Starting phenix.real_space_refine on Wed Nov 20 06:42:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/11_2024/8c82_16469.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/11_2024/8c82_16469.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/11_2024/8c82_16469.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/11_2024/8c82_16469.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/11_2024/8c82_16469.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c82_16469/11_2024/8c82_16469.cif" } 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= 0.000 sd= 0.026 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 P 2 5.49 5 S 110 5.16 5 C 13534 2.51 5 N 3486 2.21 5 O 3938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21070 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1496 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 10, 'TRANS': 172} Chain: "B" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3943 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 25, 'TRANS': 479} Chain: "C" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4382 Classifications: {'peptide': 554} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 524} Chain: "D" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 569 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "E" Number of atoms: 1496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1496 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 10, 'TRANS': 172} Chain: "F" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3943 Classifications: {'peptide': 505} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 479} Chain: "G" Number of atoms: 4382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4382 Classifications: {'peptide': 554} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 524} Chain: "H" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 569 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'Z8A': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PLP': 1, 'Q7G': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 130 Unusual residues: {'Q7G': 1, 'Z8A': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 13.69, per 1000 atoms: 0.65 Number of scatterers: 21070 At special positions: 0 Unit cell: (106.26, 175.56, 122.892, 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) S 110 16.00 P 2 15.00 O 3938 8.00 N 3486 7.00 C 13534 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.16 Conformation dependent library (CDL) restraints added in 2.9 seconds 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4932 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 14 sheets defined 53.2% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.13 Creating SS restraints... Processing helix chain 'A' and resid 62 through 72 removed outlier: 4.130A pdb=" N LEU A 72 " --> pdb=" O ASP A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 removed outlier: 3.515A pdb=" N GLN A 82 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 103 removed outlier: 4.139A pdb=" N VAL A 90 " --> pdb=" O TRP A 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N PHE A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 128 Processing helix chain 'A' and resid 146 through 151 Processing helix chain 'A' and resid 152 through 155 Processing helix chain 'A' and resid 158 through 179 Proline residue: A 168 - end of helix removed outlier: 4.066A pdb=" N ALA A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 4.035A pdb=" N TRP A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 206 Proline residue: A 203 - end of helix Processing helix chain 'B' and resid 53 through 73 Processing helix chain 'B' and resid 81 through 85 removed outlier: 3.801A pdb=" N LYS B 85 " --> pdb=" O GLN B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 100 removed outlier: 3.662A pdb=" N ASP B 94 " --> pdb=" O PRO B 90 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 removed outlier: 4.888A pdb=" N TRP B 116 " --> pdb=" O ASP B 112 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N VAL B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 176 removed outlier: 3.586A pdb=" N GLU B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N VAL B 167 " --> pdb=" O PRO B 163 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS B 169 " --> pdb=" O LYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 204 removed outlier: 3.678A pdb=" N TYR B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.583A pdb=" N THR B 226 " --> pdb=" O PRO B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 239 through 250 removed outlier: 4.218A pdb=" N ARG B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 removed outlier: 3.777A pdb=" N LEU B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.831A pdb=" N LEU B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.762A pdb=" N HIS B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 339' Processing helix chain 'B' and resid 342 through 347 Processing helix chain 'B' and resid 368 through 379 removed outlier: 4.193A pdb=" N ILE B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 389 through 406 removed outlier: 3.813A pdb=" N VAL B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 4.136A pdb=" N GLN B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE B 424 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 432 removed outlier: 4.040A pdb=" N SER B 432 " --> pdb=" O SER B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 459 Processing helix chain 'B' and resid 461 through 476 Processing helix chain 'B' and resid 482 through 503 removed outlier: 3.622A pdb=" N GLU B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR B 503 " --> pdb=" O ALA B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.533A pdb=" N GLN B 516 " --> pdb=" O VAL B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 554 Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 33 through 37 removed outlier: 3.957A pdb=" N LEU C 37 " --> pdb=" O PRO C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 85 removed outlier: 4.059A pdb=" N SER C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 114 removed outlier: 3.582A pdb=" N ILE C 114 " --> pdb=" O TYR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 122 removed outlier: 5.360A pdb=" N ASP C 120 " --> pdb=" O ARG C 117 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE C 122 " --> pdb=" O ASP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 186 Processing helix chain 'C' and resid 200 through 215 removed outlier: 3.562A pdb=" N ILE C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 233 removed outlier: 4.321A pdb=" N PHE C 233 " --> pdb=" O ASN C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 272 through 286 Processing helix chain 'C' and resid 313 through 325 removed outlier: 3.506A pdb=" N LEU C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 removed outlier: 4.129A pdb=" N ILE C 349 " --> pdb=" O GLY C 345 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE C 350 " --> pdb=" O VAL C 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 345 through 350' Processing helix chain 'C' and resid 353 through 357 removed outlier: 3.588A pdb=" N VAL C 357 " --> pdb=" O PRO C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 4.026A pdb=" N ARG C 384 " --> pdb=" O TRP C 380 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 399 through 414 removed outlier: 3.550A pdb=" N LEU C 403 " --> pdb=" O PRO C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 444 Processing helix chain 'C' and resid 464 through 476 removed outlier: 4.094A pdb=" N ALA C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 523 Processing helix chain 'C' and resid 541 through 553 Proline residue: C 550 - end of helix Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 29 through 45 removed outlier: 3.820A pdb=" N HIS D 45 " --> pdb=" O THR D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 69 Processing helix chain 'E' and resid 62 through 72 removed outlier: 4.103A pdb=" N LEU E 72 " --> pdb=" O ASP E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 103 removed outlier: 4.305A pdb=" N VAL E 90 " --> pdb=" O TRP E 86 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE E 103 " --> pdb=" O PHE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 128 Processing helix chain 'E' and resid 146 through 151 Processing helix chain 'E' and resid 152 through 155 Processing helix chain 'E' and resid 158 through 179 Proline residue: E 168 - end of helix removed outlier: 3.807A pdb=" N ALA E 179 " --> pdb=" O SER E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.556A pdb=" N TRP E 188 " --> pdb=" O LYS E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 Processing helix chain 'F' and resid 53 through 73 removed outlier: 3.625A pdb=" N VAL F 59 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU F 60 " --> pdb=" O ARG F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 85 removed outlier: 4.136A pdb=" N LYS F 85 " --> pdb=" O GLN F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 100 Processing helix chain 'F' and resid 110 through 120 removed outlier: 4.885A pdb=" N TRP F 116 " --> pdb=" O ASP F 112 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL F 118 " --> pdb=" O GLN F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 161 through 176 Processing helix chain 'F' and resid 189 through 204 removed outlier: 3.661A pdb=" N TYR F 193 " --> pdb=" O GLN F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 216 Processing helix chain 'F' and resid 217 through 222 Processing helix chain 'F' and resid 223 through 226 removed outlier: 3.603A pdb=" N THR F 226 " --> pdb=" O PRO F 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 223 through 226' Processing helix chain 'F' and resid 239 through 250 removed outlier: 4.157A pdb=" N ARG F 250 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 279 removed outlier: 3.865A pdb=" N LEU F 264 " --> pdb=" O ASP F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 314 removed outlier: 3.827A pdb=" N LEU F 306 " --> pdb=" O PRO F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 339 removed outlier: 3.764A pdb=" N HIS F 338 " --> pdb=" O GLY F 334 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE F 339 " --> pdb=" O LEU F 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 334 through 339' Processing helix chain 'F' and resid 342 through 347 Processing helix chain 'F' and resid 368 through 379 removed outlier: 4.157A pdb=" N ILE F 377 " --> pdb=" O LEU F 373 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 384 Processing helix chain 'F' and resid 389 through 406 removed outlier: 3.822A pdb=" N VAL F 393 " --> pdb=" O PRO F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 407 through 427 removed outlier: 4.106A pdb=" N GLN F 411 " --> pdb=" O ASN F 407 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASP F 427 " --> pdb=" O SER F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 459 Processing helix chain 'F' and resid 461 through 476 Processing helix chain 'F' and resid 482 through 503 removed outlier: 3.635A pdb=" N GLU F 486 " --> pdb=" O ILE F 482 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN F 502 " --> pdb=" O HIS F 498 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR F 503 " --> pdb=" O ALA F 499 " (cutoff:3.500A) Processing helix chain 'F' and resid 513 through 517 removed outlier: 3.528A pdb=" N GLN F 516 " --> pdb=" O VAL F 513 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 554 Processing helix chain 'G' and resid 19 through 28 Processing helix chain 'G' and resid 33 through 37 removed outlier: 3.804A pdb=" N LEU G 37 " --> pdb=" O PRO G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 85 removed outlier: 3.962A pdb=" N SER G 61 " --> pdb=" O PRO G 57 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR G 68 " --> pdb=" O THR G 64 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 71 " --> pdb=" O ASN G 67 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE G 72 " --> pdb=" O TYR G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 94 removed outlier: 3.731A pdb=" N LEU G 91 " --> pdb=" O ASN G 88 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ASP G 92 " --> pdb=" O LYS G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 114 removed outlier: 3.649A pdb=" N ARG G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE G 114 " --> pdb=" O TYR G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 122 removed outlier: 5.395A pdb=" N ASP G 120 " --> pdb=" O ARG G 117 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE G 122 " --> pdb=" O ASP G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 186 Processing helix chain 'G' and resid 200 through 215 removed outlier: 3.553A pdb=" N ILE G 204 " --> pdb=" O THR G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 233 removed outlier: 4.338A pdb=" N PHE G 233 " --> pdb=" O ASN G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 250 through 261 Processing helix chain 'G' and resid 272 through 286 Processing helix chain 'G' and resid 313 through 325 removed outlier: 3.630A pdb=" N LEU G 317 " --> pdb=" O ASN G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 350 removed outlier: 4.128A pdb=" N ILE G 349 " --> pdb=" O GLY G 345 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE G 350 " --> pdb=" O VAL G 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 345 through 350' Processing helix chain 'G' and resid 378 through 389 removed outlier: 3.927A pdb=" N ARG G 384 " --> pdb=" O TRP G 380 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU G 387 " --> pdb=" O ASP G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 Processing helix chain 'G' and resid 399 through 414 Processing helix chain 'G' and resid 421 through 444 Processing helix chain 'G' and resid 464 through 476 removed outlier: 4.079A pdb=" N ALA G 468 " --> pdb=" O SER G 464 " (cutoff:3.500A) Processing helix chain 'G' and resid 504 through 523 Processing helix chain 'G' and resid 541 through 553 Proline residue: G 550 - end of helix Processing helix chain 'H' and resid 13 through 21 Processing helix chain 'H' and resid 25 through 45 removed outlier: 3.874A pdb=" N THR H 30 " --> pdb=" O GLY H 26 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE H 31 " --> pdb=" O ILE H 27 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS H 45 " --> pdb=" O THR H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 69 Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57 Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 124 removed outlier: 5.966A pdb=" N ILE B 133 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU B 506 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N PHE B 148 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 211 removed outlier: 3.516A pdb=" N ILE B 349 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LYS B 286 " --> pdb=" O ARG B 316 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE B 318 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE B 288 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ASP B 320 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N THR B 290 " --> pdb=" O ASP B 320 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 231 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL B 289 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 233 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N GLU B 291 " --> pdb=" O VAL B 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 434 through 436 removed outlier: 3.898A pdb=" N THR B 508 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 126 through 127 removed outlier: 4.113A pdb=" N ARG C 135 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ALA C 153 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 9.433A pdb=" N ILE C 140 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N SER C 151 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N HIS C 142 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR C 149 " --> pdb=" O HIS C 142 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ALA C 479 " --> pdb=" O PRO C 156 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET C 158 " --> pdb=" O ALA C 479 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 218 through 222 removed outlier: 3.652A pdb=" N GLY C 362 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE C 359 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N MET C 361 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N ILE C 297 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N PHE C 329 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE C 299 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N ASP C 331 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA C 301 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP C 246 " --> pdb=" O CYS C 300 " (cutoff:3.500A) removed outlier: 8.653A pdb=" N GLU C 302 " --> pdb=" O ASP C 246 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 455 through 460 removed outlier: 3.563A pdb=" N ARG C 494 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N VAL C 481 " --> pdb=" O ARG C 496 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 55 through 57 Processing sheet with id=AA9, first strand: chain 'F' and resid 123 through 124 removed outlier: 5.944A pdb=" N ILE F 133 " --> pdb=" O ASN F 146 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU F 142 " --> pdb=" O ARG F 137 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU F 506 " --> pdb=" O ASN F 146 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N PHE F 148 " --> pdb=" O LEU F 506 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 207 through 211 removed outlier: 3.513A pdb=" N ILE F 349 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LYS F 286 " --> pdb=" O ARG F 316 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE F 318 " --> pdb=" O LYS F 286 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE F 288 " --> pdb=" O PHE F 318 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ASP F 320 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N THR F 290 " --> pdb=" O ASP F 320 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL F 231 " --> pdb=" O PHE F 287 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL F 289 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL F 233 " --> pdb=" O VAL F 289 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N GLU F 291 " --> pdb=" O VAL F 233 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 434 through 436 removed outlier: 3.923A pdb=" N THR F 508 " --> pdb=" O LYS F 526 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 126 through 127 removed outlier: 4.117A pdb=" N ARG G 135 " --> pdb=" O THR G 127 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA G 153 " --> pdb=" O ASP G 138 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N ILE G 140 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N SER G 151 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N HIS G 142 " --> pdb=" O THR G 149 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR G 149 " --> pdb=" O HIS G 142 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ALA G 479 " --> pdb=" O PRO G 156 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N MET G 158 " --> pdb=" O ALA G 479 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 218 through 222 removed outlier: 3.705A pdb=" N GLY G 362 " --> pdb=" O TYR G 374 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE G 359 " --> pdb=" O LEU G 328 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET G 361 " --> pdb=" O ILE G 330 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE G 297 " --> pdb=" O TYR G 327 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N PHE G 329 " --> pdb=" O ILE G 297 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE G 299 " --> pdb=" O PHE G 329 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ASP G 331 " --> pdb=" O ILE G 299 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ALA G 301 " --> pdb=" O ASP G 331 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP G 246 " --> pdb=" O CYS G 300 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N GLU G 302 " --> pdb=" O ASP G 246 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 455 through 460 removed outlier: 3.684A pdb=" N ARG G 494 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL G 481 " --> pdb=" O ARG G 496 " (cutoff:3.500A) 984 hydrogen bonds defined for protein. 2829 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: 6.70 Time building geometry restraints manager: 5.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5160 1.33 - 1.45: 4111 1.45 - 1.57: 12125 1.57 - 1.69: 2 1.69 - 1.81: 166 Bond restraints: 21564 Sorted by residual: bond pdb=" N PRO B 86 " pdb=" CD PRO B 86 " ideal model delta sigma weight residual 1.473 1.539 -0.066 1.40e-02 5.10e+03 2.23e+01 bond pdb=" C4 Z8A E 301 " pdb=" O2 Z8A E 301 " ideal model delta sigma weight residual 1.412 1.355 0.057 2.00e-02 2.50e+03 8.05e+00 bond pdb=" N TYR G 485 " pdb=" CA TYR G 485 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.29e-02 6.01e+03 6.07e+00 bond pdb=" C3 Z8A E 301 " pdb=" O1 Z8A E 301 " ideal model delta sigma weight residual 1.413 1.365 0.048 2.00e-02 2.50e+03 5.66e+00 bond pdb=" N TYR C 485 " pdb=" CA TYR C 485 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.41e-02 5.03e+03 4.91e+00 ... (remaining 21559 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 28431 1.56 - 3.13: 646 3.13 - 4.69: 135 4.69 - 6.25: 36 6.25 - 7.82: 18 Bond angle restraints: 29266 Sorted by residual: angle pdb=" C GLN B 84 " pdb=" CA GLN B 84 " pdb=" CB GLN B 84 " ideal model delta sigma weight residual 110.88 104.00 6.88 1.57e+00 4.06e-01 1.92e+01 angle pdb=" N PHE D 48 " pdb=" CA PHE D 48 " pdb=" C PHE D 48 " ideal model delta sigma weight residual 114.31 109.01 5.30 1.29e+00 6.01e-01 1.69e+01 angle pdb=" CA LYS B 85 " pdb=" C LYS B 85 " pdb=" N PRO B 86 " ideal model delta sigma weight residual 118.44 124.52 -6.08 1.59e+00 3.96e-01 1.46e+01 angle pdb=" N PRO B 86 " pdb=" CA PRO B 86 " pdb=" CB PRO B 86 " ideal model delta sigma weight residual 103.25 107.00 -3.75 1.05e+00 9.07e-01 1.28e+01 angle pdb=" N PRO B 86 " pdb=" CA PRO B 86 " pdb=" C PRO B 86 " ideal model delta sigma weight residual 112.47 105.39 7.08 2.06e+00 2.36e-01 1.18e+01 ... (remaining 29261 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.40: 12714 29.40 - 58.79: 453 58.79 - 88.19: 72 88.19 - 117.59: 36 117.59 - 146.99: 11 Dihedral angle restraints: 13286 sinusoidal: 5630 harmonic: 7656 Sorted by residual: dihedral pdb=" CA LYS B 85 " pdb=" C LYS B 85 " pdb=" N PRO B 86 " pdb=" CA PRO B 86 " ideal model delta harmonic sigma weight residual -180.00 -53.94 -126.06 0 5.00e+00 4.00e-02 6.36e+02 dihedral pdb=" C4 Z8A E 301 " pdb=" C2 Z8A E 301 " pdb=" C3 Z8A E 301 " pdb=" N1 Z8A E 301 " ideal model delta sinusoidal sigma weight residual 304.92 157.93 146.99 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C16 Z8A E 301 " pdb=" C17 Z8A E 301 " pdb=" C18 Z8A E 301 " pdb=" C6 Z8A E 301 " ideal model delta sinusoidal sigma weight residual 59.65 -154.76 -145.59 1 3.00e+01 1.11e-03 1.95e+01 ... (remaining 13283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2969 0.067 - 0.134: 342 0.134 - 0.200: 10 0.200 - 0.267: 3 0.267 - 0.334: 4 Chirality restraints: 3328 Sorted by residual: chirality pdb=" C4 Z8A A 301 " pdb=" C3 Z8A A 301 " pdb=" C5 Z8A A 301 " pdb=" O2 Z8A A 301 " both_signs ideal model delta sigma weight residual False -2.29 -2.62 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" C51 Q7G E 302 " pdb=" C41 Q7G E 302 " pdb=" C61 Q7G E 302 " pdb=" O51 Q7G E 302 " both_signs ideal model delta sigma weight residual False -2.21 -2.52 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C51 Q7G C 602 " pdb=" C41 Q7G C 602 " pdb=" C61 Q7G C 602 " pdb=" O51 Q7G C 602 " both_signs ideal model delta sigma weight residual False -2.21 -2.51 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3325 not shown) Planarity restraints: 3688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 Q7G E 302 " -0.016 2.00e-02 2.50e+03 5.76e-02 4.15e+01 pdb=" C13 Q7G E 302 " -0.009 2.00e-02 2.50e+03 pdb=" C14 Q7G E 302 " -0.095 2.00e-02 2.50e+03 pdb=" C15 Q7G E 302 " 0.069 2.00e-02 2.50e+03 pdb=" C16 Q7G E 302 " 0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 212 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO A 213 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 213 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 213 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP G 556 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ASP G 556 " 0.031 2.00e-02 2.50e+03 pdb=" O ASP G 556 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS G 557 " -0.010 2.00e-02 2.50e+03 ... (remaining 3685 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 205 2.67 - 3.22: 19041 3.22 - 3.78: 29332 3.78 - 4.34: 38780 4.34 - 4.90: 68830 Nonbonded interactions: 156188 Sorted by model distance: nonbonded pdb=" OD1 ASP C 238 " pdb=" N LYS C 239 " model vdw 2.108 3.120 nonbonded pdb=" OD1 ASP G 238 " pdb=" N LYS G 239 " model vdw 2.220 3.120 nonbonded pdb=" OH TYR F 460 " pdb=" OE1 GLU F 488 " model vdw 2.240 3.040 nonbonded pdb=" O PHE B 491 " pdb=" OG SER B 494 " model vdw 2.250 3.040 nonbonded pdb=" O GLN F 77 " pdb=" OG SER F 80 " model vdw 2.280 3.040 ... (remaining 156183 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and (resid 39 through 221 or resid 301)) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 8 through 561 or resid 601)) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 4.940 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: 0.040 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 46.900 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.090 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 : 0.003 0.066 21564 Z= 0.200 Angle : 0.622 7.815 29266 Z= 0.329 Chirality : 0.044 0.334 3328 Planarity : 0.004 0.058 3688 Dihedral : 17.017 146.987 8354 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.09 % Allowed : 0.17 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 0.90 (0.16), residues: 2602 helix: 2.30 (0.16), residues: 1152 sheet: 0.69 (0.32), residues: 234 loop : -1.19 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 112 HIS 0.006 0.001 HIS G 78 PHE 0.030 0.001 PHE E 163 TYR 0.018 0.001 TYR G 510 ARG 0.004 0.000 ARG B 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 338 time to evaluate : 2.515 Fit side-chains revert: symmetry clash REVERT: A 86 TRP cc_start: 0.7150 (m-10) cc_final: 0.4899 (m-90) REVERT: A 163 PHE cc_start: 0.8676 (t80) cc_final: 0.8151 (t80) REVERT: A 209 ARG cc_start: 0.6282 (mmt-90) cc_final: 0.5941 (mmt-90) REVERT: A 220 GLN cc_start: 0.8094 (mt0) cc_final: 0.7841 (mt0) REVERT: B 265 GLU cc_start: 0.6925 (tt0) cc_final: 0.6705 (tt0) REVERT: B 274 GLN cc_start: 0.8238 (tp40) cc_final: 0.7957 (tm-30) REVERT: C 409 SER cc_start: 0.8404 (m) cc_final: 0.8108 (m) REVERT: C 534 ASP cc_start: 0.8245 (m-30) cc_final: 0.7626 (p0) REVERT: D 7 SER cc_start: 0.8826 (t) cc_final: 0.8590 (p) REVERT: E 174 VAL cc_start: 0.8418 (t) cc_final: 0.7986 (p) REVERT: E 209 ARG cc_start: 0.6422 (mmt-90) cc_final: 0.5949 (mpt180) REVERT: F 99 ASP cc_start: 0.8604 (t0) cc_final: 0.8142 (t0) REVERT: F 274 GLN cc_start: 0.8202 (tp40) cc_final: 0.7920 (tm-30) REVERT: G 97 ASP cc_start: 0.7805 (t0) cc_final: 0.7228 (t70) REVERT: G 409 SER cc_start: 0.8671 (t) cc_final: 0.8458 (t) REVERT: G 548 ARG cc_start: 0.7367 (tpp80) cc_final: 0.6691 (mtp180) REVERT: H 5 LYS cc_start: 0.7966 (tppt) cc_final: 0.7703 (tttm) outliers start: 2 outliers final: 0 residues processed: 340 average time/residue: 0.3571 time to fit residues: 184.5510 Evaluate side-chains 218 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 217 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 150 optimal weight: 0.5980 chunk 234 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 128 HIS E 189 ASN F 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21564 Z= 0.255 Angle : 0.606 8.683 29266 Z= 0.310 Chirality : 0.045 0.251 3328 Planarity : 0.005 0.052 3688 Dihedral : 11.792 148.820 3346 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.57 % Favored : 96.39 % Rotamer: Outliers : 1.25 % Allowed : 6.40 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 0.90 (0.16), residues: 2602 helix: 2.35 (0.16), residues: 1180 sheet: 0.22 (0.34), residues: 216 loop : -1.20 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 540 HIS 0.006 0.001 HIS G 203 PHE 0.020 0.002 PHE F 364 TYR 0.024 0.002 TYR C 510 ARG 0.006 0.001 ARG D 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 2.524 Fit side-chains REVERT: A 86 TRP cc_start: 0.7229 (m-10) cc_final: 0.4869 (m-90) REVERT: A 220 GLN cc_start: 0.7798 (mt0) cc_final: 0.7581 (mt0) REVERT: B 99 ASP cc_start: 0.8383 (t0) cc_final: 0.8054 (t0) REVERT: B 274 GLN cc_start: 0.8118 (tp40) cc_final: 0.7757 (tm-30) REVERT: C 409 SER cc_start: 0.8438 (m) cc_final: 0.8167 (m) REVERT: C 534 ASP cc_start: 0.8613 (m-30) cc_final: 0.7619 (p0) REVERT: C 540 TRP cc_start: 0.8623 (m-10) cc_final: 0.8381 (m-10) REVERT: D 7 SER cc_start: 0.8949 (t) cc_final: 0.8595 (p) REVERT: E 174 VAL cc_start: 0.8577 (t) cc_final: 0.8281 (p) REVERT: E 177 HIS cc_start: 0.8143 (OUTLIER) cc_final: 0.7362 (t-90) REVERT: E 209 ARG cc_start: 0.6781 (mmt-90) cc_final: 0.6477 (mpt180) REVERT: F 99 ASP cc_start: 0.8413 (t0) cc_final: 0.7997 (t0) REVERT: F 265 GLU cc_start: 0.6953 (tt0) cc_final: 0.6700 (tt0) REVERT: F 274 GLN cc_start: 0.8186 (tp40) cc_final: 0.7829 (tm-30) REVERT: F 463 GLU cc_start: 0.7646 (mp0) cc_final: 0.7386 (mp0) REVERT: G 97 ASP cc_start: 0.7893 (t0) cc_final: 0.7326 (t70) REVERT: G 116 MET cc_start: 0.7359 (tpp) cc_final: 0.7084 (tpp) REVERT: G 409 SER cc_start: 0.8795 (t) cc_final: 0.8587 (t) REVERT: G 548 ARG cc_start: 0.7298 (tpp80) cc_final: 0.6918 (mtp180) REVERT: G 556 ASP cc_start: 0.7722 (t70) cc_final: 0.7128 (t70) REVERT: H 5 LYS cc_start: 0.7979 (tppt) cc_final: 0.7624 (tttm) outliers start: 29 outliers final: 22 residues processed: 242 average time/residue: 0.3584 time to fit residues: 133.1012 Evaluate side-chains 225 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 2.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain E residue 177 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 499 MET Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 41 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 130 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 0.8980 chunk 159 optimal weight: 0.0050 chunk 64 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 237 GLN E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN F 477 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21564 Z= 0.234 Angle : 0.565 7.569 29266 Z= 0.288 Chirality : 0.044 0.348 3328 Planarity : 0.005 0.081 3688 Dihedral : 9.716 142.800 3346 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.42 % Favored : 96.54 % Rotamer: Outliers : 1.82 % Allowed : 8.95 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 0.96 (0.16), residues: 2602 helix: 2.45 (0.15), residues: 1170 sheet: 0.53 (0.32), residues: 244 loop : -1.30 (0.16), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 540 HIS 0.004 0.001 HIS G 203 PHE 0.021 0.002 PHE E 172 TYR 0.021 0.001 TYR C 510 ARG 0.004 0.000 ARG G 212 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 2.494 Fit side-chains REVERT: A 86 TRP cc_start: 0.7266 (m-10) cc_final: 0.4882 (m-90) REVERT: A 163 PHE cc_start: 0.8817 (t80) cc_final: 0.8608 (t80) REVERT: B 114 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: B 274 GLN cc_start: 0.8098 (tp40) cc_final: 0.7724 (tm-30) REVERT: B 279 LYS cc_start: 0.6334 (pttt) cc_final: 0.5782 (ttmt) REVERT: C 272 MET cc_start: 0.6899 (mmt) cc_final: 0.6472 (mmt) REVERT: C 409 SER cc_start: 0.8382 (m) cc_final: 0.8128 (m) REVERT: D 7 SER cc_start: 0.8926 (t) cc_final: 0.8533 (p) REVERT: E 174 VAL cc_start: 0.8594 (t) cc_final: 0.8280 (p) REVERT: E 177 HIS cc_start: 0.8116 (OUTLIER) cc_final: 0.7368 (t-90) REVERT: E 209 ARG cc_start: 0.6849 (mmt-90) cc_final: 0.6549 (mpt180) REVERT: F 99 ASP cc_start: 0.8424 (t0) cc_final: 0.8013 (t0) REVERT: F 114 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: F 274 GLN cc_start: 0.8133 (tp40) cc_final: 0.7730 (tm-30) REVERT: F 424 PHE cc_start: 0.8210 (OUTLIER) cc_final: 0.7963 (t80) REVERT: F 463 GLU cc_start: 0.7620 (mp0) cc_final: 0.7282 (mp0) REVERT: G 97 ASP cc_start: 0.7943 (t0) cc_final: 0.7380 (t70) REVERT: G 116 MET cc_start: 0.7325 (tpp) cc_final: 0.7074 (tpp) REVERT: G 272 MET cc_start: 0.6938 (mmt) cc_final: 0.6466 (mmt) REVERT: G 548 ARG cc_start: 0.7418 (tpp80) cc_final: 0.6845 (mtp180) REVERT: H 8 MET cc_start: 0.8380 (ttt) cc_final: 0.8062 (ttt) outliers start: 42 outliers final: 24 residues processed: 233 average time/residue: 0.3478 time to fit residues: 125.4561 Evaluate side-chains 218 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 177 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 424 PHE Chi-restraints excluded: chain F residue 470 SER Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 231 optimal weight: 0.2980 chunk 176 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 112 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 235 optimal weight: 2.9990 chunk 249 optimal weight: 0.0040 chunk 123 optimal weight: 0.1980 chunk 223 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 375 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21564 Z= 0.120 Angle : 0.488 7.364 29266 Z= 0.244 Chirality : 0.041 0.409 3328 Planarity : 0.004 0.084 3688 Dihedral : 9.095 142.418 3346 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.92 % Favored : 97.04 % Rotamer: Outliers : 1.43 % Allowed : 9.72 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 1.26 (0.17), residues: 2602 helix: 2.65 (0.15), residues: 1172 sheet: 0.59 (0.32), residues: 268 loop : -1.09 (0.17), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 540 HIS 0.002 0.000 HIS C 514 PHE 0.015 0.001 PHE A 163 TYR 0.019 0.001 TYR F 71 ARG 0.003 0.000 ARG G 212 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 2.420 Fit side-chains REVERT: A 86 TRP cc_start: 0.7230 (m-10) cc_final: 0.4841 (m-90) REVERT: B 274 GLN cc_start: 0.8052 (tp40) cc_final: 0.7703 (mt0) REVERT: C 409 SER cc_start: 0.8272 (m) cc_final: 0.8040 (m) REVERT: D 7 SER cc_start: 0.8861 (t) cc_final: 0.8457 (p) REVERT: E 174 VAL cc_start: 0.8603 (t) cc_final: 0.8289 (p) REVERT: E 177 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7325 (t-90) REVERT: F 99 ASP cc_start: 0.8390 (t0) cc_final: 0.8034 (t0) REVERT: F 114 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.8028 (mp10) REVERT: F 274 GLN cc_start: 0.8039 (tp40) cc_final: 0.7387 (tp40) REVERT: F 279 LYS cc_start: 0.5920 (pttt) cc_final: 0.5419 (ttmt) REVERT: F 424 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7687 (t80) REVERT: F 463 GLU cc_start: 0.7568 (mp0) cc_final: 0.7194 (mp0) REVERT: G 97 ASP cc_start: 0.7944 (t0) cc_final: 0.7324 (t70) REVERT: G 272 MET cc_start: 0.6690 (mmt) cc_final: 0.6319 (mmt) REVERT: G 548 ARG cc_start: 0.7418 (tpp80) cc_final: 0.6704 (mtp180) REVERT: G 552 ASP cc_start: 0.8331 (m-30) cc_final: 0.8048 (m-30) REVERT: H 8 MET cc_start: 0.8237 (ttt) cc_final: 0.7869 (ttt) outliers start: 33 outliers final: 14 residues processed: 233 average time/residue: 0.3347 time to fit residues: 122.4344 Evaluate side-chains 211 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 194 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 452 ASP Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain E residue 177 HIS Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 424 PHE Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 207 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 102 optimal weight: 0.0060 chunk 212 optimal weight: 2.9990 chunk 172 optimal weight: 0.0970 chunk 0 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21564 Z= 0.239 Angle : 0.551 10.163 29266 Z= 0.281 Chirality : 0.044 0.365 3328 Planarity : 0.004 0.088 3688 Dihedral : 8.868 136.422 3346 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.04 % Favored : 95.93 % Rotamer: Outliers : 1.77 % Allowed : 10.59 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 1.19 (0.17), residues: 2602 helix: 2.57 (0.15), residues: 1184 sheet: 0.63 (0.33), residues: 244 loop : -1.14 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 540 HIS 0.004 0.001 HIS G 203 PHE 0.030 0.002 PHE A 163 TYR 0.022 0.001 TYR G 510 ARG 0.003 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 194 time to evaluate : 2.704 Fit side-chains REVERT: B 114 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7873 (mp10) REVERT: B 274 GLN cc_start: 0.8062 (tp40) cc_final: 0.7705 (mt0) REVERT: B 279 LYS cc_start: 0.6014 (pttt) cc_final: 0.5563 (ttmt) REVERT: C 409 SER cc_start: 0.8362 (m) cc_final: 0.8117 (m) REVERT: D 7 SER cc_start: 0.8854 (t) cc_final: 0.8430 (p) REVERT: E 174 VAL cc_start: 0.8612 (t) cc_final: 0.8318 (p) REVERT: F 99 ASP cc_start: 0.8435 (t0) cc_final: 0.8073 (t0) REVERT: F 114 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7998 (mp10) REVERT: F 274 GLN cc_start: 0.8072 (tp40) cc_final: 0.7682 (tm-30) REVERT: F 279 LYS cc_start: 0.6075 (pttt) cc_final: 0.5585 (ttmt) REVERT: F 463 GLU cc_start: 0.7623 (mp0) cc_final: 0.7237 (mp0) REVERT: G 97 ASP cc_start: 0.7862 (t0) cc_final: 0.7302 (t70) REVERT: G 272 MET cc_start: 0.6996 (mmt) cc_final: 0.6555 (mmt) REVERT: G 548 ARG cc_start: 0.7415 (tpp80) cc_final: 0.6813 (mtp180) REVERT: H 8 MET cc_start: 0.8342 (ttt) cc_final: 0.8013 (ttt) outliers start: 41 outliers final: 31 residues processed: 225 average time/residue: 0.3380 time to fit residues: 118.8030 Evaluate side-chains 219 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 186 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 499 MET Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 83 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 146 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 249 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 115 optimal weight: 0.0770 chunk 20 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 131 optimal weight: 0.6980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 67 ASN ** G 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21564 Z= 0.164 Angle : 0.507 7.466 29266 Z= 0.257 Chirality : 0.042 0.354 3328 Planarity : 0.004 0.088 3688 Dihedral : 8.626 135.293 3346 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.86 % Allowed : 10.85 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 1.30 (0.17), residues: 2602 helix: 2.66 (0.15), residues: 1172 sheet: 0.71 (0.32), residues: 278 loop : -1.09 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 540 HIS 0.002 0.001 HIS F 421 PHE 0.023 0.001 PHE A 163 TYR 0.018 0.001 TYR F 71 ARG 0.003 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 2.532 Fit side-chains REVERT: B 114 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: B 274 GLN cc_start: 0.8052 (tp40) cc_final: 0.7698 (mt0) REVERT: B 377 ILE cc_start: 0.8358 (tp) cc_final: 0.8142 (mt) REVERT: C 107 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7716 (pm20) REVERT: D 7 SER cc_start: 0.8837 (t) cc_final: 0.8412 (p) REVERT: E 174 VAL cc_start: 0.8620 (t) cc_final: 0.8335 (p) REVERT: F 99 ASP cc_start: 0.8420 (t0) cc_final: 0.8069 (t0) REVERT: F 114 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7999 (mp10) REVERT: F 274 GLN cc_start: 0.8050 (tp40) cc_final: 0.7393 (tp40) REVERT: F 279 LYS cc_start: 0.5912 (pttt) cc_final: 0.5472 (ttmt) REVERT: F 463 GLU cc_start: 0.7591 (mp0) cc_final: 0.7196 (mp0) REVERT: G 97 ASP cc_start: 0.7803 (t0) cc_final: 0.7233 (t70) REVERT: G 272 MET cc_start: 0.6796 (mmt) cc_final: 0.6406 (mmt) REVERT: G 548 ARG cc_start: 0.7413 (tpp80) cc_final: 0.6794 (mtp180) REVERT: H 8 MET cc_start: 0.8328 (ttt) cc_final: 0.7988 (ttt) outliers start: 43 outliers final: 27 residues processed: 230 average time/residue: 0.3510 time to fit residues: 124.7871 Evaluate side-chains 220 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 190 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain E residue 177 HIS Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 283 ILE Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 240 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 210 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 248 optimal weight: 0.8980 chunk 155 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21564 Z= 0.225 Angle : 0.543 7.536 29266 Z= 0.278 Chirality : 0.044 0.454 3328 Planarity : 0.004 0.089 3688 Dihedral : 8.521 131.374 3346 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.77 % Allowed : 11.62 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 1.20 (0.17), residues: 2602 helix: 2.59 (0.15), residues: 1184 sheet: 0.61 (0.34), residues: 244 loop : -1.14 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 540 HIS 0.003 0.001 HIS G 203 PHE 0.024 0.001 PHE E 172 TYR 0.020 0.001 TYR G 510 ARG 0.003 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 2.434 Fit side-chains REVERT: B 114 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: B 274 GLN cc_start: 0.8071 (tp40) cc_final: 0.7710 (mt0) REVERT: B 377 ILE cc_start: 0.8376 (tp) cc_final: 0.8132 (mt) REVERT: C 107 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7714 (pm20) REVERT: D 7 SER cc_start: 0.8843 (t) cc_final: 0.8403 (p) REVERT: E 174 VAL cc_start: 0.8624 (t) cc_final: 0.8331 (p) REVERT: F 99 ASP cc_start: 0.8475 (t0) cc_final: 0.8111 (t0) REVERT: F 114 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8003 (mp10) REVERT: F 274 GLN cc_start: 0.8060 (tp40) cc_final: 0.7663 (tm-30) REVERT: F 279 LYS cc_start: 0.5968 (pttt) cc_final: 0.5510 (ttmt) REVERT: F 463 GLU cc_start: 0.7622 (mp0) cc_final: 0.7232 (mp0) REVERT: G 97 ASP cc_start: 0.7851 (t0) cc_final: 0.7632 (t70) REVERT: G 272 MET cc_start: 0.6919 (mmt) cc_final: 0.6484 (mmt) REVERT: G 548 ARG cc_start: 0.7424 (tpp80) cc_final: 0.6777 (mtp180) REVERT: H 8 MET cc_start: 0.8339 (ttt) cc_final: 0.7994 (ttt) outliers start: 41 outliers final: 32 residues processed: 223 average time/residue: 0.3435 time to fit residues: 118.8917 Evaluate side-chains 219 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 500 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 153 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 148 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 21564 Z= 0.319 Angle : 0.602 8.072 29266 Z= 0.311 Chirality : 0.047 0.486 3328 Planarity : 0.005 0.089 3688 Dihedral : 8.537 129.258 3346 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.16 % Allowed : 11.93 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 2602 helix: 2.53 (0.15), residues: 1170 sheet: 0.14 (0.35), residues: 216 loop : -1.28 (0.16), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 540 HIS 0.004 0.001 HIS G 203 PHE 0.037 0.002 PHE A 172 TYR 0.024 0.002 TYR G 510 ARG 0.003 0.000 ARG G 344 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 191 time to evaluate : 2.575 Fit side-chains REVERT: A 163 PHE cc_start: 0.8329 (t80) cc_final: 0.8051 (t80) REVERT: A 220 GLN cc_start: 0.7764 (mt0) cc_final: 0.7551 (mt0) REVERT: B 114 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7941 (mt0) REVERT: B 274 GLN cc_start: 0.8120 (tp40) cc_final: 0.7755 (mt0) REVERT: B 279 LYS cc_start: 0.6131 (pttt) cc_final: 0.5681 (ttmt) REVERT: B 377 ILE cc_start: 0.8472 (tp) cc_final: 0.8119 (mt) REVERT: B 427 ASP cc_start: 0.7238 (m-30) cc_final: 0.6950 (t70) REVERT: C 97 ASP cc_start: 0.8255 (t0) cc_final: 0.7964 (p0) REVERT: C 107 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7802 (pm20) REVERT: D 7 SER cc_start: 0.8839 (t) cc_final: 0.8402 (p) REVERT: E 174 VAL cc_start: 0.8611 (t) cc_final: 0.8330 (p) REVERT: F 99 ASP cc_start: 0.8417 (t0) cc_final: 0.8029 (t0) REVERT: F 114 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7862 (mt0) REVERT: F 274 GLN cc_start: 0.8151 (tp40) cc_final: 0.7766 (tm-30) REVERT: F 279 LYS cc_start: 0.6226 (pttt) cc_final: 0.5766 (ttmt) REVERT: F 463 GLU cc_start: 0.7661 (mp0) cc_final: 0.7288 (mp0) REVERT: G 272 MET cc_start: 0.7011 (mmt) cc_final: 0.6560 (mmt) REVERT: G 548 ARG cc_start: 0.7405 (tpp80) cc_final: 0.6737 (mtp180) REVERT: H 8 MET cc_start: 0.8363 (ttt) cc_final: 0.8038 (ttt) outliers start: 50 outliers final: 39 residues processed: 235 average time/residue: 0.3430 time to fit residues: 125.3924 Evaluate side-chains 230 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 2.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 409 SER Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 238 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 231 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 209 optimal weight: 0.4980 chunk 219 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21564 Z= 0.180 Angle : 0.525 7.452 29266 Z= 0.268 Chirality : 0.044 0.455 3328 Planarity : 0.004 0.087 3688 Dihedral : 8.276 128.755 3346 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.90 % Allowed : 12.45 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 1.18 (0.17), residues: 2602 helix: 2.53 (0.15), residues: 1184 sheet: 0.70 (0.32), residues: 274 loop : -1.17 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 86 HIS 0.002 0.001 HIS G 203 PHE 0.039 0.001 PHE A 172 TYR 0.018 0.001 TYR F 71 ARG 0.003 0.000 ARG C 212 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 2.501 Fit side-chains REVERT: A 220 GLN cc_start: 0.7768 (mt0) cc_final: 0.7554 (mt0) REVERT: B 114 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7890 (mt0) REVERT: B 274 GLN cc_start: 0.8097 (tp40) cc_final: 0.7747 (mt0) REVERT: B 377 ILE cc_start: 0.8378 (tp) cc_final: 0.8055 (mt) REVERT: B 463 GLU cc_start: 0.7589 (mp0) cc_final: 0.7226 (mp0) REVERT: C 97 ASP cc_start: 0.8276 (t0) cc_final: 0.8002 (p0) REVERT: C 107 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7766 (pm20) REVERT: D 7 SER cc_start: 0.8826 (t) cc_final: 0.8387 (p) REVERT: E 174 VAL cc_start: 0.8632 (t) cc_final: 0.8348 (p) REVERT: F 99 ASP cc_start: 0.8374 (t0) cc_final: 0.7996 (t0) REVERT: F 114 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7946 (mt0) REVERT: F 274 GLN cc_start: 0.8086 (tp40) cc_final: 0.7696 (tm-30) REVERT: F 279 LYS cc_start: 0.5905 (pttt) cc_final: 0.5497 (ttmt) REVERT: F 463 GLU cc_start: 0.7622 (mp0) cc_final: 0.7256 (mp0) REVERT: G 97 ASP cc_start: 0.7421 (t70) cc_final: 0.7056 (t70) REVERT: G 272 MET cc_start: 0.6822 (mmt) cc_final: 0.6462 (mmt) REVERT: G 548 ARG cc_start: 0.7365 (tpp80) cc_final: 0.6693 (mtp180) REVERT: H 8 MET cc_start: 0.8299 (ttt) cc_final: 0.7945 (ttt) outliers start: 44 outliers final: 40 residues processed: 225 average time/residue: 0.3514 time to fit residues: 122.3843 Evaluate side-chains 224 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 426 SER Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 245 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 236 optimal weight: 0.6980 chunk 204 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 158 optimal weight: 0.8980 chunk 125 optimal weight: 30.0000 chunk 162 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21564 Z= 0.232 Angle : 0.553 7.629 29266 Z= 0.283 Chirality : 0.045 0.482 3328 Planarity : 0.004 0.086 3688 Dihedral : 8.193 125.530 3346 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.82 % Allowed : 12.53 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 1.09 (0.17), residues: 2602 helix: 2.60 (0.15), residues: 1172 sheet: 0.29 (0.33), residues: 254 loop : -1.20 (0.17), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 86 HIS 0.003 0.001 HIS G 203 PHE 0.043 0.002 PHE A 172 TYR 0.020 0.001 TYR C 510 ARG 0.004 0.000 ARG C 212 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5204 Ramachandran restraints generated. 2602 Oldfield, 0 Emsley, 2602 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 183 time to evaluate : 2.404 Fit side-chains REVERT: B 114 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7900 (mt0) REVERT: B 274 GLN cc_start: 0.8101 (tp40) cc_final: 0.7753 (mt0) REVERT: B 377 ILE cc_start: 0.8409 (tp) cc_final: 0.8073 (mt) REVERT: B 427 ASP cc_start: 0.7229 (m-30) cc_final: 0.6942 (t70) REVERT: C 97 ASP cc_start: 0.8281 (t0) cc_final: 0.7968 (p0) REVERT: C 107 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: D 7 SER cc_start: 0.8835 (t) cc_final: 0.8392 (p) REVERT: E 174 VAL cc_start: 0.8611 (t) cc_final: 0.8306 (p) REVERT: F 99 ASP cc_start: 0.8383 (t0) cc_final: 0.7999 (t0) REVERT: F 114 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7900 (mt0) REVERT: F 274 GLN cc_start: 0.8092 (tp40) cc_final: 0.7710 (tm-30) REVERT: F 279 LYS cc_start: 0.5978 (pttt) cc_final: 0.5564 (ttmt) REVERT: G 272 MET cc_start: 0.6932 (mmt) cc_final: 0.6528 (mmt) REVERT: G 548 ARG cc_start: 0.7386 (tpp80) cc_final: 0.6712 (mtp180) REVERT: H 8 MET cc_start: 0.8303 (ttt) cc_final: 0.7972 (ttt) outliers start: 42 outliers final: 39 residues processed: 220 average time/residue: 0.3475 time to fit residues: 118.6441 Evaluate side-chains 223 residues out of total 2314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 181 time to evaluate : 2.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 191 PHE Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain B residue 107 ASP Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 422 ASP Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 214 ILE Chi-restraints excluded: chain C residue 260 SER Chi-restraints excluded: chain C residue 342 THR Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 417 ILE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain F residue 111 THR Chi-restraints excluded: chain F residue 114 GLN Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 205 THR Chi-restraints excluded: chain F residue 327 VAL Chi-restraints excluded: chain F residue 331 THR Chi-restraints excluded: chain F residue 494 SER Chi-restraints excluded: chain G residue 104 SER Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 260 SER Chi-restraints excluded: chain G residue 342 THR Chi-restraints excluded: chain G residue 375 ILE Chi-restraints excluded: chain G residue 417 ILE Chi-restraints excluded: chain G residue 481 VAL Chi-restraints excluded: chain G residue 500 SER Chi-restraints excluded: chain H residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 258 random chunks: chunk 218 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 179 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.189051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.142618 restraints weight = 26823.472| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.57 r_work: 0.3616 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21564 Z= 0.261 Angle : 0.568 7.973 29266 Z= 0.293 Chirality : 0.045 0.462 3328 Planarity : 0.005 0.086 3688 Dihedral : 8.164 123.816 3346 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.86 % Allowed : 12.62 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.76 % 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: 0.98 (0.17), residues: 2602 helix: 2.56 (0.15), residues: 1170 sheet: 0.25 (0.36), residues: 212 loop : -1.28 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 540 HIS 0.004 0.001 HIS G 203 PHE 0.040 0.002 PHE A 172 TYR 0.021 0.001 TYR G 510 ARG 0.004 0.000 ARG C 212 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4237.53 seconds wall clock time: 78 minutes 52.74 seconds (4732.74 seconds total)