Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 00:22:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/04_2023/6btm_7286_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/04_2023/6btm_7286.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/04_2023/6btm_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_7286/04_2023/6btm_7286_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/04_2023/6btm_7286_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/04_2023/6btm_7286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/04_2023/6btm_7286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/04_2023/6btm_7286_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6btm_7286/04_2023/6btm_7286_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 10.13, per 1000 atoms: 0.54 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: 7.77 Conformation dependent library (CDL) restraints added in 3.1 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: 2.00 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: 5.14 Time building geometry restraints manager: 8.31 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: 11054 34.27 - 68.54: 104 68.54 - 102.80: 17 102.80 - 137.07: 1 137.07 - 171.34: 2 Dihedral angle restraints: 11178 sinusoidal: 4337 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 11175 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: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.380 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 50.590 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.270 ------------------------------------------------------------------------------- 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 : 11.306 171.339 6782 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 % 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 *********************** 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 : 2.456 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 499 average time/residue: 0.3324 time to fit residues: 253.2398 Evaluate side-chains 244 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0631 ------------------------------------------------------------------------------- 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: 1.9990 chunk 177 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 60 optimal weight: 0.0470 chunk 119 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 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: 0.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- 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 849 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 GLN B 872 ASN B 963 ASN B 982 ASN C 91 HIS D 142 HIS ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.111 19481 Z= 0.201 Angle : 0.879 85.295 26545 Z= 0.379 Chirality : 0.050 1.234 2869 Planarity : 0.004 0.053 3318 Dihedral : 9.825 170.799 2634 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.20 % Favored : 94.76 % Rotamer Outliers : 2.69 % 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: -1.32 (0.17), residues: 2347 helix: 0.11 (0.16), residues: 1112 sheet: -0.40 (0.43), residues: 161 loop : -2.05 (0.18), residues: 1074 *********************** 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 339 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 286 time to evaluate : 2.328 Fit side-chains outliers start: 53 outliers final: 29 residues processed: 319 average time/residue: 0.2729 time to fit residues: 140.4075 Evaluate side-chains 254 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 225 time to evaluate : 2.087 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1752 time to fit residues: 12.3163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 176 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 chunk 58 optimal weight: 9.9990 chunk 212 optimal weight: 2.9990 chunk 229 optimal weight: 4.9990 chunk 189 optimal weight: 0.7980 chunk 211 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** B 380 GLN B 453 HIS B 753 HIS B 848 GLN B 849 HIS B 982 ASN C 91 HIS C 239 HIS D 29 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: 0.7757 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.106 19481 Z= 0.281 Angle : 0.871 80.515 26545 Z= 0.374 Chirality : 0.054 1.574 2869 Planarity : 0.004 0.048 3318 Dihedral : 9.219 151.769 2634 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.18 % Favored : 93.78 % Rotamer Outliers : 1.88 % 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: -0.95 (0.17), residues: 2347 helix: 0.61 (0.16), residues: 1085 sheet: -0.10 (0.43), residues: 157 loop : -2.05 (0.17), residues: 1105 *********************** 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 268 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 231 time to evaluate : 2.371 Fit side-chains outliers start: 37 outliers final: 22 residues processed: 260 average time/residue: 0.3026 time to fit residues: 125.5088 Evaluate side-chains 217 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 195 time to evaluate : 2.446 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2016 time to fit residues: 11.8159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 110 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 101 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 213 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 202 optimal weight: 0.9980 chunk 60 optimal weight: 0.0870 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 761 ASN B 777 ASN ** C 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.105 19481 Z= 0.176 Angle : 0.808 81.673 26545 Z= 0.333 Chirality : 0.051 1.547 2869 Planarity : 0.003 0.042 3318 Dihedral : 8.792 146.691 2634 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 1.12 % 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: -0.60 (0.18), residues: 2347 helix: 0.87 (0.16), residues: 1101 sheet: 0.28 (0.44), residues: 147 loop : -1.89 (0.18), residues: 1099 *********************** 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 258 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 236 time to evaluate : 2.213 Fit side-chains outliers start: 22 outliers final: 11 residues processed: 247 average time/residue: 0.2823 time to fit residues: 112.0502 Evaluate side-chains 210 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 2.238 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1919 time to fit residues: 6.7041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 0.3980 chunk 128 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 168 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 156 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 848 GLN B 963 ASN C 91 HIS C 239 HIS ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.4003 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= 0.238 Angle : 0.832 81.698 26545 Z= 0.344 Chirality : 0.052 1.547 2869 Planarity : 0.003 0.039 3318 Dihedral : 8.598 136.401 2634 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.92 % Favored : 94.03 % Rotamer Outliers : 1.47 % 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: -0.55 (0.18), residues: 2347 helix: 0.96 (0.17), residues: 1095 sheet: 0.15 (0.43), residues: 157 loop : -1.90 (0.18), residues: 1095 *********************** 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 226 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 2.439 Fit side-chains outliers start: 29 outliers final: 17 residues processed: 221 average time/residue: 0.3025 time to fit residues: 106.5532 Evaluate side-chains 201 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 2.238 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1774 time to fit residues: 8.7691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 10.0000 chunk 203 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 104 optimal weight: 0.5980 chunk 18 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 chunk 118 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 GLN B 630 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 HIS C 91 HIS C 239 HIS ** E 33 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4234 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= 0.226 Angle : 0.822 81.914 26545 Z= 0.339 Chirality : 0.052 1.534 2869 Planarity : 0.003 0.038 3318 Dihedral : 8.367 119.161 2634 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer Outliers : 1.67 % 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: -0.41 (0.18), residues: 2347 helix: 1.11 (0.17), residues: 1085 sheet: 0.51 (0.44), residues: 147 loop : -1.88 (0.18), residues: 1115 *********************** 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 240 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 207 time to evaluate : 2.347 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 23 residues processed: 226 average time/residue: 0.3130 time to fit residues: 112.0710 Evaluate side-chains 211 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 188 time to evaluate : 2.144 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1909 time to fit residues: 10.9433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 128 optimal weight: 0.9990 chunk 165 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 225 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 HIS B 505 ASN ** B 696 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS ** E 33 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4388 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= 0.172 Angle : 0.812 82.194 26545 Z= 0.330 Chirality : 0.051 1.522 2869 Planarity : 0.003 0.037 3318 Dihedral : 8.142 102.004 2634 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 0.66 % 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: 1077 sheet: 0.51 (0.44), residues: 148 loop : -1.76 (0.18), residues: 1122 *********************** 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 227 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 214 time to evaluate : 2.309 Fit side-chains outliers start: 13 outliers final: 3 residues processed: 223 average time/residue: 0.3201 time to fit residues: 113.6061 Evaluate side-chains 200 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 197 time to evaluate : 2.323 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1946 time to fit residues: 4.1652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 205 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 133 ASN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS ** 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: 0.7727 moved from start: 0.4517 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= 0.166 Angle : 0.812 82.359 26545 Z= 0.329 Chirality : 0.051 1.513 2869 Planarity : 0.003 0.035 3318 Dihedral : 7.914 87.863 2634 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.86 % 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: -0.10 (0.18), residues: 2347 helix: 1.35 (0.17), residues: 1079 sheet: 0.56 (0.44), residues: 148 loop : -1.66 (0.18), residues: 1120 *********************** 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 225 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 208 time to evaluate : 2.302 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 216 average time/residue: 0.3049 time to fit residues: 104.2809 Evaluate side-chains 208 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 2.365 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2130 time to fit residues: 8.1223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.8980 chunk 197 optimal weight: 7.9990 chunk 210 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 64 optimal weight: 0.0070 chunk 189 optimal weight: 0.0670 chunk 198 optimal weight: 0.9980 chunk 209 optimal weight: 2.9990 chunk 138 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 HIS C 239 HIS ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.4655 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= 0.164 Angle : 0.810 82.412 26545 Z= 0.327 Chirality : 0.050 1.510 2869 Planarity : 0.003 0.034 3318 Dihedral : 7.622 88.194 2634 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer Outliers : 0.41 % 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: 1079 sheet: 0.40 (0.44), residues: 154 loop : -1.58 (0.19), residues: 1114 *********************** 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 221 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 213 time to evaluate : 2.346 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 218 average time/residue: 0.3079 time to fit residues: 107.5485 Evaluate side-chains 204 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 201 time to evaluate : 2.265 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2012 time to fit residues: 4.1433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 0.6980 chunk 135 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 214 optimal weight: 2.9990 chunk 185 optimal weight: 0.0670 chunk 19 optimal weight: 0.0060 chunk 143 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 overall best weight: 0.3734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN B 696 GLN ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN B1013 HIS C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7680 moved from start: 0.4799 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= 0.160 Angle : 0.813 82.592 26545 Z= 0.326 Chirality : 0.050 1.502 2869 Planarity : 0.003 0.034 3318 Dihedral : 7.410 88.548 2634 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 0.30 % 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: 0.11 (0.18), residues: 2347 helix: 1.51 (0.17), residues: 1076 sheet: 0.55 (0.45), residues: 143 loop : -1.50 (0.18), residues: 1128 ********************** 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 230 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 224 time to evaluate : 2.216 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 226 average time/residue: 0.3069 time to fit residues: 111.4672 Evaluate side-chains 217 residues out of total 1987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 213 time to evaluate : 2.359 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2225 time to fit residues: 4.5039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 171 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 0.9990 chunk 185 optimal weight: 0.0370 chunk 77 optimal weight: 0.0030 chunk 190 optimal weight: 5.9990 chunk 23 optimal weight: 0.0870 chunk 34 optimal weight: 9.9990 chunk 163 optimal weight: 7.9990 overall best weight: 0.4048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN C 91 HIS ** C 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 GLN F 135 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.108769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.094596 restraints weight = 34441.766| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.41 r_work: 0.3097 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4886 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= 0.161 Angle : 0.812 82.639 26545 Z= 0.327 Chirality : 0.050 1.495 2869 Planarity : 0.003 0.034 3318 Dihedral : 7.353 88.644 2634 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.30 % 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: 0.16 (0.18), residues: 2347 helix: 1.54 (0.17), residues: 1077 sheet: 0.58 (0.46), residues: 143 loop : -1.45 (0.19), residues: 1127 =============================================================================== Job complete usr+sys time: 3848.96 seconds wall clock time: 70 minutes 51.59 seconds (4251.59 seconds total)