Starting phenix.real_space_refine on Sat Feb 17 14:22:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/02_2024/6btm_7286_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/02_2024/6btm_7286.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/02_2024/6btm_7286_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/02_2024/6btm_7286_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/02_2024/6btm_7286_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/02_2024/6btm_7286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/02_2024/6btm_7286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/02_2024/6btm_7286_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/02_2024/6btm_7286_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.117 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: 5 Type Number sf(0) Gaussians Fe 13 7.16 5 S 109 5.16 5 C 12324 2.51 5 N 3102 2.21 5 O 3386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18934 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1737 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 214} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 7208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 948, 7208 Classifications: {'peptide': 948} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 31, 'TRANS': 916} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3697 Classifications: {'peptide': 457} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 436} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "D" Number of atoms: 1363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1363 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 162} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 1263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1263 Classifications: {'peptide': 161} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 153} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3300 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 387} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {'HEC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'E87': 1, 'F3S': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'E87': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7839 SG CYS B 879 55.855 63.976 77.010 1.00112.21 S ATOM 7687 SG CYS B 859 51.556 64.610 81.973 1.00106.17 S ATOM 7886 SG CYS B 885 52.353 59.128 78.996 1.00110.43 S ATOM 7658 SG CYS B 855 46.065 58.003 78.453 1.00111.33 S ATOM 7913 SG CYS B 889 47.380 52.106 76.760 1.00111.86 S ATOM 7597 SG CYS B 847 45.421 56.143 72.566 1.00110.05 S ATOM 7622 SG CYS B 850 41.188 54.019 77.047 1.00112.98 S Time building chain proxies: 9.98, per 1000 atoms: 0.53 Number of scatterers: 18934 At special positions: 0 Unit cell: (107.8, 125.4, 163.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 13 26.01 S 109 16.00 O 3386 8.00 N 3102 7.00 C 12324 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 769 " - pdb=" SG CYS B 971 " distance=2.03 Simple disulfide: pdb=" SG CYS B 938 " - pdb=" SG CYS B 965 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of additional links: simple=2, symmetry=0 Simple link: pdb=" N GLU B 71 " - pdb=" C E87 B1103 " Simple link: pdb=" N HIS E 21 " - pdb=" C E87 E 202 " Number of custom bonds: simple=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.86 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B1101 " pdb="FE3 F3S B1101 " - pdb=" SG CYS B 859 " pdb="FE4 F3S B1101 " - pdb=" SG CYS B 885 " pdb="FE1 F3S B1101 " - pdb=" SG CYS B 879 " pdb=" SF4 B1102 " pdb="FE1 SF4 B1102 " - pdb=" SG CYS B 855 " pdb="FE3 SF4 B1102 " - pdb=" SG CYS B 847 " pdb="FE2 SF4 B1102 " - pdb=" SG CYS B 889 " pdb="FE4 SF4 B1102 " - pdb=" SG CYS B 850 " Number of angles added : 21 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 10 sheets defined 44.7% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 225 through 245 removed outlier: 4.383A pdb=" N TYR A 242 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 273 through 276 No H-bonds generated for 'chain 'A' and resid 273 through 276' Processing helix chain 'A' and resid 293 through 296 No H-bonds generated for 'chain 'A' and resid 293 through 296' Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.526A pdb=" N GLN A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS A 324 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 325 " --> pdb=" O GLN A 321 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 326 " --> pdb=" O ILE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 365 No H-bonds generated for 'chain 'A' and resid 362 through 365' Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.535A pdb=" N HIS A 400 " --> pdb=" O CYS A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 417 No H-bonds generated for 'chain 'A' and resid 414 through 417' Processing helix chain 'A' and resid 431 through 434 No H-bonds generated for 'chain 'A' and resid 431 through 434' Processing helix chain 'B' and resid 134 through 142 removed outlier: 4.478A pdb=" N ILE B 140 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N LEU B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLY B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 178 Processing helix chain 'B' and resid 192 through 204 Processing helix chain 'B' and resid 219 through 229 removed outlier: 3.528A pdb=" N VAL B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 269 removed outlier: 3.930A pdb=" N GLY B 268 " --> pdb=" O GLY B 264 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG B 269 " --> pdb=" O TYR B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 291 No H-bonds generated for 'chain 'B' and resid 288 through 291' Processing helix chain 'B' and resid 301 through 315 removed outlier: 4.199A pdb=" N GLN B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 314 " --> pdb=" O GLN B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.753A pdb=" N GLU B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LYS B 334 " --> pdb=" O ALA B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 368 Processing helix chain 'B' and resid 386 through 398 removed outlier: 3.614A pdb=" N ALA B 390 " --> pdb=" O ASN B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 414 No H-bonds generated for 'chain 'B' and resid 411 through 414' Processing helix chain 'B' and resid 418 through 427 removed outlier: 3.692A pdb=" N LYS B 427 " --> pdb=" O SER B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 443 No H-bonds generated for 'chain 'B' and resid 440 through 443' Processing helix chain 'B' and resid 484 through 492 Processing helix chain 'B' and resid 498 through 504 Processing helix chain 'B' and resid 538 through 547 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 573 through 577 Processing helix chain 'B' and resid 595 through 601 removed outlier: 4.118A pdb=" N LYS B 600 " --> pdb=" O ALA B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 669 No H-bonds generated for 'chain 'B' and resid 667 through 669' Processing helix chain 'B' and resid 671 through 673 No H-bonds generated for 'chain 'B' and resid 671 through 673' Processing helix chain 'B' and resid 711 through 716 Processing helix chain 'B' and resid 719 through 721 No H-bonds generated for 'chain 'B' and resid 719 through 721' Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 768 through 776 removed outlier: 3.608A pdb=" N ALA B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS B 773 " --> pdb=" O CYS B 769 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 810 through 816 removed outlier: 3.871A pdb=" N ARG B 814 " --> pdb=" O GLY B 810 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LYS B 815 " --> pdb=" O ASP B 811 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 810 through 816' Processing helix chain 'B' and resid 827 through 830 No H-bonds generated for 'chain 'B' and resid 827 through 830' Processing helix chain 'B' and resid 939 through 948 removed outlier: 4.741A pdb=" N ALA B 944 " --> pdb=" O GLN B 940 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 947 " --> pdb=" O GLN B 943 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 992 No H-bonds generated for 'chain 'B' and resid 989 through 992' Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 37 through 63 Processing helix chain 'C' and resid 65 through 67 No H-bonds generated for 'chain 'C' and resid 65 through 67' Processing helix chain 'C' and resid 79 through 96 removed outlier: 3.758A pdb=" N HIS C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA C 92 " --> pdb=" O GLY C 88 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLY C 93 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N THR C 94 " --> pdb=" O GLY C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 102 No H-bonds generated for 'chain 'C' and resid 99 through 102' Processing helix chain 'C' and resid 106 through 110 removed outlier: 3.545A pdb=" N ALA C 110 " --> pdb=" O TRP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 120 removed outlier: 3.689A pdb=" N THR C 119 " --> pdb=" O ALA C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 132 removed outlier: 3.745A pdb=" N LEU C 128 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE C 129 " --> pdb=" O GLN C 125 " (cutoff:3.500A) Proline residue: C 130 - end of helix Processing helix chain 'C' and resid 137 through 143 removed outlier: 5.077A pdb=" N TYR C 141 " --> pdb=" O TRP C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 191 removed outlier: 3.526A pdb=" N GLY C 182 " --> pdb=" O PHE C 178 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 183 " --> pdb=" O TRP C 179 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) Proline residue: C 185 - end of helix removed outlier: 3.767A pdb=" N MET C 189 " --> pdb=" O PRO C 185 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 206 Processing helix chain 'C' and resid 214 through 247 Proline residue: C 233 - end of helix removed outlier: 3.724A pdb=" N HIS C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 285 removed outlier: 4.247A pdb=" N VAL C 264 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU C 278 " --> pdb=" O MET C 274 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS C 284 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 324 Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 343 through 361 Proline residue: C 357 - end of helix removed outlier: 4.570A pdb=" N MET C 360 " --> pdb=" O SER C 356 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TRP C 361 " --> pdb=" O PRO C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 366 No H-bonds generated for 'chain 'C' and resid 363 through 366' Processing helix chain 'C' and resid 369 through 393 removed outlier: 3.893A pdb=" N ASN C 380 " --> pdb=" O SER C 376 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE C 381 " --> pdb=" O ILE C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 403 No H-bonds generated for 'chain 'C' and resid 401 through 403' Processing helix chain 'C' and resid 411 through 433 removed outlier: 3.660A pdb=" N ILE C 416 " --> pdb=" O VAL C 412 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 417 " --> pdb=" O ASP C 413 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG C 433 " --> pdb=" O LEU C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 445 removed outlier: 4.046A pdb=" N THR C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 459 Processing helix chain 'D' and resid 13 through 25 Processing helix chain 'D' and resid 42 through 46 Processing helix chain 'D' and resid 53 through 78 removed outlier: 4.124A pdb=" N LEU D 59 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR D 60 " --> pdb=" O CYS D 56 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 123 Proline residue: D 101 - end of helix removed outlier: 3.958A pdb=" N GLU D 105 " --> pdb=" O PRO D 101 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N MET D 115 " --> pdb=" O ALA D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.564A pdb=" N ASP D 140 " --> pdb=" O ARG D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'E' and resid 79 through 84 Processing helix chain 'E' and resid 92 through 95 No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 99 through 107 removed outlier: 3.529A pdb=" N LEU E 103 " --> pdb=" O LYS E 99 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE E 106 " --> pdb=" O GLU E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 150 removed outlier: 3.574A pdb=" N VAL E 147 " --> pdb=" O SER E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 160 No H-bonds generated for 'chain 'E' and resid 158 through 160' Processing helix chain 'E' and resid 166 through 180 removed outlier: 3.756A pdb=" N TYR E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN E 180 " --> pdb=" O LYS E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 28 removed outlier: 3.927A pdb=" N LEU F 20 " --> pdb=" O MET F 16 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU F 28 " --> pdb=" O GLY F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 103 removed outlier: 4.204A pdb=" N HIS F 100 " --> pdb=" O ASN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 133 removed outlier: 3.986A pdb=" N LEU F 110 " --> pdb=" O PRO F 106 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA F 113 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE F 127 " --> pdb=" O GLY F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 151 removed outlier: 4.871A pdb=" N ARG F 144 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 151 " --> pdb=" O GLY F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 168 removed outlier: 4.811A pdb=" N ILE F 158 " --> pdb=" O PRO F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 201 removed outlier: 3.560A pdb=" N LYS F 197 " --> pdb=" O ILE F 193 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N GLY F 199 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR F 200 " --> pdb=" O GLY F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 233 removed outlier: 3.712A pdb=" N PHE F 213 " --> pdb=" O ARG F 209 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 214 " --> pdb=" O ALA F 210 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N TYR F 220 " --> pdb=" O GLY F 216 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU F 233 " --> pdb=" O LEU F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 265 removed outlier: 3.529A pdb=" N TRP F 263 " --> pdb=" O SER F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 269 No H-bonds generated for 'chain 'F' and resid 267 through 269' Processing helix chain 'F' and resid 279 through 303 removed outlier: 4.783A pdb=" N SER F 289 " --> pdb=" O SER F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 341 removed outlier: 3.679A pdb=" N ILE F 340 " --> pdb=" O GLN F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 356 removed outlier: 3.915A pdb=" N ARG F 355 " --> pdb=" O TYR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 369 removed outlier: 4.072A pdb=" N VAL F 367 " --> pdb=" O PHE F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 376 removed outlier: 3.628A pdb=" N LEU F 376 " --> pdb=" O VAL F 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 372 through 376' Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 387 through 413 Proline residue: F 411 - end of helix Processing helix chain 'F' and resid 415 through 417 No H-bonds generated for 'chain 'F' and resid 415 through 417' Processing helix chain 'F' and resid 422 through 445 removed outlier: 3.749A pdb=" N SER F 427 " --> pdb=" O PRO F 423 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR F 444 " --> pdb=" O PHE F 440 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS F 445 " --> pdb=" O THR F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 461 removed outlier: 3.770A pdb=" N HIS F 461 " --> pdb=" O GLU F 457 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 93 through 100 removed outlier: 3.863A pdb=" N LYS B 111 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N LYS B 119 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 208 through 212 removed outlier: 6.696A pdb=" N VAL B 182 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL B 211 " --> pdb=" O VAL B 182 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU B 184 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 447 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N SER B 435 " --> pdb=" O ILE B 447 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA B 449 " --> pdb=" O SER B 435 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 346 through 350 removed outlier: 6.621A pdb=" N LEU B 244 " --> pdb=" O ILE B 347 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N VAL B 349 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL B 246 " --> pdb=" O VAL B 349 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ARG B 278 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N SER B 247 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE B 280 " --> pdb=" O SER B 247 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS B 295 " --> pdb=" O GLN B 281 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLU B 283 " --> pdb=" O LYS B 295 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL B 297 " --> pdb=" O GLU B 283 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 459 through 461 Processing sheet with id= E, first strand: chain 'B' and resid 676 through 678 Processing sheet with id= F, first strand: chain 'B' and resid 605 through 607 removed outlier: 4.011A pdb=" N LEU B 613 " --> pdb=" O PHE B 690 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 618 through 621 Processing sheet with id= H, first strand: chain 'B' and resid 727 through 729 Processing sheet with id= I, first strand: chain 'B' and resid 977 through 980 removed outlier: 3.891A pdb=" N GLY B 979 " --> pdb=" O ASN B 755 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B 755 " --> pdb=" O GLY B 979 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 167 through 172 removed outlier: 4.585A pdb=" N LYS D 4 " --> pdb=" O VAL D 149 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.52 Time building geometry restraints manager: 8.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.75: 19271 1.75 - 2.34: 207 2.34 - 2.92: 0 2.92 - 3.51: 0 3.51 - 4.09: 3 Bond restraints: 19481 Sorted by residual: bond pdb=" S4 F3S B1101 " pdb="FE1 F3S B1101 " ideal model delta sigma weight residual 2.233 4.091 -1.858 2.00e-02 2.50e+03 8.63e+03 bond pdb=" S1 F3S B1101 " pdb="FE4 F3S B1101 " ideal model delta sigma weight residual 2.258 3.858 -1.600 2.00e-02 2.50e+03 6.40e+03 bond pdb=" S2 F3S B1101 " pdb="FE3 F3S B1101 " ideal model delta sigma weight residual 2.300 3.681 -1.381 2.00e-02 2.50e+03 4.77e+03 bond pdb=" C E87 B1103 " pdb=" O E87 B1103 " ideal model delta sigma weight residual 1.400 1.245 0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" C E87 E 202 " pdb=" O E87 E 202 " ideal model delta sigma weight residual 1.400 1.248 0.152 2.00e-02 2.50e+03 5.78e+01 ... (remaining 19476 not shown) Histogram of bond angle deviations from ideal: 37.55 - 65.78: 6 65.78 - 94.01: 39 94.01 - 122.23: 22808 122.23 - 150.46: 3680 150.46 - 178.69: 12 Bond angle restraints: 26545 Sorted by residual: angle pdb=" S3 F3S B1101 " pdb="FE1 F3S B1101 " pdb=" S4 F3S B1101 " ideal model delta sigma weight residual 112.59 59.34 53.25 3.00e+00 1.11e-01 3.15e+02 angle pdb=" S1 F3S B1101 " pdb="FE4 F3S B1101 " pdb=" S3 F3S B1101 " ideal model delta sigma weight residual 114.75 63.49 51.26 3.00e+00 1.11e-01 2.92e+02 angle pdb=" S1 F3S B1101 " pdb="FE4 F3S B1101 " pdb=" S2 F3S B1101 " ideal model delta sigma weight residual 103.63 65.83 37.80 3.00e+00 1.11e-01 1.59e+02 angle pdb="FE1 F3S B1101 " pdb=" S4 F3S B1101 " pdb="FE3 F3S B1101 " ideal model delta sigma weight residual 74.86 37.55 37.31 3.00e+00 1.11e-01 1.55e+02 angle pdb=" S2 F3S B1101 " pdb="FE1 F3S B1101 " pdb=" S4 F3S B1101 " ideal model delta sigma weight residual 102.84 66.13 36.71 3.00e+00 1.11e-01 1.50e+02 ... (remaining 26540 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.27: 11062 34.27 - 68.54: 107 68.54 - 102.80: 18 102.80 - 137.07: 1 137.07 - 171.34: 2 Dihedral angle restraints: 11190 sinusoidal: 4349 harmonic: 6841 Sorted by residual: dihedral pdb=" CB CYS B 769 " pdb=" SG CYS B 769 " pdb=" SG CYS B 971 " pdb=" CB CYS B 971 " ideal model delta sinusoidal sigma weight residual 93.00 155.84 -62.84 1 1.00e+01 1.00e-02 5.22e+01 dihedral pdb=" CA VAL B 880 " pdb=" C VAL B 880 " pdb=" N GLY B 881 " pdb=" CA GLY B 881 " ideal model delta harmonic sigma weight residual -180.00 -151.02 -28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA GLU E 41 " pdb=" C GLU E 41 " pdb=" N PRO E 42 " pdb=" CA PRO E 42 " ideal model delta harmonic sigma weight residual -180.00 -152.53 -27.47 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 11187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.775: 2868 3.775 - 7.550: 0 7.550 - 11.325: 0 11.325 - 15.100: 0 15.100 - 18.875: 1 Chirality restraints: 2869 Sorted by residual: chirality pdb=" S2 F3S B1101 " pdb="FE1 F3S B1101 " pdb="FE3 F3S B1101 " pdb="FE4 F3S B1101 " both_signs ideal model delta sigma weight residual False 10.77 -8.11 18.88 2.00e-01 2.50e+01 8.91e+03 chirality pdb="FE4 SF4 B1102 " pdb=" S1 SF4 B1102 " pdb=" S2 SF4 B1102 " pdb=" S3 SF4 B1102 " both_signs ideal model delta sigma weight residual False 10.55 11.06 -0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CG LEU F 277 " pdb=" CB LEU F 277 " pdb=" CD1 LEU F 277 " pdb=" CD2 LEU F 277 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 2866 not shown) Planarity restraints: 3320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" N E87 E 202 " -0.393 2.00e-02 2.50e+03 2.35e-01 6.90e+02 pdb=" CA E87 E 202 " 0.283 2.00e-02 2.50e+03 pdb=" C1 E87 E 202 " -0.079 2.00e-02 2.50e+03 pdb=" C2 E87 E 202 " 0.188 2.00e-02 2.50e+03 pdb=" O2 E87 E 202 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N E87 B1103 " -0.280 2.00e-02 2.50e+03 1.72e-01 3.69e+02 pdb=" CA E87 B1103 " 0.208 2.00e-02 2.50e+03 pdb=" C1 E87 B1103 " -0.058 2.00e-02 2.50e+03 pdb=" C2 E87 B1103 " 0.149 2.00e-02 2.50e+03 pdb=" O2 E87 B1103 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC A1004 " -0.035 2.00e-02 2.50e+03 7.29e-02 1.19e+02 pdb=" C2C HEC A1004 " 0.195 2.00e-02 2.50e+03 pdb=" C3C HEC A1004 " -0.021 2.00e-02 2.50e+03 pdb=" C4C HEC A1004 " 0.016 2.00e-02 2.50e+03 pdb=" CAC HEC A1004 " -0.067 2.00e-02 2.50e+03 pdb=" CHC HEC A1004 " -0.045 2.00e-02 2.50e+03 pdb=" CHD HEC A1004 " 0.007 2.00e-02 2.50e+03 pdb=" CMC HEC A1004 " -0.030 2.00e-02 2.50e+03 pdb=" NC HEC A1004 " -0.020 2.00e-02 2.50e+03 ... (remaining 3317 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 63 2.57 - 3.15: 15884 3.15 - 3.74: 28542 3.74 - 4.32: 41889 4.32 - 4.90: 65897 Nonbonded interactions: 152275 Sorted by model distance: nonbonded pdb=" NE2 HIS A 400 " pdb="FE HEC A1003 " model vdw 1.991 3.080 nonbonded pdb=" NE2 HIS A 265 " pdb="FE HEC A1000 " model vdw 1.992 3.080 nonbonded pdb=" NE2 HIS A 361 " pdb="FE HEC A1002 " model vdw 1.996 3.080 nonbonded pdb=" NE2 HIS A 262 " pdb="FE HEC A1001 " model vdw 1.999 3.080 nonbonded pdb=" S1 F3S B1101 " pdb="FE1 F3S B1101 " model vdw 2.181 2.688 ... (remaining 152270 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.010 Extract box with map and model: 4.790 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 54.480 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 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 : 0.022 1.858 19481 Z= 1.102 Angle : 1.400 53.253 26545 Z= 0.774 Chirality : 0.357 18.875 2869 Planarity : 0.009 0.235 3318 Dihedral : 11.417 171.339 6794 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.15 % Allowed : 1.42 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.16), residues: 2347 helix: -1.28 (0.14), residues: 1125 sheet: -0.68 (0.46), residues: 128 loop : -2.20 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.006 TRP C 163 HIS 0.020 0.003 HIS A 361 PHE 0.073 0.005 PHE A 356 TYR 0.103 0.005 TYR B 884 ARG 0.017 0.001 ARG B 878 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 498 time to evaluate : 2.262 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.7604 (mmp) cc_final: 0.7252 (mmm) REVERT: A 270 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8788 (mm-30) REVERT: A 272 ASN cc_start: 0.9165 (t0) cc_final: 0.8934 (t0) REVERT: A 322 ILE cc_start: 0.8255 (tt) cc_final: 0.8026 (tt) REVERT: A 355 ASP cc_start: 0.8428 (p0) cc_final: 0.7928 (t70) REVERT: A 362 SER cc_start: 0.9161 (p) cc_final: 0.8551 (p) REVERT: B 121 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6398 (mt-10) REVERT: B 255 ASP cc_start: 0.8035 (m-30) cc_final: 0.7794 (p0) REVERT: B 381 ILE cc_start: 0.8689 (mm) cc_final: 0.8470 (pt) REVERT: B 606 GLU cc_start: 0.7158 (tp30) cc_final: 0.6818 (tt0) REVERT: B 607 ILE cc_start: 0.9034 (mt) cc_final: 0.8778 (tp) REVERT: B 653 LYS cc_start: 0.8013 (mttt) cc_final: 0.7700 (mttm) REVERT: B 868 ARG cc_start: 0.8134 (mpt-90) cc_final: 0.7078 (mmt180) REVERT: C 5 TYR cc_start: 0.6942 (m-80) cc_final: 0.6501 (m-80) REVERT: C 109 MET cc_start: 0.8757 (mmt) cc_final: 0.8139 (mmm) REVERT: C 208 PHE cc_start: 0.7981 (m-10) cc_final: 0.7754 (m-80) REVERT: C 284 LYS cc_start: 0.8538 (mmtt) cc_final: 0.8124 (mtpt) REVERT: C 442 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7501 (mt-10) REVERT: D 32 GLU cc_start: 0.7337 (mm-30) cc_final: 0.6795 (mm-30) REVERT: D 163 THR cc_start: 0.7680 (m) cc_final: 0.7227 (t) REVERT: E 93 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8581 (mp0) REVERT: E 163 SER cc_start: 0.8722 (p) cc_final: 0.7943 (p) REVERT: F 96 ASN cc_start: 0.7294 (m-40) cc_final: 0.7035 (t0) REVERT: F 317 ASP cc_start: 0.7751 (t70) cc_final: 0.7379 (t70) REVERT: F 419 PHE cc_start: 0.6914 (p90) cc_final: 0.6547 (t80) outliers start: 3 outliers final: 0 residues processed: 499 average time/residue: 0.3070 time to fit residues: 232.6121 Evaluate side-chains 253 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 2.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 177 optimal weight: 8.9990 chunk 98 optimal weight: 7.9990 chunk 60 optimal weight: 0.0470 chunk 119 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 70 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 overall best weight: 0.9482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 273 ASN B 752 HIS B 761 ASN ** B 849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 GLN B 872 ASN B 963 ASN B 982 ASN C 91 HIS C 239 HIS D 142 HIS ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS E 180 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 19481 Z= 0.190 Angle : 0.902 95.870 26545 Z= 0.383 Chirality : 0.047 0.948 2869 Planarity : 0.004 0.052 3318 Dihedral : 10.116 167.204 2646 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.07 % Favored : 94.89 % Rotamer: Outliers : 2.53 % Allowed : 8.26 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.17), residues: 2347 helix: 0.15 (0.16), residues: 1107 sheet: -0.31 (0.44), residues: 155 loop : -2.05 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 206 HIS 0.005 0.001 HIS F 316 PHE 0.031 0.001 PHE C 269 TYR 0.013 0.001 TYR A 237 ARG 0.005 0.000 ARG B 878 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 294 time to evaluate : 2.150 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.6655 (mmp) cc_final: 0.6269 (mmm) REVERT: A 270 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8778 (mm-30) REVERT: A 295 MET cc_start: 0.9050 (mmm) cc_final: 0.8738 (mmm) REVERT: A 393 MET cc_start: 0.7823 (tpt) cc_final: 0.7031 (tpt) REVERT: A 402 LYS cc_start: 0.8640 (mtmp) cc_final: 0.8213 (mtmm) REVERT: A 419 GLU cc_start: 0.8345 (tm-30) cc_final: 0.7618 (tm-30) REVERT: A 424 TYR cc_start: 0.7354 (m-10) cc_final: 0.7125 (m-10) REVERT: A 438 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8042 (mt-10) REVERT: B 121 GLU cc_start: 0.6988 (mm-30) cc_final: 0.6406 (mt-10) REVERT: B 299 MET cc_start: 0.7462 (mtp) cc_final: 0.6920 (ttm) REVERT: B 381 ILE cc_start: 0.8791 (mm) cc_final: 0.8536 (pt) REVERT: B 606 GLU cc_start: 0.7324 (tp30) cc_final: 0.7081 (pt0) REVERT: B 653 LYS cc_start: 0.7766 (mttt) cc_final: 0.7499 (mttm) REVERT: B 659 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8135 (tt0) REVERT: B 868 ARG cc_start: 0.8074 (mpt-90) cc_final: 0.7258 (mmt180) REVERT: C 5 TYR cc_start: 0.6817 (m-80) cc_final: 0.6417 (m-80) REVERT: C 94 THR cc_start: 0.9080 (m) cc_final: 0.8746 (t) REVERT: C 109 MET cc_start: 0.8738 (mmt) cc_final: 0.7991 (mmm) REVERT: C 208 PHE cc_start: 0.8010 (m-10) cc_final: 0.7796 (m-80) REVERT: C 284 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8094 (tttt) REVERT: C 386 GLU cc_start: 0.8249 (tp30) cc_final: 0.7565 (tt0) REVERT: C 406 MET cc_start: 0.9037 (mmt) cc_final: 0.8828 (mmt) REVERT: C 442 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7145 (mt-10) REVERT: D 21 LYS cc_start: 0.8531 (mmtp) cc_final: 0.8061 (mmtm) REVERT: D 152 ASN cc_start: 0.7119 (p0) cc_final: 0.5518 (p0) REVERT: E 93 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8571 (mp0) REVERT: E 166 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7832 (mt-10) REVERT: F 96 ASN cc_start: 0.7168 (m-40) cc_final: 0.6962 (t0) REVERT: F 413 THR cc_start: 0.8927 (m) cc_final: 0.8540 (p) REVERT: F 419 PHE cc_start: 0.6508 (p90) cc_final: 0.6254 (t80) REVERT: F 424 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7598 (mp0) outliers start: 50 outliers final: 28 residues processed: 326 average time/residue: 0.2869 time to fit residues: 151.0826 Evaluate side-chains 263 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 235 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 832 GLU Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 947 LEU Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 276 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 212 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 chunk 189 optimal weight: 9.9990 chunk 211 optimal weight: 0.4980 chunk 72 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 363 GLN B 380 GLN B 453 HIS B 753 HIS B 848 GLN B 849 HIS B 982 ASN C 91 HIS C 239 HIS E 33 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 370 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 19481 Z= 0.247 Angle : 0.857 81.620 26545 Z= 0.362 Chirality : 0.052 1.509 2869 Planarity : 0.004 0.065 3318 Dihedral : 9.467 148.327 2646 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.92 % Favored : 94.03 % Rotamer: Outliers : 3.35 % Allowed : 10.29 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2347 helix: 0.66 (0.16), residues: 1084 sheet: -0.07 (0.42), residues: 157 loop : -1.99 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 206 HIS 0.006 0.001 HIS A 443 PHE 0.026 0.002 PHE C 269 TYR 0.014 0.002 TYR A 237 ARG 0.009 0.001 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 230 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6899 (mmp) cc_final: 0.6568 (mmm) REVERT: A 270 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8761 (mm-30) REVERT: A 300 ASN cc_start: 0.7659 (p0) cc_final: 0.7290 (p0) REVERT: A 398 ASP cc_start: 0.8447 (t0) cc_final: 0.8168 (t0) REVERT: A 438 GLU cc_start: 0.8500 (mt-10) cc_final: 0.7749 (mt-10) REVERT: B 299 MET cc_start: 0.7676 (mtp) cc_final: 0.7195 (ttm) REVERT: B 381 ILE cc_start: 0.8965 (mm) cc_final: 0.8658 (pt) REVERT: B 653 LYS cc_start: 0.7610 (mttt) cc_final: 0.7388 (mttm) REVERT: B 868 ARG cc_start: 0.8302 (mpt-90) cc_final: 0.7364 (mmt180) REVERT: B 997 MET cc_start: 0.7929 (tpp) cc_final: 0.7593 (tmm) REVERT: C 201 ARG cc_start: 0.8105 (tpt170) cc_final: 0.7817 (ttp-170) REVERT: C 282 MET cc_start: 0.8275 (tpt) cc_final: 0.8075 (ttt) REVERT: C 284 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8110 (tttt) REVERT: C 383 MET cc_start: 0.7779 (tpp) cc_final: 0.7497 (mmp) REVERT: C 386 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7624 (tt0) REVERT: C 406 MET cc_start: 0.9068 (mmt) cc_final: 0.8834 (mmt) REVERT: D 152 ASN cc_start: 0.7724 (p0) cc_final: 0.7196 (p0) REVERT: E 93 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8495 (mp0) REVERT: E 166 GLU cc_start: 0.8615 (mt-10) cc_final: 0.8118 (mt-10) REVERT: F 96 ASN cc_start: 0.7410 (m-40) cc_final: 0.7196 (t0) REVERT: F 369 MET cc_start: 0.8159 (mtp) cc_final: 0.7923 (ttm) REVERT: F 410 MET cc_start: 0.8711 (mmt) cc_final: 0.8455 (mmt) outliers start: 66 outliers final: 37 residues processed: 274 average time/residue: 0.2908 time to fit residues: 125.3812 Evaluate side-chains 236 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 198 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 139 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 361 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 226 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 60 optimal weight: 0.4980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 777 ASN B 848 GLN C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN F 314 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 19481 Z= 0.190 Angle : 0.809 81.671 26545 Z= 0.334 Chirality : 0.051 1.548 2869 Planarity : 0.003 0.044 3318 Dihedral : 9.130 141.746 2646 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.50 % Favored : 94.46 % Rotamer: Outliers : 2.64 % Allowed : 11.40 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.18), residues: 2347 helix: 0.80 (0.16), residues: 1101 sheet: 0.02 (0.42), residues: 157 loop : -1.88 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 206 HIS 0.004 0.001 HIS A 443 PHE 0.023 0.001 PHE C 269 TYR 0.022 0.001 TYR F 200 ARG 0.003 0.000 ARG F 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 225 time to evaluate : 2.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6700 (mmp) cc_final: 0.6418 (mmm) REVERT: A 300 ASN cc_start: 0.7720 (p0) cc_final: 0.7255 (p0) REVERT: A 398 ASP cc_start: 0.8446 (t0) cc_final: 0.8180 (t0) REVERT: A 428 LYS cc_start: 0.8136 (ptpt) cc_final: 0.7925 (ptpt) REVERT: A 438 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7897 (mt-10) REVERT: B 299 MET cc_start: 0.7598 (mtp) cc_final: 0.7025 (ttm) REVERT: B 653 LYS cc_start: 0.7623 (mttt) cc_final: 0.7390 (mttm) REVERT: B 736 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7719 (mm-30) REVERT: B 868 ARG cc_start: 0.8273 (mpt-90) cc_final: 0.7450 (mmt180) REVERT: B 997 MET cc_start: 0.7994 (tpp) cc_final: 0.7600 (tmm) REVERT: C 5 TYR cc_start: 0.6880 (m-80) cc_final: 0.6515 (m-10) REVERT: C 116 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7785 (mm-30) REVERT: C 201 ARG cc_start: 0.8043 (tpt170) cc_final: 0.7772 (ttp-170) REVERT: C 284 LYS cc_start: 0.8526 (mmtt) cc_final: 0.8089 (tttt) REVERT: C 328 GLU cc_start: 0.6966 (tp30) cc_final: 0.6642 (tp30) REVERT: C 383 MET cc_start: 0.7827 (tpp) cc_final: 0.7576 (mmp) REVERT: C 386 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: E 93 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8558 (mp0) REVERT: F 96 ASN cc_start: 0.7545 (m-40) cc_final: 0.7338 (t0) REVERT: F 309 TYR cc_start: 0.7419 (m-80) cc_final: 0.7112 (m-80) outliers start: 52 outliers final: 38 residues processed: 262 average time/residue: 0.2833 time to fit residues: 118.9957 Evaluate side-chains 239 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 200 time to evaluate : 2.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 832 GLU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 85 ASN Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.1980 chunk 128 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 168 optimal weight: 2.9990 chunk 93 optimal weight: 0.4980 chunk 193 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 203 optimal weight: 2.9990 chunk 57 optimal weight: 0.0770 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 696 GLN B 848 GLN B 963 ASN C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 19481 Z= 0.204 Angle : 0.811 81.717 26545 Z= 0.334 Chirality : 0.051 1.552 2869 Planarity : 0.003 0.040 3318 Dihedral : 8.812 131.268 2646 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.88 % Favored : 94.08 % Rotamer: Outliers : 3.19 % Allowed : 12.01 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.18), residues: 2347 helix: 1.05 (0.17), residues: 1083 sheet: 0.11 (0.43), residues: 157 loop : -1.87 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 206 HIS 0.006 0.001 HIS B 849 PHE 0.022 0.001 PHE C 269 TYR 0.028 0.001 TYR F 200 ARG 0.003 0.000 ARG B 894 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 209 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6656 (mmp) cc_final: 0.6409 (mmm) REVERT: A 288 ILE cc_start: 0.8583 (mm) cc_final: 0.8314 (mm) REVERT: A 300 ASN cc_start: 0.7956 (p0) cc_final: 0.7494 (p0) REVERT: A 385 MET cc_start: 0.8949 (tpt) cc_final: 0.8651 (tpt) REVERT: A 398 ASP cc_start: 0.8401 (t0) cc_final: 0.8165 (t0) REVERT: A 428 LYS cc_start: 0.8188 (ptpt) cc_final: 0.7934 (ptpt) REVERT: A 434 MET cc_start: 0.9284 (mmm) cc_final: 0.8967 (mmm) REVERT: A 438 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7763 (mt-10) REVERT: B 299 MET cc_start: 0.7723 (mtp) cc_final: 0.7336 (ttm) REVERT: B 564 MET cc_start: 0.8434 (tpt) cc_final: 0.8193 (mmm) REVERT: B 566 ASP cc_start: 0.8690 (OUTLIER) cc_final: 0.8386 (m-30) REVERT: B 736 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7605 (mm-30) REVERT: B 740 VAL cc_start: 0.7777 (t) cc_final: 0.7576 (m) REVERT: B 868 ARG cc_start: 0.8301 (mpt-90) cc_final: 0.7490 (mmt180) REVERT: C 109 MET cc_start: 0.8641 (tpp) cc_final: 0.8169 (mmt) REVERT: C 282 MET cc_start: 0.7966 (ttt) cc_final: 0.7686 (ttt) REVERT: C 284 LYS cc_start: 0.8523 (mmtt) cc_final: 0.8085 (tttt) REVERT: C 328 GLU cc_start: 0.7036 (tp30) cc_final: 0.6769 (tp30) REVERT: C 383 MET cc_start: 0.7832 (tpp) cc_final: 0.7601 (mmp) REVERT: C 386 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: C 406 MET cc_start: 0.8999 (mmt) cc_final: 0.8641 (mmt) REVERT: D 24 ARG cc_start: 0.8134 (mmm-85) cc_final: 0.7847 (mmm-85) REVERT: D 72 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8532 (mtm) REVERT: D 151 ASP cc_start: 0.8206 (p0) cc_final: 0.7905 (p0) REVERT: D 155 GLU cc_start: 0.7783 (pp20) cc_final: 0.7463 (pp20) REVERT: E 93 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8576 (mp0) REVERT: F 292 THR cc_start: 0.8713 (OUTLIER) cc_final: 0.8481 (m) REVERT: F 309 TYR cc_start: 0.7610 (m-80) cc_final: 0.7263 (m-80) outliers start: 63 outliers final: 44 residues processed: 258 average time/residue: 0.2799 time to fit residues: 114.6593 Evaluate side-chains 245 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 197 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 566 ASP Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 832 GLU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 226 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 118 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 ASN B 696 GLN B 848 GLN C 91 HIS C 239 HIS ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 19481 Z= 0.237 Angle : 0.822 81.811 26545 Z= 0.340 Chirality : 0.052 1.545 2869 Planarity : 0.003 0.038 3318 Dihedral : 8.667 115.697 2646 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.45 % Allowed : 12.67 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.18), residues: 2347 helix: 1.09 (0.17), residues: 1089 sheet: 0.17 (0.43), residues: 157 loop : -1.85 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 206 HIS 0.007 0.001 HIS B 849 PHE 0.022 0.001 PHE F 286 TYR 0.022 0.001 TYR F 200 ARG 0.003 0.000 ARG B 894 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 205 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6555 (mmp) cc_final: 0.6314 (mmm) REVERT: A 288 ILE cc_start: 0.8637 (mm) cc_final: 0.8354 (mm) REVERT: A 300 ASN cc_start: 0.8156 (p0) cc_final: 0.7698 (p0) REVERT: A 385 MET cc_start: 0.8908 (tpt) cc_final: 0.8615 (tpt) REVERT: A 398 ASP cc_start: 0.8494 (t0) cc_final: 0.8245 (t0) REVERT: A 428 LYS cc_start: 0.8213 (ptpt) cc_final: 0.8007 (ptpt) REVERT: A 434 MET cc_start: 0.9260 (mmm) cc_final: 0.9045 (mmm) REVERT: A 438 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8031 (mt-10) REVERT: B 299 MET cc_start: 0.7919 (mtp) cc_final: 0.7534 (ttm) REVERT: B 564 MET cc_start: 0.8534 (tpt) cc_final: 0.8321 (mmm) REVERT: B 736 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7671 (mm-30) REVERT: B 868 ARG cc_start: 0.8493 (mpt-90) cc_final: 0.7570 (mmt180) REVERT: C 284 LYS cc_start: 0.8542 (mmtt) cc_final: 0.8112 (tttt) REVERT: C 328 GLU cc_start: 0.7094 (tp30) cc_final: 0.6656 (tp30) REVERT: C 386 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7731 (tt0) REVERT: C 406 MET cc_start: 0.8969 (mmt) cc_final: 0.8613 (mmt) REVERT: D 24 ARG cc_start: 0.8260 (mmm-85) cc_final: 0.7850 (mmm-85) REVERT: D 72 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8552 (mtm) REVERT: D 155 GLU cc_start: 0.7782 (pp20) cc_final: 0.7489 (pp20) REVERT: E 93 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8547 (mp0) REVERT: F 292 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8489 (m) REVERT: F 309 TYR cc_start: 0.7687 (m-80) cc_final: 0.7325 (m-80) REVERT: F 424 GLU cc_start: 0.8237 (mp0) cc_final: 0.7963 (mp0) outliers start: 68 outliers final: 54 residues processed: 255 average time/residue: 0.3010 time to fit residues: 122.0819 Evaluate side-chains 246 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 189 time to evaluate : 2.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 786 GLU Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 832 GLU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 150 ASN Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 427 SER Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 165 optimal weight: 0.4980 chunk 190 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 225 optimal weight: 0.9980 chunk 141 optimal weight: 0.0170 chunk 137 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 139 optimal weight: 0.7980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 696 GLN C 91 HIS ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.104 19481 Z= 0.158 Angle : 0.795 82.228 26545 Z= 0.323 Chirality : 0.050 1.522 2869 Planarity : 0.003 0.036 3318 Dihedral : 8.412 100.678 2646 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.94 % Allowed : 13.18 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2347 helix: 1.27 (0.17), residues: 1080 sheet: 0.22 (0.43), residues: 157 loop : -1.74 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 206 HIS 0.015 0.001 HIS C 239 PHE 0.022 0.001 PHE F 286 TYR 0.022 0.001 TYR A 237 ARG 0.002 0.000 ARG B 788 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 213 time to evaluate : 2.926 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.6491 (mmp) cc_final: 0.6283 (mmm) REVERT: A 288 ILE cc_start: 0.8632 (mm) cc_final: 0.8351 (mm) REVERT: A 385 MET cc_start: 0.8904 (tpt) cc_final: 0.8635 (tpt) REVERT: A 398 ASP cc_start: 0.8414 (t0) cc_final: 0.8193 (t0) REVERT: A 419 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8432 (tm-30) REVERT: A 428 LYS cc_start: 0.8204 (ptpt) cc_final: 0.8002 (ptpt) REVERT: A 434 MET cc_start: 0.9260 (mmm) cc_final: 0.9049 (mmm) REVERT: A 438 GLU cc_start: 0.8540 (mt-10) cc_final: 0.7918 (mt-10) REVERT: B 108 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8084 (pp) REVERT: B 564 MET cc_start: 0.8266 (tpt) cc_final: 0.8055 (mmm) REVERT: B 736 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7854 (mm-30) REVERT: B 868 ARG cc_start: 0.8377 (mpt-90) cc_final: 0.7545 (mmt180) REVERT: B 990 LYS cc_start: 0.8951 (mttt) cc_final: 0.8705 (mptt) REVERT: C 5 TYR cc_start: 0.7211 (m-80) cc_final: 0.6876 (m-10) REVERT: C 284 LYS cc_start: 0.8509 (mmtt) cc_final: 0.8076 (tttt) REVERT: C 328 GLU cc_start: 0.6894 (tp30) cc_final: 0.6463 (tp30) REVERT: C 386 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7700 (tp30) REVERT: C 406 MET cc_start: 0.8989 (mmt) cc_final: 0.8603 (mmt) REVERT: C 448 LYS cc_start: 0.8359 (pttp) cc_final: 0.7953 (mtmm) REVERT: D 24 ARG cc_start: 0.8266 (mmm-85) cc_final: 0.7838 (mmm-85) REVERT: D 46 MET cc_start: 0.8486 (mtt) cc_final: 0.8192 (mtt) REVERT: D 72 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8468 (ttm) REVERT: D 155 GLU cc_start: 0.7740 (pp20) cc_final: 0.7474 (pp20) REVERT: E 93 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8544 (mp0) REVERT: E 166 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8052 (mp0) REVERT: F 4 PHE cc_start: 0.6435 (OUTLIER) cc_final: 0.6115 (t80) REVERT: F 309 TYR cc_start: 0.7686 (m-80) cc_final: 0.7316 (m-80) REVERT: F 369 MET cc_start: 0.8409 (ttm) cc_final: 0.8043 (ttm) REVERT: F 424 GLU cc_start: 0.8243 (mp0) cc_final: 0.8025 (mp0) REVERT: F 452 ARG cc_start: 0.8114 (ptm-80) cc_final: 0.7687 (ptm-80) outliers start: 58 outliers final: 42 residues processed: 254 average time/residue: 0.2827 time to fit residues: 115.1685 Evaluate side-chains 248 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 202 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 384 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 832 GLU Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain E residue 123 VAL Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 0.7980 chunk 134 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 143 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 177 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 505 ASN B 696 GLN B 755 ASN B 777 ASN C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN D 152 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 19481 Z= 0.183 Angle : 0.802 82.226 26545 Z= 0.326 Chirality : 0.051 1.520 2869 Planarity : 0.003 0.035 3318 Dihedral : 8.279 89.573 2646 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.35 % Allowed : 13.43 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2347 helix: 1.32 (0.17), residues: 1084 sheet: 0.30 (0.43), residues: 158 loop : -1.68 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 395 HIS 0.005 0.001 HIS C 239 PHE 0.022 0.001 PHE F 286 TYR 0.023 0.001 TYR A 237 ARG 0.002 0.000 ARG B 894 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 204 time to evaluate : 2.344 Fit side-chains revert: symmetry clash REVERT: A 244 MET cc_start: 0.6511 (mmp) cc_final: 0.6299 (mmm) REVERT: A 288 ILE cc_start: 0.8648 (mm) cc_final: 0.8351 (mm) REVERT: A 385 MET cc_start: 0.8906 (tpt) cc_final: 0.8631 (tpt) REVERT: A 398 ASP cc_start: 0.8490 (t0) cc_final: 0.8228 (t0) REVERT: A 428 LYS cc_start: 0.8216 (ptpt) cc_final: 0.8002 (ptpt) REVERT: A 434 MET cc_start: 0.9248 (mmm) cc_final: 0.9012 (mmm) REVERT: A 438 GLU cc_start: 0.8550 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 108 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8050 (pp) REVERT: B 299 MET cc_start: 0.7291 (ttm) cc_final: 0.6977 (ttm) REVERT: B 564 MET cc_start: 0.8363 (tpt) cc_final: 0.8160 (mmm) REVERT: B 736 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7846 (mm-30) REVERT: B 755 ASN cc_start: 0.8125 (OUTLIER) cc_final: 0.7730 (m110) REVERT: B 868 ARG cc_start: 0.8443 (mpt-90) cc_final: 0.7533 (mmt180) REVERT: B 932 MET cc_start: 0.8646 (tpp) cc_final: 0.8300 (tpp) REVERT: B 990 LYS cc_start: 0.8939 (mttt) cc_final: 0.8701 (mptt) REVERT: C 5 TYR cc_start: 0.7247 (m-80) cc_final: 0.6910 (m-10) REVERT: C 284 LYS cc_start: 0.8496 (mmtt) cc_final: 0.8084 (tttt) REVERT: C 328 GLU cc_start: 0.6944 (tp30) cc_final: 0.6463 (tp30) REVERT: C 386 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7782 (tp30) REVERT: C 406 MET cc_start: 0.8993 (mmt) cc_final: 0.8651 (mmt) REVERT: C 448 LYS cc_start: 0.8358 (pttp) cc_final: 0.7965 (mtmm) REVERT: D 24 ARG cc_start: 0.8340 (mmm-85) cc_final: 0.7877 (mmm-85) REVERT: D 46 MET cc_start: 0.8326 (mtt) cc_final: 0.8073 (mtt) REVERT: D 72 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8458 (ttm) REVERT: E 93 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8522 (mp0) REVERT: E 166 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8085 (mp0) REVERT: F 4 PHE cc_start: 0.6402 (OUTLIER) cc_final: 0.6168 (t80) REVERT: F 309 TYR cc_start: 0.7769 (m-80) cc_final: 0.7370 (m-80) REVERT: F 369 MET cc_start: 0.8477 (ttm) cc_final: 0.8129 (ttp) REVERT: F 452 ARG cc_start: 0.8078 (ptm-80) cc_final: 0.7663 (ptm-80) outliers start: 66 outliers final: 50 residues processed: 249 average time/residue: 0.2877 time to fit residues: 113.4534 Evaluate side-chains 253 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 198 time to evaluate : 2.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 755 ASN Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 832 GLU Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 57 ILE Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 386 GLU Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 4 PHE Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 chunk 210 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 165 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 189 optimal weight: 4.9990 chunk 198 optimal weight: 0.7980 chunk 209 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 696 GLN B 755 ASN C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 19481 Z= 0.169 Angle : 0.798 82.308 26545 Z= 0.324 Chirality : 0.050 1.515 2869 Planarity : 0.003 0.035 3318 Dihedral : 8.078 88.123 2646 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.14 % Allowed : 13.74 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.18), residues: 2347 helix: 1.41 (0.17), residues: 1077 sheet: 0.35 (0.43), residues: 158 loop : -1.60 (0.19), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 206 HIS 0.003 0.001 HIS B 999 PHE 0.023 0.001 PHE F 286 TYR 0.024 0.001 TYR A 237 ARG 0.002 0.000 ARG B 788 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 204 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6504 (mmp) cc_final: 0.6288 (mmm) REVERT: A 288 ILE cc_start: 0.8666 (mm) cc_final: 0.8375 (mm) REVERT: A 385 MET cc_start: 0.8898 (tpt) cc_final: 0.8633 (tpt) REVERT: A 398 ASP cc_start: 0.8468 (t0) cc_final: 0.8233 (t0) REVERT: A 419 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8451 (tm-30) REVERT: A 428 LYS cc_start: 0.8197 (ptpt) cc_final: 0.7988 (ptpt) REVERT: A 434 MET cc_start: 0.9224 (mmm) cc_final: 0.8981 (mmm) REVERT: B 108 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8104 (pp) REVERT: B 299 MET cc_start: 0.7252 (ttm) cc_final: 0.6973 (ttm) REVERT: B 564 MET cc_start: 0.8265 (tpt) cc_final: 0.8059 (mmm) REVERT: B 736 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7773 (mm-30) REVERT: B 755 ASN cc_start: 0.7623 (OUTLIER) cc_final: 0.7276 (m110) REVERT: B 868 ARG cc_start: 0.8415 (mpt-90) cc_final: 0.7581 (mmt180) REVERT: B 932 MET cc_start: 0.8652 (tpp) cc_final: 0.8252 (tpp) REVERT: B 990 LYS cc_start: 0.8898 (mttt) cc_final: 0.8627 (mptt) REVERT: C 5 TYR cc_start: 0.7246 (m-80) cc_final: 0.6921 (m-10) REVERT: C 284 LYS cc_start: 0.8453 (mmtt) cc_final: 0.8043 (tttt) REVERT: C 328 GLU cc_start: 0.6906 (tp30) cc_final: 0.6389 (tp30) REVERT: C 406 MET cc_start: 0.8988 (mmt) cc_final: 0.8608 (mmt) REVERT: D 24 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.7877 (mmm-85) REVERT: D 44 LYS cc_start: 0.8844 (tttt) cc_final: 0.8588 (mmmt) REVERT: D 46 MET cc_start: 0.8227 (mtt) cc_final: 0.7998 (mtt) REVERT: D 72 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8473 (ttm) REVERT: E 93 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8522 (mp0) REVERT: F 1 MET cc_start: 0.8100 (mmm) cc_final: 0.7787 (mmm) REVERT: F 309 TYR cc_start: 0.7825 (m-80) cc_final: 0.7416 (m-80) REVERT: F 368 VAL cc_start: 0.8422 (p) cc_final: 0.8221 (p) REVERT: F 452 ARG cc_start: 0.8057 (ptm-80) cc_final: 0.7643 (ptm-80) outliers start: 62 outliers final: 49 residues processed: 246 average time/residue: 0.2944 time to fit residues: 115.8428 Evaluate side-chains 249 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 197 time to evaluate : 2.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 696 GLN Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 755 ASN Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 832 GLU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 276 THR Chi-restraints excluded: chain F residue 292 THR Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 233 optimal weight: 0.9980 chunk 214 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 143 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 696 GLN B 755 ASN B1013 HIS C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 19481 Z= 0.178 Angle : 0.805 82.343 26545 Z= 0.328 Chirality : 0.051 1.515 2869 Planarity : 0.003 0.035 3318 Dihedral : 7.984 87.466 2646 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.89 % Allowed : 13.94 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.18), residues: 2347 helix: 1.39 (0.17), residues: 1083 sheet: 0.44 (0.45), residues: 147 loop : -1.59 (0.18), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 395 HIS 0.003 0.001 HIS B 999 PHE 0.023 0.001 PHE F 286 TYR 0.023 0.001 TYR A 237 ARG 0.002 0.000 ARG D 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4694 Ramachandran restraints generated. 2347 Oldfield, 0 Emsley, 2347 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 203 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 MET cc_start: 0.6505 (mmp) cc_final: 0.6288 (mmm) REVERT: A 288 ILE cc_start: 0.8667 (mm) cc_final: 0.8374 (mm) REVERT: A 385 MET cc_start: 0.8899 (tpt) cc_final: 0.8638 (tpt) REVERT: A 398 ASP cc_start: 0.8470 (t0) cc_final: 0.8234 (t0) REVERT: A 419 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8499 (tm-30) REVERT: A 428 LYS cc_start: 0.8193 (ptpt) cc_final: 0.7987 (ptpt) REVERT: A 434 MET cc_start: 0.9218 (mmm) cc_final: 0.8973 (mmm) REVERT: B 108 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8110 (pp) REVERT: B 299 MET cc_start: 0.7249 (ttm) cc_final: 0.6980 (ttm) REVERT: B 517 LYS cc_start: 0.7779 (mmtt) cc_final: 0.7101 (mmmt) REVERT: B 564 MET cc_start: 0.8290 (tpt) cc_final: 0.8085 (mmm) REVERT: B 736 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7626 (mm-30) REVERT: B 755 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.7242 (m110) REVERT: B 868 ARG cc_start: 0.8416 (mpt-90) cc_final: 0.7590 (mmt180) REVERT: B 932 MET cc_start: 0.8665 (tpp) cc_final: 0.8235 (tpp) REVERT: B 990 LYS cc_start: 0.8871 (mttt) cc_final: 0.8593 (mptt) REVERT: C 5 TYR cc_start: 0.7249 (m-80) cc_final: 0.6930 (m-10) REVERT: C 284 LYS cc_start: 0.8445 (mmtt) cc_final: 0.8041 (tttt) REVERT: C 328 GLU cc_start: 0.6917 (tp30) cc_final: 0.6416 (tp30) REVERT: C 406 MET cc_start: 0.8991 (mmt) cc_final: 0.8644 (mmt) REVERT: D 24 ARG cc_start: 0.8348 (mmm-85) cc_final: 0.8075 (mmm-85) REVERT: D 44 LYS cc_start: 0.8828 (tttt) cc_final: 0.8531 (mmmt) REVERT: D 46 MET cc_start: 0.8212 (mtt) cc_final: 0.7940 (mtt) REVERT: D 72 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8471 (ttm) REVERT: E 93 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8524 (mp0) REVERT: E 152 LEU cc_start: 0.9119 (tm) cc_final: 0.8880 (tt) REVERT: F 1 MET cc_start: 0.8094 (mmm) cc_final: 0.7783 (mmm) REVERT: F 309 TYR cc_start: 0.7913 (m-80) cc_final: 0.7499 (m-80) REVERT: F 368 VAL cc_start: 0.8442 (p) cc_final: 0.8238 (p) REVERT: F 452 ARG cc_start: 0.8183 (ptm-80) cc_final: 0.7765 (ptm-80) outliers start: 57 outliers final: 49 residues processed: 244 average time/residue: 0.2956 time to fit residues: 114.8693 Evaluate side-chains 258 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 206 time to evaluate : 2.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 364 HIS Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 443 HIS Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 402 HIS Chi-restraints excluded: chain B residue 403 THR Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 631 VAL Chi-restraints excluded: chain B residue 696 GLN Chi-restraints excluded: chain B residue 728 VAL Chi-restraints excluded: chain B residue 741 ASP Chi-restraints excluded: chain B residue 755 ASN Chi-restraints excluded: chain B residue 796 LEU Chi-restraints excluded: chain B residue 832 GLU Chi-restraints excluded: chain B residue 848 GLN Chi-restraints excluded: chain B residue 866 HIS Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 973 SER Chi-restraints excluded: chain B residue 1016 VAL Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 239 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 286 SER Chi-restraints excluded: chain C residue 289 GLU Chi-restraints excluded: chain C residue 356 SER Chi-restraints excluded: chain C residue 369 ILE Chi-restraints excluded: chain C residue 377 ILE Chi-restraints excluded: chain C residue 434 THR Chi-restraints excluded: chain D residue 40 HIS Chi-restraints excluded: chain D residue 65 ILE Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 43 TYR Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 88 SER Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 268 SER Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 350 THR Chi-restraints excluded: chain F residue 361 LEU Chi-restraints excluded: chain F residue 428 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 27 optimal weight: 0.0980 chunk 51 optimal weight: 0.9980 chunk 185 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 163 optimal weight: 0.0470 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 696 GLN B 755 ASN C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 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 = 0.3492 r_free = 0.3492 target = 0.112707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.098093 restraints weight = 35868.352| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.50 r_work: 0.3188 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.4513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 19481 Z= 0.182 Angle : 0.809 82.323 26545 Z= 0.329 Chirality : 0.051 1.516 2869 Planarity : 0.003 0.035 3318 Dihedral : 7.940 88.046 2646 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.79 % Allowed : 14.04 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.18), residues: 2347 helix: 1.43 (0.17), residues: 1082 sheet: 0.46 (0.45), residues: 147 loop : -1.57 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 795 HIS 0.003 0.001 HIS B 999 PHE 0.023 0.001 PHE F 286 TYR 0.023 0.001 TYR A 237 ARG 0.002 0.000 ARG D 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3839.89 seconds wall clock time: 71 minutes 7.90 seconds (4267.90 seconds total)