030 (m) REVERT: D 485 MET cc_start: 0.9054 (mmp) cc_final: 0.8057 (mmm) REVERT: D 513 MET cc_start: 0.9260 (mmt) cc_final: 0.8930 (mmm) REVERT: D 544 LEU cc_start: 0.8878 (tt) cc_final: 0.8451 (tp) REVERT: D 644 MET cc_start: 0.9353 (mpp) cc_final: 0.9012 (mpp) REVERT: D 698 MET cc_start: 0.9047 (tmm) cc_final: 0.8815 (tmm) REVERT: D 720 ASN cc_start: 0.9297 (t0) cc_final: 0.8832 (t0) REVERT: D 725 MET cc_start: 0.9434 (tpp) cc_final: 0.8747 (tpt) REVERT: D 743 MET cc_start: 0.7536 (tpt) cc_final: 0.7198 (tpp) REVERT: D 1040 MET cc_start: 0.8430 (ptp) cc_final: 0.8106 (mpp) REVERT: D 1143 ASP cc_start: 0.9183 (p0) cc_final: 0.8939 (t0) REVERT: D 1186 TYR cc_start: 0.8924 (m-10) cc_final: 0.8599 (m-10) REVERT: E 26 ARG cc_start: 0.9455 (tpm170) cc_final: 0.9215 (tpm170) REVERT: E 56 GLU cc_start: 0.9288 (mm-30) cc_final: 0.9012 (tp30) outliers start: 1 outliers final: 0 residues processed: 242 average time/residue: 0.1700 time to fit residues: 70.4595 Evaluate side-chains 191 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 83 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 196 optimal weight: 10.0000 chunk 53 optimal weight: 0.0870 chunk 301 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 232 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 1 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 overall best weight: 4.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN D 792 ASN ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** 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 = 0.3361 r_free = 0.3361 target = 0.054957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.034823 restraints weight = 203910.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.036032 restraints weight = 114186.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.036848 restraints weight = 76544.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.037391 restraints weight = 57831.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.037806 restraints weight = 47489.563| |-----------------------------------------------------------------------------| r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 29873 Z= 0.219 Angle : 0.645 8.446 40748 Z= 0.347 Chirality : 0.045 0.299 4752 Planarity : 0.005 0.055 5163 Dihedral : 14.267 151.832 4813 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 0.11 % Allowed : 5.02 % Favored : 94.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.13), residues: 3767 helix: 0.05 (0.14), residues: 1325 sheet: -1.20 (0.24), residues: 441 loop : -1.66 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 47 TYR 0.022 0.001 TYR C1285 PHE 0.023 0.002 PHE C1270 TRP 0.021 0.002 TRP D 686 HIS 0.007 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.22 (29868) covalent geometry : angle 0.64485 / 0.35 (40748) hydrogen bonds : bond 0.05327 / 3.71 ( 1167) hydrogen bonds : angle 5.60261 / 3.90 ( 3165) metal coordination : bond 0.00312 / 0.20 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 232 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9255 (pmm) cc_final: 0.8706 (pmm) REVERT: A 177 TYR cc_start: 0.6917 (m-10) cc_final: 0.6671 (m-10) REVERT: A 203 ILE cc_start: 0.9641 (pt) cc_final: 0.9434 (pt) REVERT: C 85 CYS cc_start: 0.9508 (m) cc_final: 0.9303 (m) REVERT: C 403 MET cc_start: 0.9352 (tmm) cc_final: 0.9067 (tmm) REVERT: C 459 MET cc_start: 0.9557 (mmp) cc_final: 0.9332 (mmm) REVERT: C 515 MET cc_start: 0.7935 (ptm) cc_final: 0.7516 (ptp) REVERT: C 516 ASP cc_start: 0.7730 (p0) cc_final: 0.7396 (p0) REVERT: C 549 ASP cc_start: 0.9359 (t0) cc_final: 0.8966 (t0) REVERT: C 653 MET cc_start: 0.8665 (tpt) cc_final: 0.8278 (tpt) REVERT: C 704 MET cc_start: 0.9501 (mmp) cc_final: 0.9280 (mmp) REVERT: C 794 LEU cc_start: 0.9615 (tt) cc_final: 0.9164 (pp) REVERT: C 799 ASN cc_start: 0.9275 (p0) cc_final: 0.9041 (p0) REVERT: C 805 MET cc_start: 0.8815 (ppp) cc_final: 0.8368 (ppp) REVERT: C 865 LEU cc_start: 0.9337 (mt) cc_final: 0.9050 (mt) REVERT: C 951 MET cc_start: 0.9226 (mmp) cc_final: 0.8949 (mmm) REVERT: C 1107 MET cc_start: 0.9299 (mpp) cc_final: 0.9068 (mpp) REVERT: C 1108 ASN cc_start: 0.9475 (m-40) cc_final: 0.8839 (t0) REVERT: C 1114 GLU cc_start: 0.9461 (tm-30) cc_final: 0.9075 (tm-30) REVERT: C 1233 LEU cc_start: 0.9617 (mp) cc_final: 0.9342 (pp) REVERT: D 120 LEU cc_start: 0.9497 (mt) cc_final: 0.9074 (tp) REVERT: D 130 MET cc_start: 0.7716 (ppp) cc_final: 0.7493 (ppp) REVERT: D 180 MET cc_start: 0.8129 (ppp) cc_final: 0.7624 (ppp) REVERT: D 329 ASP cc_start: 0.9076 (m-30) cc_final: 0.8817 (m-30) REVERT: D 330 MET cc_start: 0.9305 (tpt) cc_final: 0.8837 (tpp) REVERT: D 454 CYS cc_start: 0.9286 (m) cc_final: 0.9004 (m) REVERT: D 485 MET cc_start: 0.9119 (mmp) cc_final: 0.8017 (mmm) REVERT: D 644 MET cc_start: 0.9323 (mpp) cc_final: 0.8944 (mpp) REVERT: D 725 MET cc_start: 0.9448 (tpp) cc_final: 0.8583 (tpp) REVERT: D 792 ASN cc_start: 0.9640 (OUTLIER) cc_final: 0.9217 (t0) REVERT: D 1143 ASP cc_start: 0.9192 (p0) cc_final: 0.8877 (t0) REVERT: D 1186 TYR cc_start: 0.8964 (m-10) cc_final: 0.8644 (m-10) REVERT: D 1254 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8886 (pt0) REVERT: E 18 ASP cc_start: 0.9498 (m-30) cc_final: 0.9253 (t0) outliers start: 3 outliers final: 0 residues processed: 235 average time/residue: 0.1759 time to fit residues: 70.2795 Evaluate side-chains 185 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 277 optimal weight: 10.0000 chunk 121 optimal weight: 0.0270 chunk 178 optimal weight: 0.9990 chunk 370 optimal weight: 40.0000 chunk 369 optimal weight: 7.9990 chunk 298 optimal weight: 9.9990 chunk 251 optimal weight: 9.9990 chunk 139 optimal weight: 20.0000 chunk 48 optimal weight: 50.0000 chunk 270 optimal weight: 0.9990 chunk 376 optimal weight: 40.0000 overall best weight: 4.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN D 232 ASN ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 29 GLN ** 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 = 0.3367 r_free = 0.3367 target = 0.055119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.035168 restraints weight = 201688.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.036384 restraints weight = 112068.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.037225 restraints weight = 74985.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.037819 restraints weight = 56456.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.038184 restraints weight = 45897.386| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29873 Z= 0.184 Angle : 0.617 9.125 40748 Z= 0.332 Chirality : 0.044 0.299 4752 Planarity : 0.004 0.052 5163 Dihedral : 14.230 153.181 4813 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.13), residues: 3767 helix: 0.17 (0.14), residues: 1319 sheet: -1.20 (0.24), residues: 438 loop : -1.63 (0.14), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 842 TYR 0.014 0.001 TYR D 631 PHE 0.015 0.001 PHE D 461 TRP 0.020 0.001 TRP D 686 HIS 0.006 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (29868) covalent geometry : angle 0.61650 / 0.33 (40748) hydrogen bonds : bond 0.04896 / 3.42 ( 1167) hydrogen bonds : angle 5.42429 / 3.77 ( 3165) metal coordination : bond 0.00235 / 0.13 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 224 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9292 (pmm) cc_final: 0.8690 (pmm) REVERT: A 177 TYR cc_start: 0.6970 (m-10) cc_final: 0.6625 (m-10) REVERT: A 203 ILE cc_start: 0.9625 (pt) cc_final: 0.9419 (pt) REVERT: C 85 CYS cc_start: 0.9440 (m) cc_final: 0.9219 (m) REVERT: C 403 MET cc_start: 0.9349 (tmm) cc_final: 0.9059 (tmm) REVERT: C 459 MET cc_start: 0.9560 (mmp) cc_final: 0.9327 (mmm) REVERT: C 515 MET cc_start: 0.7863 (ptm) cc_final: 0.7414 (ptp) REVERT: C 516 ASP cc_start: 0.7689 (p0) cc_final: 0.7351 (p0) REVERT: C 549 ASP cc_start: 0.9349 (t0) cc_final: 0.8956 (t0) REVERT: C 653 MET cc_start: 0.8701 (tpt) cc_final: 0.8394 (tpt) REVERT: C 704 MET cc_start: 0.9486 (mmp) cc_final: 0.9266 (mmp) REVERT: C 805 MET cc_start: 0.8845 (ppp) cc_final: 0.8377 (ppp) REVERT: C 951 MET cc_start: 0.9246 (mmp) cc_final: 0.8968 (mmm) REVERT: C 1107 MET cc_start: 0.9307 (mpp) cc_final: 0.9069 (mpp) REVERT: C 1108 ASN cc_start: 0.9450 (m-40) cc_final: 0.8813 (t0) REVERT: C 1114 GLU cc_start: 0.9458 (tm-30) cc_final: 0.9080 (tm-30) REVERT: C 1233 LEU cc_start: 0.9588 (mp) cc_final: 0.9320 (pp) REVERT: C 1329 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8757 (mt-10) REVERT: D 56 LEU cc_start: 0.9321 (tp) cc_final: 0.8952 (tt) REVERT: D 120 LEU cc_start: 0.9522 (mt) cc_final: 0.9067 (tp) REVERT: D 180 MET cc_start: 0.8175 (ppp) cc_final: 0.7596 (ppp) REVERT: D 232 ASN cc_start: 0.9295 (OUTLIER) cc_final: 0.9077 (m-40) REVERT: D 329 ASP cc_start: 0.9036 (m-30) cc_final: 0.8782 (m-30) REVERT: D 330 MET cc_start: 0.9331 (tpt) cc_final: 0.8814 (tpp) REVERT: D 355 ILE cc_start: 0.9638 (tp) cc_final: 0.9424 (tp) REVERT: D 454 CYS cc_start: 0.9225 (m) cc_final: 0.8931 (m) REVERT: D 485 MET cc_start: 0.9120 (mmp) cc_final: 0.8114 (mmm) REVERT: D 644 MET cc_start: 0.9320 (mpp) cc_final: 0.8905 (mpp) REVERT: D 725 MET cc_start: 0.9424 (tpp) cc_final: 0.8619 (tpp) REVERT: D 743 MET cc_start: 0.8049 (tpt) cc_final: 0.7779 (tpp) REVERT: D 1040 MET cc_start: 0.8524 (ptp) cc_final: 0.8196 (mpp) REVERT: D 1143 ASP cc_start: 0.9185 (p0) cc_final: 0.8956 (t0) REVERT: D 1186 TYR cc_start: 0.8957 (m-10) cc_final: 0.8621 (m-10) REVERT: E 18 ASP cc_start: 0.9486 (m-30) cc_final: 0.9227 (t0) REVERT: E 30 MET cc_start: 0.9181 (mmp) cc_final: 0.8639 (mmm) outliers start: 3 outliers final: 0 residues processed: 227 average time/residue: 0.1732 time to fit residues: 66.8971 Evaluate side-chains 182 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 305 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 179 optimal weight: 7.9990 chunk 345 optimal weight: 50.0000 chunk 205 optimal weight: 6.9990 chunk 332 optimal weight: 50.0000 chunk 254 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** D 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 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 = 0.3353 r_free = 0.3353 target = 0.054475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.034579 restraints weight = 205737.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.035762 restraints weight = 114867.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.036600 restraints weight = 77209.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.037151 restraints weight = 58327.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.037542 restraints weight = 47839.346| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29873 Z= 0.224 Angle : 0.646 8.830 40748 Z= 0.346 Chirality : 0.045 0.291 4752 Planarity : 0.005 0.063 5163 Dihedral : 14.234 153.545 4813 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.13), residues: 3767 helix: 0.18 (0.14), residues: 1314 sheet: -1.40 (0.24), residues: 446 loop : -1.64 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 191 TYR 0.018 0.001 TYR D 631 PHE 0.024 0.002 PHE C 186 TRP 0.018 0.002 TRP D 686 HIS 0.006 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.22 (29868) covalent geometry : angle 0.64603 / 0.35 (40748) hydrogen bonds : bond 0.04904 / 3.44 ( 1167) hydrogen bonds : angle 5.39496 / 3.74 ( 3165) metal coordination : bond 0.00279 / 0.14 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9280 (pmm) cc_final: 0.8616 (pmm) REVERT: A 145 LYS cc_start: 0.9486 (tmtt) cc_final: 0.9042 (tptt) REVERT: A 177 TYR cc_start: 0.7151 (m-10) cc_final: 0.6746 (m-10) REVERT: A 203 ILE cc_start: 0.9645 (pt) cc_final: 0.9439 (pt) REVERT: C 85 CYS cc_start: 0.9447 (m) cc_final: 0.9231 (m) REVERT: C 403 MET cc_start: 0.9362 (tmm) cc_final: 0.9062 (tmm) REVERT: C 459 MET cc_start: 0.9561 (mmp) cc_final: 0.9329 (mmm) REVERT: C 515 MET cc_start: 0.7954 (ptm) cc_final: 0.7517 (ptp) REVERT: C 516 ASP cc_start: 0.7896 (p0) cc_final: 0.7520 (p0) REVERT: C 549 ASP cc_start: 0.9377 (t0) cc_final: 0.8967 (t0) REVERT: C 653 MET cc_start: 0.8782 (tpt) cc_final: 0.8374 (tpt) REVERT: C 704 MET cc_start: 0.9460 (mmp) cc_final: 0.9236 (mmp) REVERT: C 805 MET cc_start: 0.8838 (ppp) cc_final: 0.8357 (ppp) REVERT: C 951 MET cc_start: 0.9253 (mmp) cc_final: 0.9000 (mmm) REVERT: C 1107 MET cc_start: 0.9297 (mpp) cc_final: 0.9054 (mpp) REVERT: C 1108 ASN cc_start: 0.9476 (m-40) cc_final: 0.8816 (t0) REVERT: C 1114 GLU cc_start: 0.9454 (tm-30) cc_final: 0.9066 (tm-30) REVERT: C 1232 MET cc_start: 0.9266 (mmm) cc_final: 0.9049 (mmm) REVERT: C 1233 LEU cc_start: 0.9594 (mp) cc_final: 0.9326 (pp) REVERT: C 1274 GLU cc_start: 0.9199 (pm20) cc_final: 0.8948 (pm20) REVERT: C 1275 VAL cc_start: 0.9613 (t) cc_final: 0.9353 (t) REVERT: C 1329 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8774 (mt-10) REVERT: D 56 LEU cc_start: 0.9294 (tp) cc_final: 0.8904 (tt) REVERT: D 120 LEU cc_start: 0.9546 (mt) cc_final: 0.9085 (tp) REVERT: D 130 MET cc_start: 0.7859 (ppp) cc_final: 0.7570 (ppp) REVERT: D 180 MET cc_start: 0.8236 (ppp) cc_final: 0.7493 (ppp) REVERT: D 192 MET cc_start: 0.9091 (ttp) cc_final: 0.8605 (tmm) REVERT: D 329 ASP cc_start: 0.9039 (m-30) cc_final: 0.8771 (m-30) REVERT: D 330 MET cc_start: 0.9382 (tpt) cc_final: 0.8929 (tpp) REVERT: D 454 CYS cc_start: 0.9198 (m) cc_final: 0.8897 (m) REVERT: D 485 MET cc_start: 0.9147 (mmp) cc_final: 0.8090 (mmm) REVERT: D 644 MET cc_start: 0.9315 (mpp) cc_final: 0.8920 (mpp) REVERT: D 725 MET cc_start: 0.9386 (tpp) cc_final: 0.8533 (tpp) REVERT: D 1143 ASP cc_start: 0.9180 (p0) cc_final: 0.8901 (t0) REVERT: D 1186 TYR cc_start: 0.8963 (m-10) cc_final: 0.8609 (m-10) REVERT: D 1254 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8864 (mt-10) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1710 time to fit residues: 64.8762 Evaluate side-chains 177 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 332 optimal weight: 50.0000 chunk 137 optimal weight: 9.9990 chunk 195 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 174 optimal weight: 0.9980 chunk 227 optimal weight: 9.9990 chunk 184 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 273 optimal weight: 0.6980 chunk 231 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.055664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.035812 restraints weight = 201128.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.037032 restraints weight = 110574.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.037864 restraints weight = 73395.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.038468 restraints weight = 55079.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.038821 restraints weight = 44740.080| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29873 Z= 0.128 Angle : 0.609 9.992 40748 Z= 0.321 Chirality : 0.045 0.296 4752 Planarity : 0.004 0.085 5163 Dihedral : 14.181 153.918 4813 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3767 helix: 0.30 (0.14), residues: 1316 sheet: -1.25 (0.24), residues: 443 loop : -1.60 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 191 TYR 0.013 0.001 TYR D1363 PHE 0.027 0.001 PHE C 186 TRP 0.017 0.001 TRP D 686 HIS 0.004 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.13 (29868) covalent geometry : angle 0.60879 / 0.32 (40748) hydrogen bonds : bond 0.04570 / 3.21 ( 1167) hydrogen bonds : angle 5.16510 / 3.57 ( 3165) metal coordination : bond 0.00181 / 0.09 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9312 (pmm) cc_final: 0.8590 (pmm) REVERT: A 145 LYS cc_start: 0.9493 (tmtt) cc_final: 0.9059 (tptt) REVERT: A 203 ILE cc_start: 0.9639 (pt) cc_final: 0.9433 (pt) REVERT: A 205 MET cc_start: 0.8639 (pmm) cc_final: 0.8428 (pmm) REVERT: C 85 CYS cc_start: 0.9429 (m) cc_final: 0.9204 (m) REVERT: C 403 MET cc_start: 0.9366 (tmm) cc_final: 0.9079 (tmm) REVERT: C 459 MET cc_start: 0.9552 (mmp) cc_final: 0.9315 (mmm) REVERT: C 515 MET cc_start: 0.7807 (ptm) cc_final: 0.7190 (ptp) REVERT: C 516 ASP cc_start: 0.7821 (p0) cc_final: 0.7437 (p0) REVERT: C 527 LYS cc_start: 0.9481 (mttt) cc_final: 0.9232 (mtmm) REVERT: C 549 ASP cc_start: 0.9332 (t0) cc_final: 0.8933 (t0) REVERT: C 653 MET cc_start: 0.8752 (tpt) cc_final: 0.8430 (tpt) REVERT: C 704 MET cc_start: 0.9394 (mmp) cc_final: 0.9180 (mmp) REVERT: C 764 CYS cc_start: 0.9585 (t) cc_final: 0.9355 (t) REVERT: C 805 MET cc_start: 0.8878 (ppp) cc_final: 0.8489 (ppp) REVERT: C 951 MET cc_start: 0.9242 (mmp) cc_final: 0.9000 (mmm) REVERT: C 1107 MET cc_start: 0.9312 (mpp) cc_final: 0.9053 (mpp) REVERT: C 1108 ASN cc_start: 0.9422 (m-40) cc_final: 0.8637 (t0) REVERT: C 1114 GLU cc_start: 0.9418 (tm-30) cc_final: 0.9039 (tm-30) REVERT: C 1232 MET cc_start: 0.9308 (mmm) cc_final: 0.9059 (mmm) REVERT: C 1329 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8669 (mt-10) REVERT: D 56 LEU cc_start: 0.9202 (tp) cc_final: 0.8956 (tp) REVERT: D 120 LEU cc_start: 0.9546 (mt) cc_final: 0.9085 (tp) REVERT: D 180 MET cc_start: 0.8271 (ppp) cc_final: 0.7556 (ppp) REVERT: D 192 MET cc_start: 0.9038 (ttp) cc_final: 0.8569 (tmm) REVERT: D 245 LEU cc_start: 0.9528 (tp) cc_final: 0.9184 (tp) REVERT: D 329 ASP cc_start: 0.9068 (m-30) cc_final: 0.8838 (m-30) REVERT: D 330 MET cc_start: 0.9353 (tpt) cc_final: 0.8861 (tpp) REVERT: D 355 ILE cc_start: 0.9676 (tp) cc_final: 0.9394 (tp) REVERT: D 454 CYS cc_start: 0.9173 (m) cc_final: 0.8970 (m) REVERT: D 478 LEU cc_start: 0.9779 (mm) cc_final: 0.9534 (mt) REVERT: D 485 MET cc_start: 0.9148 (mmp) cc_final: 0.8132 (mmm) REVERT: D 644 MET cc_start: 0.9292 (mpp) cc_final: 0.8870 (mpp) REVERT: D 725 MET cc_start: 0.9375 (tpp) cc_final: 0.8508 (tpp) REVERT: D 743 MET cc_start: 0.8206 (tpt) cc_final: 0.7855 (tpp) REVERT: D 1040 MET cc_start: 0.8515 (ptp) cc_final: 0.8229 (mpp) REVERT: D 1143 ASP cc_start: 0.9108 (p0) cc_final: 0.8802 (t0) REVERT: D 1186 TYR cc_start: 0.8912 (m-10) cc_final: 0.8568 (m-10) REVERT: E 18 ASP cc_start: 0.9485 (m-30) cc_final: 0.9245 (t0) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1713 time to fit residues: 68.5189 Evaluate side-chains 186 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 146 optimal weight: 0.9990 chunk 256 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 291 optimal weight: 8.9990 chunk 348 optimal weight: 40.0000 chunk 45 optimal weight: 40.0000 chunk 340 optimal weight: 50.0000 chunk 86 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 147 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 196 GLN D 771 GLN ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.053600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.034274 restraints weight = 203983.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.035437 restraints weight = 115115.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.036229 restraints weight = 77883.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.036760 restraints weight = 59040.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.037210 restraints weight = 48424.514| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 29873 Z= 0.288 Angle : 0.716 8.194 40748 Z= 0.379 Chirality : 0.046 0.282 4752 Planarity : 0.005 0.067 5163 Dihedral : 14.264 154.023 4813 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 0.04 % Allowed : 3.04 % Favored : 96.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.13), residues: 3767 helix: 0.13 (0.14), residues: 1317 sheet: -1.52 (0.23), residues: 467 loop : -1.69 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 901 TYR 0.047 0.002 TYR C1251 PHE 0.024 0.002 PHE D 461 TRP 0.017 0.002 TRP D 686 HIS 0.009 0.002 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.29 (29868) covalent geometry : angle 0.71556 / 0.38 (40748) hydrogen bonds : bond 0.05052 / 3.54 ( 1167) hydrogen bonds : angle 5.47068 / 3.78 ( 3165) metal coordination : bond 0.00389 / 0.19 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9323 (pmm) cc_final: 0.8629 (pmm) REVERT: A 145 LYS cc_start: 0.9506 (tmtt) cc_final: 0.9083 (tptt) REVERT: A 177 TYR cc_start: 0.6915 (m-10) cc_final: 0.6568 (m-10) REVERT: A 205 MET cc_start: 0.8737 (pmm) cc_final: 0.8522 (pmm) REVERT: C 403 MET cc_start: 0.9390 (tmm) cc_final: 0.9093 (tmm) REVERT: C 459 MET cc_start: 0.9562 (mmp) cc_final: 0.9221 (mmm) REVERT: C 515 MET cc_start: 0.8059 (ptm) cc_final: 0.7501 (ptp) REVERT: C 516 ASP cc_start: 0.7854 (p0) cc_final: 0.7527 (p0) REVERT: C 527 LYS cc_start: 0.9466 (mttt) cc_final: 0.9225 (mttp) REVERT: C 549 ASP cc_start: 0.9387 (t0) cc_final: 0.8978 (t0) REVERT: C 653 MET cc_start: 0.8752 (tpt) cc_final: 0.8294 (tpt) REVERT: C 704 MET cc_start: 0.9459 (mmp) cc_final: 0.9244 (mmp) REVERT: C 805 MET cc_start: 0.8905 (ppp) cc_final: 0.8476 (ppp) REVERT: C 951 MET cc_start: 0.9204 (mmp) cc_final: 0.8991 (mmm) REVERT: C 1107 MET cc_start: 0.9337 (mpp) cc_final: 0.9063 (mpp) REVERT: C 1108 ASN cc_start: 0.9503 (m-40) cc_final: 0.8882 (t0) REVERT: C 1114 GLU cc_start: 0.9408 (tm-30) cc_final: 0.8383 (tm-30) REVERT: C 1230 MET cc_start: 0.8918 (tpt) cc_final: 0.8150 (tpp) REVERT: C 1272 GLU cc_start: 0.8836 (pm20) cc_final: 0.8467 (pm20) REVERT: C 1329 GLU cc_start: 0.9168 (mt-10) cc_final: 0.8776 (mt-10) REVERT: D 56 LEU cc_start: 0.9202 (tp) cc_final: 0.8990 (tp) REVERT: D 120 LEU cc_start: 0.9564 (mt) cc_final: 0.9079 (tp) REVERT: D 180 MET cc_start: 0.8378 (ppp) cc_final: 0.7701 (ppp) REVERT: D 192 MET cc_start: 0.9116 (ttp) cc_final: 0.8608 (tmm) REVERT: D 329 ASP cc_start: 0.9070 (m-30) cc_final: 0.8832 (m-30) REVERT: D 330 MET cc_start: 0.9453 (tpt) cc_final: 0.8944 (tpp) REVERT: D 355 ILE cc_start: 0.9671 (tp) cc_final: 0.9429 (tp) REVERT: D 454 CYS cc_start: 0.9159 (m) cc_final: 0.8878 (m) REVERT: D 485 MET cc_start: 0.9166 (mmp) cc_final: 0.8165 (mmm) REVERT: D 644 MET cc_start: 0.9254 (mpp) cc_final: 0.8837 (mpp) REVERT: D 725 MET cc_start: 0.9422 (tpp) cc_final: 0.8586 (tpp) REVERT: D 743 MET cc_start: 0.8345 (tpt) cc_final: 0.8120 (tpp) REVERT: D 1143 ASP cc_start: 0.9178 (p0) cc_final: 0.8941 (t0) REVERT: D 1186 TYR cc_start: 0.8914 (m-10) cc_final: 0.8571 (m-10) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.1725 time to fit residues: 64.6142 Evaluate side-chains 173 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 350 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 270 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 243 optimal weight: 3.9990 chunk 210 optimal weight: 3.9990 chunk 375 optimal weight: 20.0000 chunk 187 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.054561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.034748 restraints weight = 200068.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.035975 restraints weight = 112371.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.036783 restraints weight = 75499.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.037389 restraints weight = 57001.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.037744 restraints weight = 46458.397| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 29873 Z= 0.169 Angle : 0.635 11.566 40748 Z= 0.335 Chirality : 0.045 0.290 4752 Planarity : 0.004 0.054 5163 Dihedral : 14.226 154.377 4813 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.14), residues: 3767 helix: 0.31 (0.14), residues: 1305 sheet: -1.40 (0.23), residues: 465 loop : -1.62 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 901 TYR 0.015 0.001 TYR D 631 PHE 0.022 0.002 PHE D 227 TRP 0.020 0.002 TRP D 686 HIS 0.006 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (29868) covalent geometry : angle 0.63504 / 0.34 (40748) hydrogen bonds : bond 0.04608 / 3.24 ( 1167) hydrogen bonds : angle 5.23773 / 3.63 ( 3165) metal coordination : bond 0.00214 / 0.11 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9320 (pmm) cc_final: 0.8577 (pmm) REVERT: A 145 LYS cc_start: 0.9518 (tmtt) cc_final: 0.9080 (tptt) REVERT: A 158 ARG cc_start: 0.8741 (mpt90) cc_final: 0.8452 (mpt180) REVERT: A 177 TYR cc_start: 0.7007 (m-10) cc_final: 0.6689 (m-10) REVERT: C 403 MET cc_start: 0.9388 (tmm) cc_final: 0.9104 (tmm) REVERT: C 459 MET cc_start: 0.9578 (mmp) cc_final: 0.9264 (mmp) REVERT: C 516 ASP cc_start: 0.7793 (p0) cc_final: 0.7394 (p0) REVERT: C 527 LYS cc_start: 0.9417 (mttt) cc_final: 0.9188 (mtpp) REVERT: C 549 ASP cc_start: 0.9402 (t0) cc_final: 0.9014 (t0) REVERT: C 653 MET cc_start: 0.8841 (tpt) cc_final: 0.8446 (tpt) REVERT: C 681 MET cc_start: 0.9417 (mmp) cc_final: 0.9195 (mmp) REVERT: C 704 MET cc_start: 0.9435 (mmp) cc_final: 0.9227 (mmp) REVERT: C 805 MET cc_start: 0.8947 (ppp) cc_final: 0.8467 (ppp) REVERT: C 951 MET cc_start: 0.9246 (mmp) cc_final: 0.9026 (mmm) REVERT: C 1107 MET cc_start: 0.9315 (mpp) cc_final: 0.9039 (mpp) REVERT: C 1108 ASN cc_start: 0.9490 (m-40) cc_final: 0.8680 (t0) REVERT: C 1114 GLU cc_start: 0.9390 (tm-30) cc_final: 0.9003 (tm-30) REVERT: C 1272 GLU cc_start: 0.8925 (pm20) cc_final: 0.8442 (pm20) REVERT: C 1274 GLU cc_start: 0.9251 (pm20) cc_final: 0.8871 (pm20) REVERT: C 1329 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8691 (mt-10) REVERT: D 56 LEU cc_start: 0.9198 (tp) cc_final: 0.8986 (tp) REVERT: D 120 LEU cc_start: 0.9580 (mt) cc_final: 0.9067 (tp) REVERT: D 180 MET cc_start: 0.8419 (ppp) cc_final: 0.8073 (ppp) REVERT: D 192 MET cc_start: 0.9083 (ttp) cc_final: 0.8592 (tmm) REVERT: D 245 LEU cc_start: 0.9571 (tp) cc_final: 0.9288 (tp) REVERT: D 329 ASP cc_start: 0.9041 (m-30) cc_final: 0.8817 (m-30) REVERT: D 330 MET cc_start: 0.9355 (tpt) cc_final: 0.8913 (tpt) REVERT: D 355 ILE cc_start: 0.9661 (tp) cc_final: 0.9428 (tp) REVERT: D 485 MET cc_start: 0.9130 (mmp) cc_final: 0.8040 (mmm) REVERT: D 622 ASP cc_start: 0.9101 (t70) cc_final: 0.8886 (t0) REVERT: D 644 MET cc_start: 0.9298 (mpp) cc_final: 0.8867 (mpp) REVERT: D 725 MET cc_start: 0.9439 (tpp) cc_final: 0.8618 (tpp) REVERT: D 743 MET cc_start: 0.8223 (tpt) cc_final: 0.7989 (tpp) REVERT: D 1040 MET cc_start: 0.8517 (ptp) cc_final: 0.8199 (mpp) REVERT: D 1143 ASP cc_start: 0.9161 (p0) cc_final: 0.8853 (t0) REVERT: D 1186 TYR cc_start: 0.8939 (m-10) cc_final: 0.8581 (m-10) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1842 time to fit residues: 70.9231 Evaluate side-chains 177 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 168 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 238 optimal weight: 6.9990 chunk 322 optimal weight: 9.9990 chunk 352 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 320 optimal weight: 9.9990 chunk 359 optimal weight: 1.9990 chunk 187 optimal weight: 9.9990 chunk 219 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 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 = 0.3333 r_free = 0.3333 target = 0.053849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.033805 restraints weight = 205039.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.034955 restraints weight = 115386.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.035739 restraints weight = 78039.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.036306 restraints weight = 59070.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.036712 restraints weight = 48510.851| |-----------------------------------------------------------------------------| r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 29873 Z= 0.240 Angle : 0.676 9.786 40748 Z= 0.359 Chirality : 0.045 0.281 4752 Planarity : 0.005 0.057 5163 Dihedral : 14.260 154.213 4813 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.14), residues: 3767 helix: 0.19 (0.14), residues: 1311 sheet: -1.48 (0.23), residues: 466 loop : -1.67 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 901 TYR 0.020 0.002 TYR D 631 PHE 0.019 0.002 PHE D 461 TRP 0.019 0.002 TRP D 686 HIS 0.007 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.24 (29868) covalent geometry : angle 0.67640 / 0.36 (40748) hydrogen bonds : bond 0.04801 / 3.36 ( 1167) hydrogen bonds : angle 5.35106 / 3.70 ( 3165) metal coordination : bond 0.00355 / 0.18 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9320 (pmm) cc_final: 0.8603 (pmm) REVERT: A 145 LYS cc_start: 0.9533 (tmtt) cc_final: 0.9090 (tptt) REVERT: A 177 TYR cc_start: 0.7068 (m-10) cc_final: 0.6687 (m-10) REVERT: B 51 MET cc_start: 0.9270 (tpt) cc_final: 0.9067 (tpp) REVERT: C 403 MET cc_start: 0.9393 (tmm) cc_final: 0.9105 (tmm) REVERT: C 446 ASP cc_start: 0.8805 (m-30) cc_final: 0.8604 (m-30) REVERT: C 459 MET cc_start: 0.9577 (mmp) cc_final: 0.9227 (mmm) REVERT: C 515 MET cc_start: 0.8224 (ptm) cc_final: 0.7861 (ptm) REVERT: C 516 ASP cc_start: 0.7770 (p0) cc_final: 0.7406 (p0) REVERT: C 527 LYS cc_start: 0.9430 (mttt) cc_final: 0.9170 (mttp) REVERT: C 549 ASP cc_start: 0.9403 (t0) cc_final: 0.9028 (t0) REVERT: C 653 MET cc_start: 0.8778 (tpt) cc_final: 0.8308 (tpt) REVERT: C 681 MET cc_start: 0.9427 (mmp) cc_final: 0.9221 (mmp) REVERT: C 704 MET cc_start: 0.9434 (mmp) cc_final: 0.9231 (mmp) REVERT: C 805 MET cc_start: 0.8936 (ppp) cc_final: 0.8454 (ppp) REVERT: C 951 MET cc_start: 0.9216 (mmp) cc_final: 0.8985 (mmm) REVERT: C 1107 MET cc_start: 0.9345 (mpp) cc_final: 0.9062 (mpp) REVERT: C 1108 ASN cc_start: 0.9525 (m-40) cc_final: 0.8837 (t0) REVERT: C 1114 GLU cc_start: 0.9377 (tm-30) cc_final: 0.8971 (tm-30) REVERT: C 1272 GLU cc_start: 0.8989 (pm20) cc_final: 0.8581 (pm20) REVERT: C 1273 MET cc_start: 0.9204 (mmp) cc_final: 0.8765 (mmp) REVERT: C 1274 GLU cc_start: 0.9342 (pm20) cc_final: 0.9042 (pm20) REVERT: C 1329 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8682 (mt-10) REVERT: D 56 LEU cc_start: 0.9235 (tp) cc_final: 0.9030 (tp) REVERT: D 120 LEU cc_start: 0.9605 (mt) cc_final: 0.9103 (tp) REVERT: D 180 MET cc_start: 0.8447 (ppp) cc_final: 0.8092 (ppp) REVERT: D 192 MET cc_start: 0.9102 (ttp) cc_final: 0.8658 (tmm) REVERT: D 245 LEU cc_start: 0.9580 (tp) cc_final: 0.9298 (tp) REVERT: D 329 ASP cc_start: 0.9036 (m-30) cc_final: 0.8776 (m-30) REVERT: D 330 MET cc_start: 0.9405 (tpt) cc_final: 0.8931 (tpt) REVERT: D 454 CYS cc_start: 0.9242 (m) cc_final: 0.9029 (m) REVERT: D 485 MET cc_start: 0.9125 (mmp) cc_final: 0.8048 (mmm) REVERT: D 644 MET cc_start: 0.9250 (mpp) cc_final: 0.8841 (mpp) REVERT: D 725 MET cc_start: 0.9407 (tpp) cc_final: 0.8600 (tpp) REVERT: D 743 MET cc_start: 0.8277 (tpt) cc_final: 0.8071 (tpp) REVERT: D 1040 MET cc_start: 0.8545 (ptp) cc_final: 0.8202 (mpp) REVERT: D 1143 ASP cc_start: 0.9174 (p0) cc_final: 0.8755 (t0) REVERT: D 1186 TYR cc_start: 0.8895 (m-10) cc_final: 0.8545 (m-10) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1711 time to fit residues: 63.1507 Evaluate side-chains 171 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 66 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 202 optimal weight: 8.9990 chunk 234 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN D1227 HIS ** D1326 GLN ** 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 = 0.3367 r_free = 0.3367 target = 0.055084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.035017 restraints weight = 201662.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.036217 restraints weight = 111804.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.037034 restraints weight = 74800.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.037637 restraints weight = 56460.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.037982 restraints weight = 45965.749| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29873 Z= 0.139 Angle : 0.632 10.159 40748 Z= 0.331 Chirality : 0.045 0.288 4752 Planarity : 0.004 0.058 5163 Dihedral : 14.216 154.523 4813 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.14), residues: 3767 helix: 0.37 (0.14), residues: 1302 sheet: -1.35 (0.24), residues: 460 loop : -1.58 (0.14), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 901 TYR 0.013 0.001 TYR D1363 PHE 0.023 0.001 PHE C1270 TRP 0.021 0.002 TRP D 686 HIS 0.005 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (29868) covalent geometry : angle 0.63161 / 0.33 (40748) hydrogen bonds : bond 0.04504 / 3.17 ( 1167) hydrogen bonds : angle 5.13499 / 3.55 ( 3165) metal coordination : bond 0.00125 / 0.06 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7534 Ramachandran restraints generated. 3767 Oldfield, 0 Emsley, 3767 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9262 (pmm) cc_final: 0.8528 (pmm) REVERT: A 145 LYS cc_start: 0.9530 (tmtt) cc_final: 0.9109 (tptt) REVERT: A 158 ARG cc_start: 0.8725 (mpt90) cc_final: 0.8452 (mpt180) REVERT: A 177 TYR cc_start: 0.7028 (m-10) cc_final: 0.6714 (m-10) REVERT: C 403 MET cc_start: 0.9397 (tmm) cc_final: 0.9100 (tmm) REVERT: C 459 MET cc_start: 0.9563 (mmp) cc_final: 0.9260 (mmp) REVERT: C 515 MET cc_start: 0.8022 (ptm) cc_final: 0.7551 (ptm) REVERT: C 516 ASP cc_start: 0.7748 (p0) cc_final: 0.7404 (p0) REVERT: C 527 LYS cc_start: 0.9369 (mttt) cc_final: 0.9107 (mtpp) REVERT: C 549 ASP cc_start: 0.9387 (t0) cc_final: 0.9003 (t0) REVERT: C 681 MET cc_start: 0.9404 (mmp) cc_final: 0.9180 (mmp) REVERT: C 704 MET cc_start: 0.9380 (mmp) cc_final: 0.9172 (mmp) REVERT: C 805 MET cc_start: 0.8946 (ppp) cc_final: 0.8463 (ppp) REVERT: C 951 MET cc_start: 0.9217 (mmp) cc_final: 0.8970 (mmm) REVERT: C 1107 MET cc_start: 0.9323 (mpp) cc_final: 0.9033 (mpp) REVERT: C 1108 ASN cc_start: 0.9448 (m-40) cc_final: 0.8558 (t0) REVERT: C 1114 GLU cc_start: 0.9344 (tm-30) cc_final: 0.8950 (tm-30) REVERT: C 1272 GLU cc_start: 0.8921 (pm20) cc_final: 0.8487 (pm20) REVERT: C 1273 MET cc_start: 0.9165 (mmp) cc_final: 0.8778 (mmp) REVERT: C 1279 GLU cc_start: 0.9561 (tp30) cc_final: 0.9340 (tp30) REVERT: C 1290 MET cc_start: 0.9145 (ttt) cc_final: 0.8943 (ppp) REVERT: C 1329 GLU cc_start: 0.9182 (mt-10) cc_final: 0.8603 (mt-10) REVERT: D 56 LEU cc_start: 0.9227 (tp) cc_final: 0.9017 (tp) REVERT: D 120 LEU cc_start: 0.9586 (mt) cc_final: 0.9071 (tp) REVERT: D 180 MET cc_start: 0.8487 (ppp) cc_final: 0.7255 (tmm) REVERT: D 245 LEU cc_start: 0.9569 (tp) cc_final: 0.9300 (tp) REVERT: D 329 ASP cc_start: 0.9025 (m-30) cc_final: 0.8810 (m-30) REVERT: D 330 MET cc_start: 0.9369 (tpt) cc_final: 0.8850 (tpt) REVERT: D 355 ILE cc_start: 0.9640 (tp) cc_final: 0.9412 (tp) REVERT: D 466 MET cc_start: 0.9101 (pmm) cc_final: 0.8875 (pmm) REVERT: D 485 MET cc_start: 0.9110 (mmp) cc_final: 0.8103 (mmm) REVERT: D 644 MET cc_start: 0.9270 (mpp) cc_final: 0.8851 (mpp) REVERT: D 725 MET cc_start: 0.9399 (tpp) cc_final: 0.8597 (tpp) REVERT: D 743 MET cc_start: 0.8195 (tpt) cc_final: 0.7962 (tpp) REVERT: D 1040 MET cc_start: 0.8573 (ptp) cc_final: 0.8243 (mpp) REVERT: D 1143 ASP cc_start: 0.9139 (p0) cc_final: 0.8719 (t0) REVERT: D 1186 TYR cc_start: 0.8873 (m-10) cc_final: 0.8516 (m-10) REVERT: D 1254 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8905 (mt-10) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1756 time to fit residues: 66.9248 Evaluate side-chains 175 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 271 optimal weight: 9.9990 chunk 275 optimal weight: 5.9990 chunk 308 optimal weight: 0.7980 chunk 236 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 chunk 212 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 368 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 49 optimal weight: 50.0000 chunk 322 optimal weight: 10.0000 overall best weight: 6.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D1326 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 = 0.3325 r_free = 0.3325 target = 0.053448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.033702 restraints weight = 208454.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.034885 restraints weight = 116553.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.035662 restraints weight = 77941.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.036222 restraints weight = 58955.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.036567 restraints weight = 48233.467| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 29873 Z= 0.295 Angle : 0.734 9.442 40748 Z= 0.387 Chirality : 0.046 0.277 4752 Planarity : 0.005 0.065 5163 Dihedral : 14.309 154.272 4813 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.13), residues: 3767 helix: 0.11 (0.14), residues: 1307 sheet: -1.55 (0.23), residues: 462 loop : -1.70 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 901 TYR 0.021 0.002 TYR D 457 PHE 0.023 0.002 PHE D1145 TRP 0.021 0.002 TRP D 686 HIS 0.010 0.002 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.30 (29868) covalent geometry : angle 0.73390 / 0.39 (40748) hydrogen bonds : bond 0.05046 / 3.53 ( 1167) hydrogen bonds : angle 5.44523 / 3.76 ( 3165) metal coordination : bond 0.00463 / 0.24 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5304.35 seconds wall clock time: 92 minutes 39.85 seconds (5559.85 seconds total)