Starting phenix.real_space_refine on Mon Sep 14 09:47:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7pyk_13718/09_2026/7pyk_13718.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pyk_13718/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pyk_13718/09_2026/7pyk_13718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pyk_13718/09_2026/7pyk_13718.map" model { file = "/net/cci-nas-00/data/ceres_data/7pyk_13718/09_2026/7pyk_13718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pyk_13718/09_2026/7pyk_13718.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7pyk_13718/09_2026/7pyk_13718.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7pyk_13718/09_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: {'RNAv2': 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: 5.79, 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: 2.34 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 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: 3.35 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: 6.88 Time building geometry restraints manager: 3.05 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: 40060 2.54 - 5.09: 622 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: 17286 29.55 - 59.10: 761 59.10 - 88.65: 53 88.65 - 118.21: 3 118.21 - 147.76: 5 Dihedral angle restraints: 18108 sinusoidal: 7228 harmonic: 10880 Sorted by residual: dihedral pdb=" C4' C R 5 " pdb=" C3' C R 5 " pdb=" C2' C R 5 " pdb=" C1' C R 5 " ideal model delta sinusoidal sigma weight residual 36.34 -35.48 71.82 1 3.10e+00 1.04e-01 6.87e+02 dihedral pdb=" O4' C R 5 " pdb=" C4' C R 5 " pdb=" C3' C R 5 " pdb=" C2' C R 5 " ideal model delta sinusoidal sigma weight residual -35.15 21.54 -56.69 1 4.00e+00 6.25e-02 2.70e+02 dihedral pdb=" O4' C R 5 " pdb=" C2' C R 5 " pdb=" C1' C R 5 " pdb=" C3' C R 5 " ideal model delta sinusoidal sigma weight residual -94.41 -38.23 -56.18 3 3.80e+00 6.93e-02 1.46e+02 ... (remaining 18105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3662 0.056 - 0.111: 935 0.111 - 0.167: 133 0.167 - 0.222: 14 0.222 - 0.278: 8 Chirality restraints: 4752 Sorted by residual: chirality pdb=" C2' C R 5 " pdb=" C3' C R 5 " pdb=" O2' C R 5 " pdb=" C1' C R 5 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" C3' C R 5 " pdb=" C4' C R 5 " pdb=" O3' C R 5 " pdb=" C2' C R 5 " both_signs ideal model delta sigma weight residual False -2.50 -2.76 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" P C R 5 " pdb=" OP1 C R 5 " pdb=" OP2 C R 5 " pdb=" O5' C R 5 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 32.390 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.700 ------------------------------------------------------------------------------- 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 : 0.787 12.723 40748 Z= 0.468 Chirality : 0.050 0.278 4752 Planarity : 0.005 0.062 5163 Dihedral : 15.535 147.756 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 0.78734 / 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 : 0.915 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: 0.1527 time to fit residues: 65.5987 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 : 1.114 ------------------------------------------------------------------------------- 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 69 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 = 0.3401 r_free = 0.3401 target = 0.056432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.036501 restraints weight = 199803.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.037785 restraints weight = 109578.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.038660 restraints weight = 72602.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.039237 restraints weight = 54320.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.039694 restraints weight = 44195.726| |-----------------------------------------------------------------------------| r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 29873 Z= 0.133 Angle : 0.659 21.292 40748 Z= 0.344 Chirality : 0.050 1.198 4752 Planarity : 0.005 0.060 5163 Dihedral : 14.418 150.205 4813 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 0.07 % Allowed : 5.16 % Favored : 94.76 % 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: -1.54 (0.13), residues: 3767 helix: -0.07 (0.14), residues: 1317 sheet: -1.24 (0.24), residues: 457 loop : -1.64 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 25 TYR 0.015 0.001 TYR D 165 PHE 0.018 0.001 PHE C1270 TRP 0.029 0.002 TRP D 686 HIS 0.004 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (29868) covalent geometry : angle 0.65851 / 0.34 (40748) hydrogen bonds : bond 0.05719 / 4.00 ( 1167) hydrogen bonds : angle 5.78016 / 4.03 ( 3165) metal coordination : bond 0.03400 / 1.48 ( 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 244 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 242 time to evaluate : 1.212 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: 0.9324 (pmm) cc_final: 0.8848 (pmm) REVERT: A 205 MET cc_start: 0.8519 (pmm) cc_final: 0.8286 (pmm) REVERT: C 85 CYS cc_start: 0.9410 (m) cc_final: 0.9164 (m) REVERT: C 403 MET cc_start: 0.9317 (tmm) cc_final: 0.9006 (tmm) REVERT: C 459 MET cc_start: 0.9540 (mmp) cc_final: 0.9304 (mmm) REVERT: C 515 MET cc_start: 0.7786 (ptm) cc_final: 0.7245 (ptp) REVERT: C 549 ASP cc_start: 0.9313 (t0) cc_final: 0.8938 (t0) REVERT: C 653 MET cc_start: 0.8597 (tpt) cc_final: 0.8203 (tpt) REVERT: C 704 MET cc_start: 0.9471 (mmp) cc_final: 0.9221 (mmp) REVERT: C 805 MET cc_start: 0.8783 (ppp) cc_final: 0.8301 (ppp) REVERT: C 865 LEU cc_start: 0.9333 (mt) cc_final: 0.9084 (mt) REVERT: C 1114 GLU cc_start: 0.9501 (tm-30) cc_final: 0.9143 (tm-30) REVERT: D 120 LEU cc_start: 0.9532 (mt) cc_final: 0.9136 (tp) REVERT: D 130 MET cc_start: 0.7663 (ppp) cc_final: 0.7322 (ppp) REVERT: D 180 MET cc_start: 0.7916 (ppp) cc_final: 0.7409 (ppp) REVERT: D 265 LEU cc_start: 0.9844 (mp) cc_final: 0.9607 (pp) REVERT: D 329 ASP cc_start: 0.9037 (m-30) cc_final: 0.8770 (m-30) REVERT: D 330 MET cc_start: 0.9268 (tpt) cc_final: 0.9029 (tpp) REVERT: D 355 ILE cc_start: 0.9634 (tp) cc_final: 0.9433 (tp) REVERT: D 454 CYS cc_start: 0.9266 (m) cc_final: 0.9029 (m) REVERT: D 485 MET cc_start: 0.9051 (mmp) cc_final: 0.8059 (mmm) REVERT: D 513 MET cc_start: 0.9257 (mmt) cc_final: 0.8927 (mmm) REVERT: D 544 LEU cc_start: 0.8879 (tt) cc_final: 0.8469 (tp) REVERT: D 644 MET cc_start: 0.9349 (mpp) cc_final: 0.9016 (mpp) REVERT: D 698 MET cc_start: 0.9037 (tmm) cc_final: 0.8800 (tmm) REVERT: D 720 ASN cc_start: 0.9290 (t0) cc_final: 0.8819 (t0) REVERT: D 725 MET cc_start: 0.9423 (tpp) cc_final: 0.8735 (tpt) REVERT: D 743 MET cc_start: 0.7523 (tpt) cc_final: 0.7185 (tpp) REVERT: D 1040 MET cc_start: 0.8442 (ptp) cc_final: 0.8117 (mpp) REVERT: D 1143 ASP cc_start: 0.9175 (p0) cc_final: 0.8928 (t0) REVERT: D 1186 TYR cc_start: 0.8920 (m-10) cc_final: 0.8596 (m-10) REVERT: E 26 ARG cc_start: 0.9481 (tpm170) cc_final: 0.9213 (tpm170) REVERT: E 56 GLU cc_start: 0.9291 (mm-30) cc_final: 0.9021 (tp30) outliers start: 2 outliers final: 0 residues processed: 244 average time/residue: 0.1613 time to fit residues: 67.7184 Evaluate side-chains 190 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.165 ------------------------------------------------------------------------------- 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: 0.0370 chunk 90 optimal weight: 10.0000 chunk 196 optimal weight: 8.9990 chunk 53 optimal weight: 0.0770 chunk 301 optimal weight: 30.0000 chunk 283 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 232 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 1 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 overall best weight: 4.0222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** 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 659 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.055467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.035648 restraints weight = 202741.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.036904 restraints weight = 111967.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.037733 restraints weight = 74563.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.038298 restraints weight = 55924.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.038738 restraints weight = 45704.378| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29873 Z= 0.191 Angle : 0.635 12.092 40748 Z= 0.338 Chirality : 0.046 0.660 4752 Planarity : 0.004 0.056 5163 Dihedral : 14.319 151.057 4813 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.04 % Allowed : 4.65 % Favored : 95.31 % 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: -1.44 (0.13), residues: 3767 helix: 0.06 (0.14), residues: 1331 sheet: -1.15 (0.24), residues: 428 loop : -1.64 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 47 TYR 0.020 0.001 TYR C1285 PHE 0.020 0.001 PHE C1270 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 0.00389 / 0.19 (29868) covalent geometry : angle 0.63480 / 0.34 (40748) hydrogen bonds : bond 0.05261 / 3.67 ( 1167) hydrogen bonds : angle 5.55717 / 3.87 ( 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 238 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 1.229 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: 0.9262 (pmm) cc_final: 0.8709 (pmm) REVERT: A 205 MET cc_start: 0.8535 (pmm) cc_final: 0.8262 (pmm) REVERT: C 85 CYS cc_start: 0.9497 (m) cc_final: 0.9287 (m) REVERT: C 403 MET cc_start: 0.9334 (tmm) cc_final: 0.9044 (tmm) REVERT: C 459 MET cc_start: 0.9559 (mmp) cc_final: 0.9328 (mmm) REVERT: C 515 MET cc_start: 0.7855 (ptm) cc_final: 0.7306 (ptp) REVERT: C 516 ASP cc_start: 0.7722 (p0) cc_final: 0.7423 (p0) REVERT: C 549 ASP cc_start: 0.9345 (t0) cc_final: 0.8963 (t0) REVERT: C 653 MET cc_start: 0.8632 (tpt) cc_final: 0.8237 (tpt) REVERT: C 704 MET cc_start: 0.9503 (mmp) cc_final: 0.9283 (mmp) REVERT: C 794 LEU cc_start: 0.9645 (tt) cc_final: 0.9064 (pp) REVERT: C 799 ASN cc_start: 0.9252 (p0) cc_final: 0.9020 (p0) REVERT: C 805 MET cc_start: 0.8818 (ppp) cc_final: 0.8365 (ppp) REVERT: C 865 LEU cc_start: 0.9308 (mt) cc_final: 0.9054 (mt) REVERT: C 951 MET cc_start: 0.9247 (mmp) cc_final: 0.8927 (mmm) REVERT: C 1107 MET cc_start: 0.9301 (mpp) cc_final: 0.9054 (mpp) REVERT: C 1108 ASN cc_start: 0.9403 (m-40) cc_final: 0.8753 (t0) REVERT: C 1114 GLU cc_start: 0.9464 (tm-30) cc_final: 0.9093 (tm-30) REVERT: C 1233 LEU cc_start: 0.9637 (mp) cc_final: 0.9348 (pp) REVERT: C 1273 MET cc_start: 0.9101 (mmp) cc_final: 0.8660 (mpp) REVERT: D 120 LEU cc_start: 0.9511 (mt) cc_final: 0.9106 (tp) REVERT: D 180 MET cc_start: 0.8099 (ppp) cc_final: 0.7599 (ppp) REVERT: D 265 LEU cc_start: 0.9852 (mp) cc_final: 0.9626 (pp) REVERT: D 329 ASP cc_start: 0.9082 (m-30) cc_final: 0.8802 (m-30) REVERT: D 330 MET cc_start: 0.9290 (tpt) cc_final: 0.8829 (tpp) REVERT: D 454 CYS cc_start: 0.9281 (m) cc_final: 0.9008 (m) REVERT: D 485 MET cc_start: 0.9125 (mmp) cc_final: 0.7999 (mmm) REVERT: D 513 MET cc_start: 0.9337 (mmt) cc_final: 0.8990 (mmm) REVERT: D 644 MET cc_start: 0.9323 (mpp) cc_final: 0.8950 (mpp) REVERT: D 720 ASN cc_start: 0.9270 (t0) cc_final: 0.8745 (t0) REVERT: D 725 MET cc_start: 0.9411 (tpp) cc_final: 0.8604 (tpp) REVERT: D 1143 ASP cc_start: 0.9183 (p0) cc_final: 0.8887 (t0) REVERT: D 1186 TYR cc_start: 0.8963 (m-10) cc_final: 0.8646 (m-10) REVERT: D 1254 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8950 (pt0) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.1686 time to fit residues: 68.7321 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 : 1.093 ------------------------------------------------------------------------------- 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: 2.9990 chunk 178 optimal weight: 1.9990 chunk 370 optimal weight: 40.0000 chunk 369 optimal weight: 8.9990 chunk 298 optimal weight: 5.9990 chunk 251 optimal weight: 10.0000 chunk 139 optimal weight: 0.9980 chunk 48 optimal weight: 40.0000 chunk 270 optimal weight: 0.9990 chunk 376 optimal weight: 50.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 D 232 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 = 0.3389 r_free = 0.3389 target = 0.055857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.036039 restraints weight = 200397.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.037277 restraints weight = 110349.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.038142 restraints weight = 73467.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.038763 restraints weight = 54951.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.039136 restraints weight = 44370.128| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29873 Z= 0.143 Angle : 0.606 9.198 40748 Z= 0.321 Chirality : 0.045 0.434 4752 Planarity : 0.004 0.054 5163 Dihedral : 14.239 151.827 4813 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.11 % Allowed : 3.33 % Favored : 96.56 % 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: -1.36 (0.13), residues: 3767 helix: 0.18 (0.14), residues: 1331 sheet: -1.14 (0.25), residues: 423 loop : -1.61 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 346 TYR 0.012 0.001 TYR D 795 PHE 0.019 0.001 PHE C 186 TRP 0.018 0.001 TRP D 686 HIS 0.004 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (29868) covalent geometry : angle 0.60552 / 0.32 (40748) hydrogen bonds : bond 0.04850 / 3.40 ( 1167) hydrogen bonds : angle 5.34107 / 3.71 ( 3165) metal coordination : bond 0.00198 / 0.11 ( 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 238 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 235 time to evaluate : 1.183 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: 0.9274 (pmm) cc_final: 0.8675 (pmm) REVERT: A 205 MET cc_start: 0.8483 (pmm) cc_final: 0.8242 (pmm) REVERT: C 85 CYS cc_start: 0.9415 (m) cc_final: 0.9181 (m) REVERT: C 403 MET cc_start: 0.9337 (tmm) cc_final: 0.9033 (tmm) REVERT: C 459 MET cc_start: 0.9547 (mmp) cc_final: 0.9314 (mmm) REVERT: C 515 MET cc_start: 0.7798 (ptm) cc_final: 0.7363 (ptp) REVERT: C 516 ASP cc_start: 0.7694 (p0) cc_final: 0.7324 (p0) REVERT: C 527 LYS cc_start: 0.9503 (mttt) cc_final: 0.9252 (mtmm) REVERT: C 549 ASP cc_start: 0.9354 (t0) cc_final: 0.8972 (t0) REVERT: C 653 MET cc_start: 0.8647 (tpt) cc_final: 0.8327 (tpt) REVERT: C 704 MET cc_start: 0.9471 (mmp) cc_final: 0.9253 (mmp) REVERT: C 794 LEU cc_start: 0.9593 (tt) cc_final: 0.8996 (pp) REVERT: C 805 MET cc_start: 0.8819 (ppp) cc_final: 0.8293 (ppp) REVERT: C 865 LEU cc_start: 0.9286 (mt) cc_final: 0.9011 (mt) REVERT: C 883 LEU cc_start: 0.9055 (mp) cc_final: 0.8855 (mp) REVERT: C 951 MET cc_start: 0.9272 (mmp) cc_final: 0.8988 (mmm) REVERT: C 1107 MET cc_start: 0.9304 (mpp) cc_final: 0.9045 (mpp) REVERT: C 1108 ASN cc_start: 0.9364 (m-40) cc_final: 0.8649 (t0) REVERT: C 1114 GLU cc_start: 0.9440 (tm-30) cc_final: 0.8490 (tm-30) REVERT: C 1230 MET cc_start: 0.8696 (tpt) cc_final: 0.8011 (tpp) REVERT: C 1329 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8724 (mt-10) REVERT: D 56 LEU cc_start: 0.9290 (tp) cc_final: 0.8947 (tt) REVERT: D 120 LEU cc_start: 0.9524 (mt) cc_final: 0.9082 (tp) REVERT: D 180 MET cc_start: 0.8112 (ppp) cc_final: 0.7530 (ppp) REVERT: D 232 ASN cc_start: 0.9251 (OUTLIER) cc_final: 0.8528 (p0) REVERT: D 252 LEU cc_start: 0.8760 (pt) cc_final: 0.8256 (tp) REVERT: D 265 LEU cc_start: 0.9850 (mp) cc_final: 0.9614 (pp) REVERT: D 298 MET cc_start: 0.9315 (tpt) cc_final: 0.9001 (tpp) REVERT: D 329 ASP cc_start: 0.9070 (m-30) cc_final: 0.8816 (m-30) REVERT: D 330 MET cc_start: 0.9302 (tpt) cc_final: 0.8800 (tpp) REVERT: D 355 ILE cc_start: 0.9634 (tp) cc_final: 0.9410 (tp) REVERT: D 454 CYS cc_start: 0.9235 (m) cc_final: 0.8967 (m) REVERT: D 478 LEU cc_start: 0.9762 (mm) cc_final: 0.9522 (mt) REVERT: D 485 MET cc_start: 0.9115 (mmp) cc_final: 0.8088 (mmm) REVERT: D 644 MET cc_start: 0.9316 (mpp) cc_final: 0.8898 (mpp) REVERT: D 720 ASN cc_start: 0.9269 (t0) cc_final: 0.8729 (t0) REVERT: D 725 MET cc_start: 0.9415 (tpp) cc_final: 0.8573 (tpp) REVERT: D 743 MET cc_start: 0.7862 (tpt) cc_final: 0.7618 (tpp) REVERT: D 1040 MET cc_start: 0.8514 (ptp) cc_final: 0.8171 (mpp) REVERT: D 1143 ASP cc_start: 0.9167 (p0) cc_final: 0.8948 (t0) REVERT: D 1186 TYR cc_start: 0.8955 (m-10) cc_final: 0.8637 (m-10) REVERT: D 1254 GLU cc_start: 0.9186 (mt-10) cc_final: 0.8841 (pt0) REVERT: E 18 ASP cc_start: 0.9494 (m-30) cc_final: 0.9242 (t0) outliers start: 3 outliers final: 0 residues processed: 238 average time/residue: 0.1753 time to fit residues: 71.4627 Evaluate side-chains 190 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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: 10.0000 chunk 345 optimal weight: 50.0000 chunk 205 optimal weight: 10.0000 chunk 332 optimal weight: 50.0000 chunk 254 optimal weight: 6.9990 chunk 256 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 154 optimal weight: 0.0040 overall best weight: 5.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 HIS ** 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 739 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 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 = 0.054448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.034528 restraints weight = 207720.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.035694 restraints weight = 116971.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.036505 restraints weight = 78951.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.037072 restraints weight = 59550.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.037474 restraints weight = 48947.203| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29873 Z= 0.250 Angle : 0.681 8.813 40748 Z= 0.361 Chirality : 0.046 0.320 4752 Planarity : 0.005 0.051 5163 Dihedral : 14.274 153.232 4813 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.90 % 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 (0.13), residues: 3767 helix: 0.10 (0.14), residues: 1326 sheet: -1.26 (0.24), residues: 440 loop : -1.68 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 332 TYR 0.025 0.002 TYR D 631 PHE 0.023 0.002 PHE C 186 TRP 0.019 0.002 TRP D 686 HIS 0.007 0.002 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.25 (29868) covalent geometry : angle 0.68105 / 0.36 (40748) hydrogen bonds : bond 0.05020 / 3.51 ( 1167) hydrogen bonds : angle 5.45241 / 3.78 ( 3165) metal coordination : bond 0.00282 / 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 222 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 221 time to evaluate : 1.180 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: 0.9297 (pmm) cc_final: 0.8652 (pmm) REVERT: A 145 LYS cc_start: 0.9483 (tmtt) cc_final: 0.9042 (tptt) REVERT: A 177 TYR cc_start: 0.6874 (m-10) cc_final: 0.6506 (m-10) REVERT: A 203 ILE cc_start: 0.9653 (pt) cc_final: 0.9442 (pt) REVERT: C 85 CYS cc_start: 0.9434 (m) cc_final: 0.9213 (m) REVERT: C 403 MET cc_start: 0.9381 (tmm) cc_final: 0.9074 (tmm) REVERT: C 459 MET cc_start: 0.9549 (mmp) cc_final: 0.9316 (mmm) REVERT: C 515 MET cc_start: 0.7967 (ptm) cc_final: 0.7555 (ptp) REVERT: C 516 ASP cc_start: 0.7868 (p0) cc_final: 0.7516 (p0) REVERT: C 527 LYS cc_start: 0.9514 (mttt) cc_final: 0.9283 (mtmm) REVERT: C 549 ASP cc_start: 0.9375 (t0) cc_final: 0.8985 (t0) REVERT: C 653 MET cc_start: 0.8746 (tpt) cc_final: 0.8345 (tpt) REVERT: C 704 MET cc_start: 0.9488 (mmp) cc_final: 0.9256 (mmp) REVERT: C 805 MET cc_start: 0.8833 (ppp) cc_final: 0.8363 (ppp) REVERT: C 951 MET cc_start: 0.9225 (mmp) cc_final: 0.8954 (mmm) REVERT: C 1114 GLU cc_start: 0.9452 (tm-30) cc_final: 0.8488 (tm-30) REVERT: C 1230 MET cc_start: 0.8891 (tpt) cc_final: 0.8147 (tpp) REVERT: C 1233 LEU cc_start: 0.9581 (mp) cc_final: 0.9327 (pp) REVERT: C 1329 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8780 (mt-10) REVERT: D 56 LEU cc_start: 0.9311 (tp) cc_final: 0.8916 (tt) REVERT: D 120 LEU cc_start: 0.9538 (mt) cc_final: 0.9090 (tp) REVERT: D 180 MET cc_start: 0.8175 (ppp) cc_final: 0.7450 (ppp) REVERT: D 298 MET cc_start: 0.9365 (tpt) cc_final: 0.9059 (tpp) REVERT: D 329 ASP cc_start: 0.9042 (m-30) cc_final: 0.8802 (m-30) REVERT: D 330 MET cc_start: 0.9386 (tpt) cc_final: 0.8815 (tpp) REVERT: D 454 CYS cc_start: 0.9208 (m) cc_final: 0.8917 (m) REVERT: D 485 MET cc_start: 0.9140 (mmp) cc_final: 0.7977 (mmm) REVERT: D 644 MET cc_start: 0.9315 (mpp) cc_final: 0.8886 (mpp) REVERT: D 725 MET cc_start: 0.9374 (tpp) cc_final: 0.8564 (tpp) REVERT: D 792 ASN cc_start: 0.9639 (OUTLIER) cc_final: 0.9132 (t0) REVERT: D 1143 ASP cc_start: 0.9201 (p0) cc_final: 0.8935 (t0) REVERT: D 1186 TYR cc_start: 0.8917 (m-10) cc_final: 0.8567 (m-10) REVERT: D 1254 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8820 (mt-10) outliers start: 1 outliers final: 0 residues processed: 222 average time/residue: 0.1761 time to fit residues: 67.1722 Evaluate side-chains 179 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 178 time to evaluate : 1.226 ------------------------------------------------------------------------------- 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: 6.9990 chunk 195 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 174 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 184 optimal weight: 4.9990 chunk 270 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 231 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 739 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.055401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.035706 restraints weight = 198058.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.036909 restraints weight = 110600.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.037765 restraints weight = 74556.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.038402 restraints weight = 55977.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.038774 restraints weight = 45285.457| |-----------------------------------------------------------------------------| r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29873 Z= 0.133 Angle : 0.609 8.441 40748 Z= 0.320 Chirality : 0.045 0.326 4752 Planarity : 0.004 0.071 5163 Dihedral : 14.197 153.122 4813 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % 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: -1.26 (0.14), residues: 3767 helix: 0.32 (0.14), residues: 1313 sheet: -1.25 (0.24), residues: 423 loop : -1.55 (0.14), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 191 TYR 0.017 0.001 TYR D 631 PHE 0.025 0.001 PHE C 186 TRP 0.019 0.001 TRP D 686 HIS 0.005 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (29868) covalent geometry : angle 0.60933 / 0.32 (40748) hydrogen bonds : bond 0.04573 / 3.21 ( 1167) hydrogen bonds : angle 5.15270 / 3.57 ( 3165) metal coordination : bond 0.00184 / 0.10 ( 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 235 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 1.130 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: 0.9322 (pmm) cc_final: 0.8649 (pmm) REVERT: A 145 LYS cc_start: 0.9493 (tmtt) cc_final: 0.9058 (tptt) REVERT: C 85 CYS cc_start: 0.9430 (m) cc_final: 0.9200 (m) REVERT: C 403 MET cc_start: 0.9367 (tmm) cc_final: 0.9084 (tmm) REVERT: C 459 MET cc_start: 0.9551 (mmp) cc_final: 0.9312 (mmm) REVERT: C 515 MET cc_start: 0.7797 (ptm) cc_final: 0.7187 (ptp) REVERT: C 516 ASP cc_start: 0.7835 (p0) cc_final: 0.7449 (p0) REVERT: C 527 LYS cc_start: 0.9480 (mttt) cc_final: 0.9235 (mtmm) REVERT: C 546 GLU cc_start: 0.8984 (pm20) cc_final: 0.8752 (pm20) REVERT: C 549 ASP cc_start: 0.9382 (t0) cc_final: 0.8997 (t0) REVERT: C 653 MET cc_start: 0.8754 (tpt) cc_final: 0.8424 (tpt) REVERT: C 704 MET cc_start: 0.9415 (mmp) cc_final: 0.9202 (mmp) REVERT: C 805 MET cc_start: 0.8889 (ppp) cc_final: 0.8500 (ppp) REVERT: C 951 MET cc_start: 0.9242 (mmp) cc_final: 0.9032 (mmm) REVERT: C 1107 MET cc_start: 0.9313 (mpp) cc_final: 0.9056 (mpp) REVERT: C 1108 ASN cc_start: 0.9415 (m-40) cc_final: 0.8605 (t0) REVERT: C 1114 GLU cc_start: 0.9434 (tm-30) cc_final: 0.9041 (tm-30) REVERT: C 1232 MET cc_start: 0.9301 (mmm) cc_final: 0.9064 (mmm) REVERT: C 1233 LEU cc_start: 0.9624 (mp) cc_final: 0.9320 (pp) REVERT: C 1273 MET cc_start: 0.9026 (mmp) cc_final: 0.8354 (tpt) REVERT: C 1275 VAL cc_start: 0.9612 (t) cc_final: 0.9362 (t) REVERT: C 1304 MET cc_start: 0.9541 (ttm) cc_final: 0.9251 (mmt) REVERT: C 1329 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8683 (mt-10) REVERT: D 56 LEU cc_start: 0.9260 (tp) cc_final: 0.8876 (tt) REVERT: D 120 LEU cc_start: 0.9540 (mt) cc_final: 0.9083 (tp) REVERT: D 180 MET cc_start: 0.8269 (ppp) cc_final: 0.7565 (ppp) REVERT: D 192 MET cc_start: 0.9051 (ttp) cc_final: 0.8585 (tmm) REVERT: D 245 LEU cc_start: 0.9396 (tp) cc_final: 0.9139 (tp) REVERT: D 298 MET cc_start: 0.9376 (tpt) cc_final: 0.9048 (tpp) REVERT: D 329 ASP cc_start: 0.9043 (m-30) cc_final: 0.8783 (m-30) REVERT: D 330 MET cc_start: 0.9357 (tpt) cc_final: 0.8772 (tpp) REVERT: D 355 ILE cc_start: 0.9661 (tp) cc_final: 0.9379 (tp) REVERT: D 454 CYS cc_start: 0.9191 (m) cc_final: 0.8975 (m) REVERT: D 466 MET cc_start: 0.8981 (pmm) cc_final: 0.8778 (pmm) REVERT: D 485 MET cc_start: 0.9141 (mmp) cc_final: 0.8145 (mmm) REVERT: D 644 MET cc_start: 0.9303 (mpp) cc_final: 0.8864 (mpp) REVERT: D 725 MET cc_start: 0.9382 (tpp) cc_final: 0.8516 (tpp) REVERT: D 743 MET cc_start: 0.8232 (tpt) cc_final: 0.7889 (tpp) REVERT: D 1040 MET cc_start: 0.8487 (ptp) cc_final: 0.8180 (mpp) REVERT: D 1143 ASP cc_start: 0.9126 (p0) cc_final: 0.8825 (t0) REVERT: D 1186 TYR cc_start: 0.8918 (m-10) cc_final: 0.8576 (m-10) REVERT: D 1254 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8811 (mt-10) REVERT: E 18 ASP cc_start: 0.9498 (m-30) cc_final: 0.9259 (t0) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1759 time to fit residues: 71.0656 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 : 1.220 ------------------------------------------------------------------------------- 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: 0.9980 chunk 256 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 348 optimal weight: 40.0000 chunk 45 optimal weight: 40.0000 chunk 340 optimal weight: 40.0000 chunk 86 optimal weight: 20.0000 chunk 216 optimal weight: 0.7980 chunk 76 optimal weight: 0.0170 overall best weight: 2.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 276 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 = 0.3381 r_free = 0.3381 target = 0.055547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.035479 restraints weight = 202557.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.036712 restraints weight = 112119.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.037549 restraints weight = 75032.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.038159 restraints weight = 56543.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.038521 restraints weight = 45887.145| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1896 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= 0.145 Angle : 0.617 8.735 40748 Z= 0.325 Chirality : 0.045 0.321 4752 Planarity : 0.004 0.074 5163 Dihedral : 14.174 153.156 4813 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: -1.22 (0.14), residues: 3767 helix: 0.41 (0.14), residues: 1307 sheet: -1.25 (0.24), residues: 438 loop : -1.55 (0.14), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 901 TYR 0.031 0.001 TYR A 68 PHE 0.016 0.001 PHE C 186 TRP 0.016 0.001 TRP D 686 HIS 0.005 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (29868) covalent geometry : angle 0.61721 / 0.32 (40748) hydrogen bonds : bond 0.04531 / 3.18 ( 1167) hydrogen bonds : angle 5.13812 / 3.56 ( 3165) metal coordination : bond 0.00167 / 0.09 ( 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 232 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 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: 0.9289 (pmm) cc_final: 0.8578 (pmm) REVERT: A 145 LYS cc_start: 0.9499 (tmtt) cc_final: 0.9060 (tptt) REVERT: A 177 TYR cc_start: 0.6875 (m-10) cc_final: 0.6569 (m-10) REVERT: C 85 CYS cc_start: 0.9419 (m) cc_final: 0.9197 (m) REVERT: C 403 MET cc_start: 0.9360 (tmm) cc_final: 0.9066 (tmm) REVERT: C 459 MET cc_start: 0.9546 (mmp) cc_final: 0.9306 (mmm) REVERT: C 516 ASP cc_start: 0.7843 (p0) cc_final: 0.7409 (p0) REVERT: C 549 ASP cc_start: 0.9368 (t0) cc_final: 0.8976 (t0) REVERT: C 653 MET cc_start: 0.8727 (tpt) cc_final: 0.8379 (tpt) REVERT: C 704 MET cc_start: 0.9414 (mmp) cc_final: 0.9166 (mmp) REVERT: C 764 CYS cc_start: 0.9612 (t) cc_final: 0.9350 (t) REVERT: C 805 MET cc_start: 0.8885 (ppp) cc_final: 0.8486 (ppp) REVERT: C 951 MET cc_start: 0.9219 (mmp) cc_final: 0.8999 (mmm) REVERT: C 1107 MET cc_start: 0.9322 (mpp) cc_final: 0.9057 (mpp) REVERT: C 1108 ASN cc_start: 0.9415 (m-40) cc_final: 0.8644 (t0) REVERT: C 1114 GLU cc_start: 0.9426 (tm-30) cc_final: 0.9060 (tm-30) REVERT: C 1232 MET cc_start: 0.9261 (mmm) cc_final: 0.9015 (mmm) REVERT: C 1233 LEU cc_start: 0.9607 (mp) cc_final: 0.9305 (pp) REVERT: C 1273 MET cc_start: 0.9088 (mmp) cc_final: 0.8433 (tpt) REVERT: C 1304 MET cc_start: 0.9522 (ttm) cc_final: 0.9247 (mmt) REVERT: C 1329 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8676 (mt-10) REVERT: D 56 LEU cc_start: 0.9175 (tp) cc_final: 0.8924 (tp) REVERT: D 120 LEU cc_start: 0.9540 (mt) cc_final: 0.9067 (tp) REVERT: D 180 MET cc_start: 0.8290 (ppp) cc_final: 0.7951 (ppp) REVERT: D 192 MET cc_start: 0.9061 (ttp) cc_final: 0.8589 (tmm) REVERT: D 245 LEU cc_start: 0.9562 (tp) cc_final: 0.9284 (tp) REVERT: D 298 MET cc_start: 0.9334 (tpt) cc_final: 0.9030 (tpp) REVERT: D 329 ASP cc_start: 0.9075 (m-30) cc_final: 0.8831 (m-30) REVERT: D 330 MET cc_start: 0.9364 (tpt) cc_final: 0.8880 (tpp) REVERT: D 355 ILE cc_start: 0.9685 (tp) cc_final: 0.9431 (tp) REVERT: D 454 CYS cc_start: 0.9164 (m) cc_final: 0.8880 (m) REVERT: D 485 MET cc_start: 0.9119 (mmp) cc_final: 0.8095 (mmm) REVERT: D 644 MET cc_start: 0.9293 (mpp) cc_final: 0.8871 (mpp) REVERT: D 720 ASN cc_start: 0.9198 (t0) cc_final: 0.8657 (t0) REVERT: D 725 MET cc_start: 0.9390 (tpp) cc_final: 0.8569 (tpp) REVERT: D 743 MET cc_start: 0.8317 (tpt) cc_final: 0.8009 (tpp) REVERT: D 1040 MET cc_start: 0.8508 (ptp) cc_final: 0.8161 (mpp) REVERT: D 1143 ASP cc_start: 0.9150 (p0) cc_final: 0.8905 (t0) REVERT: D 1186 TYR cc_start: 0.8876 (m-10) cc_final: 0.8508 (m-10) REVERT: E 18 ASP cc_start: 0.9472 (m-30) cc_final: 0.9231 (t0) REVERT: E 36 ASP cc_start: 0.8824 (p0) cc_final: 0.8611 (p0) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1726 time to fit residues: 69.0970 Evaluate side-chains 185 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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: 50.0000 chunk 37 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 243 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 375 optimal weight: 20.0000 chunk 187 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN ** 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 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 = 0.3389 r_free = 0.3389 target = 0.055890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.035755 restraints weight = 201357.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.036987 restraints weight = 111568.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.037829 restraints weight = 74760.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.038448 restraints weight = 56313.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.038826 restraints weight = 45818.106| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29873 Z= 0.128 Angle : 0.617 10.170 40748 Z= 0.322 Chirality : 0.045 0.321 4752 Planarity : 0.004 0.056 5163 Dihedral : 14.142 153.283 4813 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % 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: -1.14 (0.14), residues: 3767 helix: 0.50 (0.15), residues: 1302 sheet: -1.21 (0.24), residues: 428 loop : -1.51 (0.14), residues: 2037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 26 TYR 0.012 0.001 TYR D1363 PHE 0.016 0.001 PHE C 186 TRP 0.016 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 0.61714 / 0.32 (40748) hydrogen bonds : bond 0.04450 / 3.13 ( 1167) hydrogen bonds : angle 5.05024 / 3.51 ( 3165) metal coordination : bond 0.00137 / 0.07 ( 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 232 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.182 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: 0.9259 (pmm) cc_final: 0.8544 (pmm) REVERT: A 145 LYS cc_start: 0.9501 (tmtt) cc_final: 0.9080 (tptt) REVERT: A 158 ARG cc_start: 0.8717 (mpt90) cc_final: 0.8456 (mpt180) REVERT: A 177 TYR cc_start: 0.6824 (m-10) cc_final: 0.6505 (m-10) REVERT: C 85 CYS cc_start: 0.9415 (m) cc_final: 0.9207 (m) REVERT: C 403 MET cc_start: 0.9358 (tmm) cc_final: 0.9066 (tmm) REVERT: C 459 MET cc_start: 0.9525 (mmp) cc_final: 0.9200 (mmp) REVERT: C 515 MET cc_start: 0.8004 (ptm) cc_final: 0.7577 (ptm) REVERT: C 516 ASP cc_start: 0.7836 (p0) cc_final: 0.7444 (p0) REVERT: C 527 LYS cc_start: 0.9386 (mttt) cc_final: 0.9163 (mtpp) REVERT: C 549 ASP cc_start: 0.9368 (t0) cc_final: 0.9003 (t0) REVERT: C 653 MET cc_start: 0.8684 (tpt) cc_final: 0.8377 (tpt) REVERT: C 681 MET cc_start: 0.9369 (mmp) cc_final: 0.9160 (mmp) REVERT: C 805 MET cc_start: 0.8939 (ppp) cc_final: 0.8493 (ppp) REVERT: C 951 MET cc_start: 0.9200 (mmp) cc_final: 0.8985 (mmm) REVERT: C 1107 MET cc_start: 0.9326 (mpp) cc_final: 0.9049 (mpp) REVERT: C 1108 ASN cc_start: 0.9411 (m-40) cc_final: 0.8559 (t0) REVERT: C 1114 GLU cc_start: 0.9421 (tm-30) cc_final: 0.8371 (tm-30) REVERT: C 1230 MET cc_start: 0.8898 (tpt) cc_final: 0.8412 (tpp) REVERT: C 1304 MET cc_start: 0.9506 (ttm) cc_final: 0.9203 (mmt) REVERT: C 1329 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8584 (mt-10) REVERT: D 56 LEU cc_start: 0.9190 (tp) cc_final: 0.8947 (tp) REVERT: D 120 LEU cc_start: 0.9542 (mt) cc_final: 0.9065 (tp) REVERT: D 180 MET cc_start: 0.8315 (ppp) cc_final: 0.7886 (ppp) REVERT: D 192 MET cc_start: 0.9043 (ttp) cc_final: 0.8573 (tmm) REVERT: D 245 LEU cc_start: 0.9550 (tp) cc_final: 0.9259 (tp) REVERT: D 298 MET cc_start: 0.9355 (tpt) cc_final: 0.9046 (tpp) REVERT: D 329 ASP cc_start: 0.9068 (m-30) cc_final: 0.8854 (m-30) REVERT: D 330 MET cc_start: 0.9306 (tpt) cc_final: 0.8791 (tpt) REVERT: D 355 ILE cc_start: 0.9654 (tp) cc_final: 0.9378 (tp) REVERT: D 443 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8800 (tm-30) REVERT: D 454 CYS cc_start: 0.9155 (m) cc_final: 0.8954 (m) REVERT: D 485 MET cc_start: 0.9111 (mmp) cc_final: 0.8069 (mmm) REVERT: D 622 ASP cc_start: 0.9089 (t70) cc_final: 0.8876 (t0) REVERT: D 644 MET cc_start: 0.9292 (mpp) cc_final: 0.8898 (mpp) REVERT: D 720 ASN cc_start: 0.9175 (t0) cc_final: 0.8636 (t0) REVERT: D 725 MET cc_start: 0.9388 (tpp) cc_final: 0.8532 (tpp) REVERT: D 743 MET cc_start: 0.8162 (tpt) cc_final: 0.7837 (tpp) REVERT: D 1040 MET cc_start: 0.8516 (ptp) cc_final: 0.8161 (mpp) REVERT: D 1143 ASP cc_start: 0.9119 (p0) cc_final: 0.8857 (t0) REVERT: D 1186 TYR cc_start: 0.8854 (m-10) cc_final: 0.8507 (m-10) REVERT: E 18 ASP cc_start: 0.9476 (m-30) cc_final: 0.9226 (t0) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1798 time to fit residues: 71.0242 Evaluate side-chains 182 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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: 5.9990 chunk 121 optimal weight: 0.9980 chunk 238 optimal weight: 8.9990 chunk 322 optimal weight: 8.9990 chunk 352 optimal weight: 10.0000 chunk 11 optimal weight: 0.0020 chunk 320 optimal weight: 3.9990 chunk 359 optimal weight: 30.0000 chunk 187 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 overall best weight: 3.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 147 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 = 0.3377 r_free = 0.3377 target = 0.055397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.035505 restraints weight = 203233.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.036715 restraints weight = 112477.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.037580 restraints weight = 75434.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.038134 restraints weight = 56408.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.038583 restraints weight = 46152.233| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29873 Z= 0.165 Angle : 0.627 10.127 40748 Z= 0.328 Chirality : 0.045 0.318 4752 Planarity : 0.004 0.058 5163 Dihedral : 14.143 153.387 4813 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.04 % Allowed : 0.73 % Favored : 99.23 % 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: -1.16 (0.14), residues: 3767 helix: 0.49 (0.15), residues: 1307 sheet: -1.26 (0.24), residues: 449 loop : -1.53 (0.14), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 901 TYR 0.015 0.001 TYR D 631 PHE 0.015 0.001 PHE D 461 TRP 0.046 0.002 TRP C1276 HIS 0.005 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (29868) covalent geometry : angle 0.62655 / 0.33 (40748) hydrogen bonds : bond 0.04446 / 3.12 ( 1167) hydrogen bonds : angle 5.07886 / 3.51 ( 3165) metal coordination : bond 0.00185 / 0.09 ( 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 227 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 1.155 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: 0.9267 (pmm) cc_final: 0.8559 (pmm) REVERT: A 145 LYS cc_start: 0.9510 (tmtt) cc_final: 0.9090 (tptt) REVERT: A 177 TYR cc_start: 0.6913 (m-10) cc_final: 0.6504 (m-10) REVERT: C 85 CYS cc_start: 0.9425 (m) cc_final: 0.9200 (m) REVERT: C 403 MET cc_start: 0.9355 (tmm) cc_final: 0.9070 (tmm) REVERT: C 446 ASP cc_start: 0.8709 (m-30) cc_final: 0.8370 (m-30) REVERT: C 459 MET cc_start: 0.9537 (mmp) cc_final: 0.9204 (mmp) REVERT: C 515 MET cc_start: 0.8072 (ptm) cc_final: 0.7589 (ptm) REVERT: C 516 ASP cc_start: 0.7833 (p0) cc_final: 0.7464 (p0) REVERT: C 527 LYS cc_start: 0.9407 (mttt) cc_final: 0.9159 (mtpp) REVERT: C 546 GLU cc_start: 0.9011 (pm20) cc_final: 0.8764 (pm20) REVERT: C 549 ASP cc_start: 0.9384 (t0) cc_final: 0.9012 (t0) REVERT: C 653 MET cc_start: 0.8672 (tpt) cc_final: 0.8308 (tpt) REVERT: C 704 MET cc_start: 0.9453 (mmp) cc_final: 0.9218 (mmp) REVERT: C 805 MET cc_start: 0.8909 (ppp) cc_final: 0.8450 (ppp) REVERT: C 951 MET cc_start: 0.9207 (mmp) cc_final: 0.9004 (mmm) REVERT: C 1107 MET cc_start: 0.9331 (mpp) cc_final: 0.9055 (mpp) REVERT: C 1108 ASN cc_start: 0.9439 (m-40) cc_final: 0.8638 (t0) REVERT: C 1114 GLU cc_start: 0.9432 (tm-30) cc_final: 0.8386 (tm-30) REVERT: C 1230 MET cc_start: 0.8903 (tpt) cc_final: 0.8087 (tpp) REVERT: C 1304 MET cc_start: 0.9505 (ttm) cc_final: 0.9200 (mmt) REVERT: C 1329 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8614 (mt-10) REVERT: D 56 LEU cc_start: 0.9183 (tp) cc_final: 0.8950 (tp) REVERT: D 120 LEU cc_start: 0.9542 (mt) cc_final: 0.9062 (tp) REVERT: D 180 MET cc_start: 0.8403 (ppp) cc_final: 0.7168 (tmm) REVERT: D 192 MET cc_start: 0.9088 (ttp) cc_final: 0.8630 (tmm) REVERT: D 245 LEU cc_start: 0.9573 (tp) cc_final: 0.9313 (tp) REVERT: D 298 MET cc_start: 0.9370 (tpt) cc_final: 0.9067 (tpp) REVERT: D 329 ASP cc_start: 0.9008 (m-30) cc_final: 0.8758 (m-30) REVERT: D 330 MET cc_start: 0.9327 (tpt) cc_final: 0.8875 (tpt) REVERT: D 355 ILE cc_start: 0.9654 (tp) cc_final: 0.9413 (tp) REVERT: D 454 CYS cc_start: 0.9157 (m) cc_final: 0.8884 (m) REVERT: D 485 MET cc_start: 0.9179 (mmp) cc_final: 0.8098 (mmm) REVERT: D 644 MET cc_start: 0.9273 (mpp) cc_final: 0.8865 (mpp) REVERT: D 725 MET cc_start: 0.9383 (tpp) cc_final: 0.8570 (tpp) REVERT: D 743 MET cc_start: 0.8184 (tpt) cc_final: 0.7934 (tpp) REVERT: D 1143 ASP cc_start: 0.9149 (p0) cc_final: 0.8851 (t0) REVERT: D 1186 TYR cc_start: 0.8847 (m-10) cc_final: 0.8480 (m-10) REVERT: E 26 ARG cc_start: 0.9472 (tpm170) cc_final: 0.9216 (tpm170) outliers start: 1 outliers final: 1 residues processed: 227 average time/residue: 0.1759 time to fit residues: 68.5200 Evaluate side-chains 181 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 1.187 ------------------------------------------------------------------------------- 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: 3.9990 chunk 0 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 244 optimal weight: 10.0000 chunk 202 optimal weight: 10.0000 chunk 234 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 80 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 D 419 HIS D 771 GLN ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.053841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.033770 restraints weight = 206151.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.034941 restraints weight = 115682.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.035727 restraints weight = 77882.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.036327 restraints weight = 59028.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.036647 restraints weight = 47972.214| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 29873 Z= 0.278 Angle : 0.729 9.665 40748 Z= 0.384 Chirality : 0.046 0.312 4752 Planarity : 0.005 0.058 5163 Dihedral : 14.247 153.416 4813 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -1.42 (0.14), residues: 3767 helix: 0.28 (0.14), residues: 1305 sheet: -1.47 (0.23), residues: 488 loop : -1.67 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 101 TYR 0.018 0.002 TYR D 631 PHE 0.022 0.002 PHE D 461 TRP 0.059 0.003 TRP C1276 HIS 0.009 0.002 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.28 (29868) covalent geometry : angle 0.72887 / 0.38 (40748) hydrogen bonds : bond 0.04925 / 3.44 ( 1167) hydrogen bonds : angle 5.33358 / 3.68 ( 3165) metal coordination : bond 0.00377 / 0.19 ( 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 218 residues out of total 3211 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 1.269 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: 0.9287 (pmm) cc_final: 0.8617 (pmm) REVERT: A 145 LYS cc_start: 0.9520 (tmtt) cc_final: 0.9086 (tptt) REVERT: A 177 TYR cc_start: 0.7241 (m-10) cc_final: 0.6804 (m-10) REVERT: A 203 ILE cc_start: 0.9629 (pt) cc_final: 0.9415 (pt) REVERT: C 85 CYS cc_start: 0.9488 (m) cc_final: 0.9268 (m) REVERT: C 403 MET cc_start: 0.9408 (tmm) cc_final: 0.9138 (tmm) REVERT: C 446 ASP cc_start: 0.8799 (m-30) cc_final: 0.8493 (m-30) REVERT: C 459 MET cc_start: 0.9576 (mmp) cc_final: 0.9227 (mmm) REVERT: C 515 MET cc_start: 0.8186 (ptm) cc_final: 0.7814 (ptm) REVERT: C 516 ASP cc_start: 0.7847 (p0) cc_final: 0.7490 (p0) REVERT: C 527 LYS cc_start: 0.9441 (mttt) cc_final: 0.9168 (mttp) REVERT: C 546 GLU cc_start: 0.9073 (pm20) cc_final: 0.8810 (pm20) REVERT: C 549 ASP cc_start: 0.9435 (t0) cc_final: 0.9048 (t0) REVERT: C 653 MET cc_start: 0.8770 (tpt) cc_final: 0.8326 (tpt) REVERT: C 681 MET cc_start: 0.9436 (mmp) cc_final: 0.9210 (mmp) REVERT: C 704 MET cc_start: 0.9507 (mmp) cc_final: 0.9269 (mmp) REVERT: C 805 MET cc_start: 0.8973 (ppp) cc_final: 0.8588 (ppp) REVERT: C 951 MET cc_start: 0.9244 (mmp) cc_final: 0.8987 (mmm) REVERT: C 1107 MET cc_start: 0.9339 (mpp) cc_final: 0.9070 (mpp) REVERT: C 1108 ASN cc_start: 0.9502 (m-40) cc_final: 0.8865 (t0) REVERT: C 1114 GLU cc_start: 0.9404 (tm-30) cc_final: 0.8967 (tm-30) REVERT: C 1304 MET cc_start: 0.9556 (ttm) cc_final: 0.9246 (mmt) REVERT: C 1329 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8735 (mt-10) REVERT: D 56 LEU cc_start: 0.9198 (tp) cc_final: 0.8986 (tp) REVERT: D 120 LEU cc_start: 0.9584 (mt) cc_final: 0.9074 (tp) REVERT: D 180 MET cc_start: 0.8458 (ppp) cc_final: 0.8069 (ppp) REVERT: D 192 MET cc_start: 0.9161 (ttp) cc_final: 0.8725 (tmm) REVERT: D 245 LEU cc_start: 0.9594 (tp) cc_final: 0.9343 (tp) REVERT: D 298 MET cc_start: 0.9398 (tpt) cc_final: 0.9090 (tpp) REVERT: D 329 ASP cc_start: 0.9056 (m-30) cc_final: 0.8828 (m-30) REVERT: D 330 MET cc_start: 0.9371 (tpt) cc_final: 0.8939 (tpt) REVERT: D 443 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8859 (tm-30) REVERT: D 454 CYS cc_start: 0.9171 (m) cc_final: 0.8893 (m) REVERT: D 485 MET cc_start: 0.9180 (mmp) cc_final: 0.8089 (mmm) REVERT: D 644 MET cc_start: 0.9280 (mpp) cc_final: 0.8858 (mpp) REVERT: D 724 MET cc_start: 0.9312 (ptp) cc_final: 0.9097 (ptp) REVERT: D 725 MET cc_start: 0.9411 (tpp) cc_final: 0.8564 (tpp) REVERT: D 743 MET cc_start: 0.8240 (tpt) cc_final: 0.8021 (tpp) REVERT: D 1040 MET cc_start: 0.8509 (ptp) cc_final: 0.8264 (mpp) REVERT: D 1143 ASP cc_start: 0.9214 (p0) cc_final: 0.8935 (t0) REVERT: D 1186 TYR cc_start: 0.8884 (m-10) cc_final: 0.8492 (m-10) REVERT: E 26 ARG cc_start: 0.9480 (tpm170) cc_final: 0.9236 (tpm170) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1756 time to fit residues: 65.3615 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 : 1.139 ------------------------------------------------------------------------------- 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: 3.9990 chunk 275 optimal weight: 0.9990 chunk 308 optimal weight: 0.9980 chunk 236 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 368 optimal weight: 50.0000 chunk 51 optimal weight: 8.9990 chunk 49 optimal weight: 50.0000 chunk 322 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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** 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 = 0.3363 r_free = 0.3363 target = 0.054943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.035264 restraints weight = 200352.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.036505 restraints weight = 112182.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.037318 restraints weight = 75001.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.037931 restraints weight = 56616.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.038307 restraints weight = 46148.776| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2325 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= 0.154 Angle : 0.639 10.175 40748 Z= 0.335 Chirality : 0.045 0.318 4752 Planarity : 0.004 0.059 5163 Dihedral : 14.200 153.667 4813 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 13.22 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: -1.21 (0.14), residues: 3767 helix: 0.49 (0.15), residues: 1300 sheet: -1.29 (0.23), residues: 477 loop : -1.58 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 901 TYR 0.013 0.001 TYR D 631 PHE 0.021 0.002 PHE D 227 TRP 0.070 0.003 TRP C1276 HIS 0.005 0.001 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.15 (29868) covalent geometry : angle 0.63945 / 0.34 (40748) hydrogen bonds : bond 0.04509 / 3.16 ( 1167) hydrogen bonds : angle 5.11254 / 3.53 ( 3165) metal coordination : bond 0.00161 / 0.08 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5398.42 seconds wall clock time: 94 minutes 3.01 seconds (5643.01 seconds total)