Starting phenix.real_space_refine on Sun Feb 18 05:34:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfi_25873/02_2024/7tfi_25873_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfi_25873/02_2024/7tfi_25873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfi_25873/02_2024/7tfi_25873.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfi_25873/02_2024/7tfi_25873.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfi_25873/02_2024/7tfi_25873_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tfi_25873/02_2024/7tfi_25873_updated.pdb" } resolution = 3.41 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= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 370 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Se 18 7.20 5 P 56 5.49 5 Mg 4 5.21 5 S 81 5.16 5 C 12861 2.51 5 N 3507 2.21 5 O 4046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 369": "OE1" <-> "OE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "B GLU 301": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 289": "OE1" <-> "OE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "E GLU 142": "OE1" <-> "OE2" Residue "E GLU 311": "OE1" <-> "OE2" Residue "G GLU 55": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20573 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3097 Classifications: {'peptide': 391} Link IDs: {'PTRANS': 14, 'TRANS': 376} Chain breaks: 2 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2510 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 9, 'TRANS': 310} Chain: "C" Number of atoms: 2615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2615 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain: "D" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2622 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 318} Chain: "E" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2694 Classifications: {'peptide': 341} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 326} Chain breaks: 1 Chain: "F" Number of atoms: 2011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2011 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain: "G" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2014 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "H" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "I" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 449 Classifications: {'DNA': 22} Link IDs: {'rna3p': 21} Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.19, per 1000 atoms: 0.54 Number of scatterers: 20573 At special positions: 0 Unit cell: (120.06, 123.372, 144.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Se 18 33.99 S 81 16.00 P 56 15.00 Mg 4 11.99 O 4046 8.00 N 3507 7.00 C 12861 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.77 Conformation dependent library (CDL) restraints added in 3.6 seconds 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4720 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 102 helices and 18 sheets defined 43.8% alpha, 11.9% beta 15 base pairs and 32 stacking pairs defined. Time for finding SS restraints: 8.69 Creating SS restraints... Processing helix chain 'A' and resid 298 through 301 No H-bonds generated for 'chain 'A' and resid 298 through 301' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 314 through 324 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 359 through 369 Processing helix chain 'A' and resid 385 through 389 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 401 through 406 Processing helix chain 'A' and resid 436 through 445 Processing helix chain 'A' and resid 461 through 468 Proline residue: A 465 - end of helix removed outlier: 4.469A pdb=" N ARG A 468 " --> pdb=" O PRO A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 493 Processing helix chain 'A' and resid 500 through 510 removed outlier: 4.394A pdb=" N ASP A 504 " --> pdb=" O PRO A 500 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 527 removed outlier: 4.259A pdb=" N THR A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 542 Processing helix chain 'A' and resid 551 through 559 Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 574 through 583 removed outlier: 3.530A pdb=" N ASP A 583 " --> pdb=" O ALA A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 595 removed outlier: 3.731A pdb=" N ASN A 595 " --> pdb=" O MET A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 631 removed outlier: 3.686A pdb=" N CYS A 620 " --> pdb=" O GLU A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 654 removed outlier: 3.596A pdb=" N LEU A 641 " --> pdb=" O TRP A 638 " (cutoff:3.500A) Proline residue: A 642 - end of helix removed outlier: 3.549A pdb=" N SER A 648 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL A 650 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR A 651 " --> pdb=" O SER A 648 " (cutoff:3.500A) Proline residue: A 652 - end of helix Processing helix chain 'A' and resid 669 through 690 Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 55 through 66 Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.992A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 157 removed outlier: 3.753A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 232 through 240 Processing helix chain 'B' and resid 245 through 256 Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 282 through 301 Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 90 through 102 removed outlier: 3.831A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.845A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 No H-bonds generated for 'chain 'C' and resid 155 through 158' Processing helix chain 'C' and resid 171 through 185 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 206 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 252 Processing helix chain 'C' and resid 256 through 269 Processing helix chain 'C' and resid 277 through 286 Processing helix chain 'C' and resid 293 through 311 Processing helix chain 'C' and resid 316 through 330 Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 43 through 54 Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 88 through 91 No H-bonds generated for 'chain 'D' and resid 88 through 91' Processing helix chain 'D' and resid 103 through 115 removed outlier: 4.077A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 159 removed outlier: 4.450A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 198 through 208 Processing helix chain 'D' and resid 216 through 223 Processing helix chain 'D' and resid 229 through 245 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 265 through 277 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 297 through 308 Processing helix chain 'D' and resid 316 through 334 Processing helix chain 'D' and resid 339 through 351 Processing helix chain 'E' and resid 20 through 35 removed outlier: 4.219A pdb=" N GLN E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 102 through 118 removed outlier: 3.712A pdb=" N ASP E 105 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ARG E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE E 107 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLU E 111 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 112 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 113 " --> pdb=" O GLN E 110 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 116 " --> pdb=" O LEU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 150 through 160 removed outlier: 4.052A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU E 159 " --> pdb=" O ARG E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 208 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 Processing helix chain 'E' and resid 296 through 308 Processing helix chain 'E' and resid 315 through 334 Processing helix chain 'E' and resid 338 through 353 Processing helix chain 'F' and resid 9 through 22 removed outlier: 3.721A pdb=" N LYS F 13 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ARG F 14 " --> pdb=" O SER F 10 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY F 18 " --> pdb=" O ARG F 14 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP F 21 " --> pdb=" O ASP F 17 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS F 22 " --> pdb=" O GLY F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 80 Processing helix chain 'F' and resid 141 through 154 removed outlier: 3.583A pdb=" N LEU F 154 " --> pdb=" O ASP F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 221 removed outlier: 4.172A pdb=" N GLY F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER F 219 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N SER F 220 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU F 221 " --> pdb=" O LYS F 217 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 19 removed outlier: 3.943A pdb=" N PHE G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 56 No H-bonds generated for 'chain 'G' and resid 54 through 56' Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 153 removed outlier: 3.985A pdb=" N GLN G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 220 removed outlier: 3.982A pdb=" N GLY G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N SER G 219 " --> pdb=" O ILE G 215 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N SER G 220 " --> pdb=" O ILE G 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 19 Processing helix chain 'H' and resid 72 through 81 Processing helix chain 'H' and resid 141 through 153 removed outlier: 4.081A pdb=" N GLN H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 163 through 165 No H-bonds generated for 'chain 'H' and resid 163 through 165' Processing helix chain 'H' and resid 209 through 220 removed outlier: 4.262A pdb=" N ASP H 214 " --> pdb=" O LYS H 210 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY H 218 " --> pdb=" O ASP H 214 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER H 219 " --> pdb=" O ILE H 215 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N SER H 220 " --> pdb=" O ILE H 216 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 471 through 474 removed outlier: 3.723A pdb=" N TYR A 352 " --> pdb=" O ILE A 473 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU A 451 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N LEU A 351 " --> pdb=" O LEU A 451 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU A 453 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET A 423 " --> pdb=" O ILE A 452 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP A 373 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE A 422 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU A 375 " --> pdb=" O ILE A 422 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.515A pdb=" N SER B 48 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 45 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 162 through 166 removed outlier: 3.917A pdb=" N GLY C 53 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 185 through 189 removed outlier: 6.367A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 186 through 190 removed outlier: 6.021A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS E 93 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER E 90 " --> pdb=" O HIS E 93 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 71 through 73 Processing sheet with id= G, first strand: chain 'F' and resid 35 through 38 removed outlier: 4.226A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 47 through 49 removed outlier: 3.584A pdb=" N GLN F 247 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU F 250 " --> pdb=" O ALA F 235 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP F 240 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG F 224 " --> pdb=" O ASP F 240 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR F 136 " --> pdb=" O GLU F 198 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 89 through 91 removed outlier: 3.914A pdb=" N ILE F 91 " --> pdb=" O ILE F 100 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ILE F 100 " --> pdb=" O ILE F 91 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 158 through 160 Processing sheet with id= K, first strand: chain 'F' and resid 167 through 172 Processing sheet with id= L, first strand: chain 'G' and resid 114 through 117 removed outlier: 3.728A pdb=" N GLU G 104 " --> pdb=" O THR G 87 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR G 87 " --> pdb=" O GLU G 104 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU G 88 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU G 59 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 66 through 68 removed outlier: 3.751A pdb=" N SER G 49 " --> pdb=" O GLN G 247 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 135 through 140 Processing sheet with id= O, first strand: chain 'G' and resid 157 through 160 Processing sheet with id= P, first strand: chain 'H' and resid 59 through 61 removed outlier: 3.693A pdb=" N PHE H 103 " --> pdb=" O ALA H 112 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 66 through 68 removed outlier: 3.675A pdb=" N ILE H 35 " --> pdb=" O ILE H 52 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP H 240 " --> pdb=" O ARG H 224 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG H 224 " --> pdb=" O ASP H 240 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.830A pdb=" N LEU H 205 " --> pdb=" O ILE H 160 " (cutoff:3.500A) 829 hydrogen bonds defined for protein. 2355 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 33 hydrogen bonds 66 hydrogen bond angles 0 basepair planarities 15 basepair parallelities 32 stacking parallelities Total time for adding SS restraints: 7.60 Time building geometry restraints manager: 9.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 6749 1.36 - 1.51: 5570 1.51 - 1.66: 8514 1.66 - 1.80: 91 1.80 - 1.95: 64 Bond restraints: 20988 Sorted by residual: bond pdb=" CB TRP C 256 " pdb=" CG TRP C 256 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.95e+00 bond pdb=" C TYR E 161 " pdb=" N SER E 162 " ideal model delta sigma weight residual 1.332 1.315 0.017 1.40e-02 5.10e+03 1.54e+00 bond pdb=" C3' DT J 19 " pdb=" O3' DT J 19 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.30e+00 bond pdb=" CG1 ILE H 215 " pdb=" CD1 ILE H 215 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.15e+00 bond pdb=" C4 ADP E 500 " pdb=" C5 ADP E 500 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 ... (remaining 20983 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.54: 524 105.54 - 113.22: 11933 113.22 - 120.91: 10048 120.91 - 128.59: 5923 128.59 - 136.27: 126 Bond angle restraints: 28554 Sorted by residual: angle pdb=" C ILE C 275 " pdb=" N ASP C 276 " pdb=" CA ASP C 276 " ideal model delta sigma weight residual 121.54 128.95 -7.41 1.91e+00 2.74e-01 1.50e+01 angle pdb=" N VAL A 469 " pdb=" CA VAL A 469 " pdb=" C VAL A 469 " ideal model delta sigma weight residual 113.20 109.53 3.67 9.60e-01 1.09e+00 1.46e+01 angle pdb=" CA LYS G 164 " pdb=" CB LYS G 164 " pdb=" CG LYS G 164 " ideal model delta sigma weight residual 114.10 120.45 -6.35 2.00e+00 2.50e-01 1.01e+01 angle pdb=" N GLU B 287 " pdb=" CA GLU B 287 " pdb=" CB GLU B 287 " ideal model delta sigma weight residual 110.28 114.87 -4.59 1.55e+00 4.16e-01 8.79e+00 angle pdb=" N GLU E 281 " pdb=" CA GLU E 281 " pdb=" CB GLU E 281 " ideal model delta sigma weight residual 110.28 114.45 -4.17 1.55e+00 4.16e-01 7.24e+00 ... (remaining 28549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.67: 12046 26.67 - 53.33: 696 53.33 - 80.00: 52 80.00 - 106.66: 7 106.66 - 133.33: 3 Dihedral angle restraints: 12804 sinusoidal: 5555 harmonic: 7249 Sorted by residual: dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 -173.80 113.79 1 2.00e+01 2.50e-03 3.37e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 65.60 -133.33 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CA THR A 599 " pdb=" C THR A 599 " pdb=" N ARG A 600 " pdb=" CA ARG A 600 " ideal model delta harmonic sigma weight residual 180.00 160.84 19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 12801 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2362 0.039 - 0.078: 726 0.078 - 0.118: 210 0.118 - 0.157: 27 0.157 - 0.196: 1 Chirality restraints: 3326 Sorted by residual: chirality pdb=" CA GLU E 111 " pdb=" N GLU E 111 " pdb=" C GLU E 111 " pdb=" CB GLU E 111 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.61e-01 chirality pdb=" CA GLU C 279 " pdb=" N GLU C 279 " pdb=" C GLU C 279 " pdb=" CB GLU C 279 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.64e-01 chirality pdb=" CA PHE H 19 " pdb=" N PHE H 19 " pdb=" C PHE H 19 " pdb=" CB PHE H 19 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 3323 not shown) Planarity restraints: 3476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 276 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C ASP C 276 " 0.067 2.00e-02 2.50e+03 pdb=" O ASP C 276 " -0.025 2.00e-02 2.50e+03 pdb=" N LEU C 277 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS H 183 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO H 184 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO H 184 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO H 184 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 327 " 0.015 2.00e-02 2.50e+03 1.38e-02 4.73e+00 pdb=" CG TRP A 327 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 327 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP A 327 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 327 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 327 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 327 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 327 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 327 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 327 " 0.002 2.00e-02 2.50e+03 ... (remaining 3473 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 211 2.62 - 3.19: 18077 3.19 - 3.76: 32149 3.76 - 4.33: 44063 4.33 - 4.90: 72517 Nonbonded interactions: 167017 Sorted by model distance: nonbonded pdb=" OG1 THR A 360 " pdb="MG MG A 902 " model vdw 2.049 2.170 nonbonded pdb=" O3G AGS A 901 " pdb="MG MG A 902 " model vdw 2.061 2.170 nonbonded pdb=" O2G AGS B 401 " pdb="MG MG B 402 " model vdw 2.093 2.170 nonbonded pdb=" O1B AGS B 401 " pdb="MG MG B 402 " model vdw 2.105 2.170 nonbonded pdb=" O3G AGS D 401 " pdb="MG MG D 402 " model vdw 2.111 2.170 ... (remaining 167012 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'F' and resid 1 through 254) selection = (chain 'G' and resid 1 through 254) 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 14.070 Check model and map are aligned: 0.340 Set scattering table: 0.200 Process input model: 62.400 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 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 0.043 20988 Z= 0.183 Angle : 0.596 7.647 28554 Z= 0.308 Chirality : 0.041 0.196 3326 Planarity : 0.004 0.055 3476 Dihedral : 15.251 133.330 8084 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.05 % Allowed : 0.23 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2458 helix: 0.94 (0.16), residues: 1145 sheet: -0.88 (0.24), residues: 490 loop : -0.74 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 327 HIS 0.009 0.001 HIS C 184 PHE 0.021 0.001 PHE H 19 TYR 0.011 0.001 TYR A 404 ARG 0.009 0.001 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 365 time to evaluate : 2.309 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7729 (tpt) cc_final: 0.7396 (tpt) REVERT: A 322 ASN cc_start: 0.7955 (m-40) cc_final: 0.7505 (m-40) REVERT: C 99 ASP cc_start: 0.7171 (m-30) cc_final: 0.6923 (m-30) REVERT: D 134 TYR cc_start: 0.8798 (p90) cc_final: 0.8469 (p90) REVERT: E 58 GLU cc_start: 0.6986 (pt0) cc_final: 0.6768 (pt0) REVERT: E 107 ILE cc_start: 0.8845 (pt) cc_final: 0.8620 (pt) REVERT: E 119 MET cc_start: 0.6824 (mmm) cc_final: 0.6498 (mmm) REVERT: E 292 HIS cc_start: 0.7763 (t70) cc_final: 0.7008 (t-90) REVERT: E 323 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7503 (tm-30) REVERT: F 199 MSE cc_start: 0.5232 (mtt) cc_final: 0.1581 (tpt) REVERT: G 30 CYS cc_start: 0.7857 (m) cc_final: 0.7516 (t) REVERT: G 80 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7975 (mmm160) REVERT: H 159 ASN cc_start: 0.8468 (p0) cc_final: 0.8191 (p0) outliers start: 1 outliers final: 0 residues processed: 366 average time/residue: 0.3253 time to fit residues: 186.0077 Evaluate side-chains 264 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 211 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 105 optimal weight: 0.0170 chunk 64 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 195 optimal weight: 0.0770 chunk 75 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 145 optimal weight: 0.5980 chunk 227 optimal weight: 0.0010 overall best weight: 0.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 GLN E 104 ASN E 224 GLN E 227 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.0900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20988 Z= 0.150 Angle : 0.533 7.441 28554 Z= 0.276 Chirality : 0.039 0.140 3326 Planarity : 0.004 0.049 3476 Dihedral : 13.661 140.382 3198 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.27 % Allowed : 8.71 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.17), residues: 2458 helix: 1.30 (0.16), residues: 1139 sheet: -0.83 (0.23), residues: 502 loop : -0.63 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 327 HIS 0.008 0.001 HIS H 64 PHE 0.026 0.001 PHE F 245 TYR 0.017 0.001 TYR B 186 ARG 0.007 0.000 ARG A 600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 295 time to evaluate : 2.581 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7706 (tpt) cc_final: 0.7316 (tpt) REVERT: A 322 ASN cc_start: 0.7974 (m-40) cc_final: 0.7458 (m-40) REVERT: C 99 ASP cc_start: 0.7235 (m-30) cc_final: 0.7001 (m-30) REVERT: E 107 ILE cc_start: 0.8764 (pt) cc_final: 0.8536 (pt) REVERT: E 119 MET cc_start: 0.6616 (mmm) cc_final: 0.6209 (mmm) REVERT: F 199 MSE cc_start: 0.5275 (mtt) cc_final: 0.1676 (tpt) REVERT: G 188 MSE cc_start: 0.3339 (OUTLIER) cc_final: 0.3132 (mmp) REVERT: H 71 ASP cc_start: 0.7049 (t70) cc_final: 0.6647 (t70) outliers start: 28 outliers final: 13 residues processed: 313 average time/residue: 0.3127 time to fit residues: 152.3928 Evaluate side-chains 283 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 269 time to evaluate : 2.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 163 VAL Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 227 ASN Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain F residue 188 MSE Chi-restraints excluded: chain G residue 188 MSE Chi-restraints excluded: chain H residue 22 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 126 optimal weight: 0.0870 chunk 70 optimal weight: 3.9990 chunk 188 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 227 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 77 optimal weight: 0.0030 chunk 182 optimal weight: 20.0000 overall best weight: 1.3572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20988 Z= 0.234 Angle : 0.533 9.029 28554 Z= 0.274 Chirality : 0.040 0.146 3326 Planarity : 0.003 0.047 3476 Dihedral : 13.724 147.330 3198 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.36 % Allowed : 11.43 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.17), residues: 2458 helix: 1.32 (0.16), residues: 1147 sheet: -0.78 (0.23), residues: 496 loop : -0.65 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 669 HIS 0.008 0.001 HIS H 64 PHE 0.024 0.001 PHE F 245 TYR 0.017 0.001 TYR B 186 ARG 0.006 0.000 ARG D 230 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 280 time to evaluate : 2.533 Fit side-chains REVERT: A 318 MET cc_start: 0.7688 (tpt) cc_final: 0.7192 (tpp) REVERT: A 322 ASN cc_start: 0.8037 (m-40) cc_final: 0.7568 (m-40) REVERT: C 99 ASP cc_start: 0.7275 (m-30) cc_final: 0.7042 (m-30) REVERT: E 119 MET cc_start: 0.6468 (mmm) cc_final: 0.6131 (mmm) REVERT: F 199 MSE cc_start: 0.5411 (mtt) cc_final: 0.1757 (tpt) outliers start: 30 outliers final: 22 residues processed: 296 average time/residue: 0.3183 time to fit residues: 148.9925 Evaluate side-chains 278 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 256 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 140 ASP Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain F residue 1 MSE Chi-restraints excluded: chain F residue 188 MSE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 159 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 224 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 chunk 152 optimal weight: 0.4980 chunk 228 optimal weight: 0.9990 chunk 241 optimal weight: 0.4980 chunk 119 optimal weight: 3.9990 chunk 216 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 321 GLN ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 224 GLN H 247 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20988 Z= 0.154 Angle : 0.498 8.873 28554 Z= 0.256 Chirality : 0.038 0.182 3326 Planarity : 0.003 0.046 3476 Dihedral : 13.590 145.835 3198 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.86 % Allowed : 12.79 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.17), residues: 2458 helix: 1.46 (0.16), residues: 1144 sheet: -0.77 (0.23), residues: 497 loop : -0.63 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 327 HIS 0.010 0.001 HIS H 64 PHE 0.023 0.001 PHE F 245 TYR 0.018 0.001 TYR B 186 ARG 0.007 0.000 ARG H 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 291 time to evaluate : 2.429 Fit side-chains REVERT: A 318 MET cc_start: 0.7704 (tpt) cc_final: 0.7331 (tpp) REVERT: A 322 ASN cc_start: 0.8035 (m-40) cc_final: 0.7430 (m-40) REVERT: C 99 ASP cc_start: 0.7246 (m-30) cc_final: 0.7032 (m-30) REVERT: E 119 MET cc_start: 0.6450 (mmm) cc_final: 0.6140 (mmm) REVERT: F 199 MSE cc_start: 0.5490 (mtt) cc_final: 0.1828 (tpt) REVERT: H 1 MSE cc_start: 0.3599 (pmm) cc_final: 0.3171 (ptp) REVERT: H 71 ASP cc_start: 0.7125 (t70) cc_final: 0.6809 (t70) REVERT: H 228 ARG cc_start: 0.7791 (ttm-80) cc_final: 0.7477 (ttm-80) outliers start: 41 outliers final: 27 residues processed: 316 average time/residue: 0.3138 time to fit residues: 154.9178 Evaluate side-chains 290 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 263 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 660 MET Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 258 ASP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 188 MSE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 159 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 201 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 99 optimal weight: 0.0470 chunk 206 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 123 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS A 562 GLN ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 20988 Z= 0.368 Angle : 0.603 8.464 28554 Z= 0.307 Chirality : 0.042 0.171 3326 Planarity : 0.004 0.048 3476 Dihedral : 13.842 154.414 3198 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.27 % Allowed : 14.43 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2458 helix: 1.20 (0.16), residues: 1144 sheet: -0.88 (0.23), residues: 503 loop : -0.66 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 298 HIS 0.010 0.001 HIS H 64 PHE 0.020 0.002 PHE F 245 TYR 0.016 0.002 TYR B 186 ARG 0.006 0.001 ARG G 44 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 253 time to evaluate : 2.593 Fit side-chains REVERT: A 318 MET cc_start: 0.7699 (tpt) cc_final: 0.7335 (tpp) REVERT: A 322 ASN cc_start: 0.8086 (m-40) cc_final: 0.7583 (m-40) REVERT: A 327 TRP cc_start: 0.7975 (t60) cc_final: 0.7750 (t60) REVERT: C 99 ASP cc_start: 0.7323 (m-30) cc_final: 0.7011 (m-30) REVERT: E 119 MET cc_start: 0.6419 (mmm) cc_final: 0.5990 (mmm) REVERT: F 199 MSE cc_start: 0.5767 (mtt) cc_final: 0.2016 (tpt) REVERT: H 1 MSE cc_start: 0.3404 (pmm) cc_final: 0.3142 (ptp) REVERT: H 101 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8267 (pp) outliers start: 50 outliers final: 35 residues processed: 282 average time/residue: 0.3056 time to fit residues: 136.2858 Evaluate side-chains 278 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 242 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 1 MSE Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 25 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 159 ASN Chi-restraints excluded: chain H residue 247 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 81 optimal weight: 0.8980 chunk 217 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 141 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 200 optimal weight: 1.9990 chunk 111 optimal weight: 0.0980 chunk 20 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20988 Z= 0.153 Angle : 0.511 8.505 28554 Z= 0.261 Chirality : 0.039 0.145 3326 Planarity : 0.003 0.048 3476 Dihedral : 13.653 147.539 3198 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.81 % Allowed : 15.79 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2458 helix: 1.38 (0.16), residues: 1148 sheet: -0.76 (0.23), residues: 497 loop : -0.70 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 669 HIS 0.012 0.001 HIS H 64 PHE 0.022 0.001 PHE F 245 TYR 0.021 0.001 TYR B 186 ARG 0.005 0.000 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 281 time to evaluate : 2.622 Fit side-chains REVERT: A 318 MET cc_start: 0.7688 (tpt) cc_final: 0.7302 (tpp) REVERT: A 322 ASN cc_start: 0.8047 (m-40) cc_final: 0.7403 (m-40) REVERT: A 327 TRP cc_start: 0.7913 (t60) cc_final: 0.7691 (t60) REVERT: C 52 TYR cc_start: 0.8393 (t80) cc_final: 0.8103 (t80) REVERT: C 99 ASP cc_start: 0.7280 (m-30) cc_final: 0.7035 (m-30) REVERT: C 215 CYS cc_start: 0.7918 (m) cc_final: 0.7637 (m) REVERT: E 119 MET cc_start: 0.6390 (mmm) cc_final: 0.5923 (mmm) REVERT: F 199 MSE cc_start: 0.5767 (mtt) cc_final: 0.2050 (tpt) REVERT: H 228 ARG cc_start: 0.7755 (ttm-80) cc_final: 0.7540 (ttm-80) outliers start: 40 outliers final: 27 residues processed: 305 average time/residue: 0.3224 time to fit residues: 156.2995 Evaluate side-chains 293 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 266 time to evaluate : 2.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 159 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 233 optimal weight: 3.9990 chunk 27 optimal weight: 0.0570 chunk 137 optimal weight: 5.9990 chunk 176 optimal weight: 20.0000 chunk 136 optimal weight: 2.9990 chunk 203 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 240 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 111 optimal weight: 0.0060 overall best weight: 1.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20988 Z= 0.240 Angle : 0.545 8.849 28554 Z= 0.275 Chirality : 0.040 0.152 3326 Planarity : 0.003 0.049 3476 Dihedral : 13.685 152.016 3198 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.27 % Allowed : 15.97 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2458 helix: 1.39 (0.16), residues: 1140 sheet: -0.75 (0.23), residues: 503 loop : -0.70 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 669 HIS 0.011 0.001 HIS H 64 PHE 0.021 0.001 PHE F 245 TYR 0.018 0.001 TYR B 186 ARG 0.005 0.000 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 259 time to evaluate : 2.973 Fit side-chains REVERT: A 318 MET cc_start: 0.7718 (tpt) cc_final: 0.7350 (tpp) REVERT: A 322 ASN cc_start: 0.8049 (m-40) cc_final: 0.7475 (m-40) REVERT: A 327 TRP cc_start: 0.7889 (t60) cc_final: 0.7679 (t60) REVERT: C 52 TYR cc_start: 0.8418 (t80) cc_final: 0.8126 (t80) REVERT: C 99 ASP cc_start: 0.7325 (m-30) cc_final: 0.6995 (m-30) REVERT: F 199 MSE cc_start: 0.5865 (mtt) cc_final: 0.2135 (tpt) REVERT: H 101 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8315 (pp) REVERT: H 228 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.7325 (ttm-80) REVERT: H 247 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7567 (mp10) outliers start: 50 outliers final: 35 residues processed: 290 average time/residue: 0.3166 time to fit residues: 144.6015 Evaluate side-chains 290 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 253 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 103 PHE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 159 ASN Chi-restraints excluded: chain H residue 247 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 149 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 153 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN E 104 ASN E 224 GLN H 64 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 20988 Z= 0.169 Angle : 0.522 9.660 28554 Z= 0.263 Chirality : 0.039 0.157 3326 Planarity : 0.003 0.049 3476 Dihedral : 13.556 148.353 3198 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.09 % Allowed : 16.11 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.17), residues: 2458 helix: 1.48 (0.16), residues: 1142 sheet: -0.66 (0.23), residues: 500 loop : -0.67 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 669 HIS 0.011 0.001 HIS H 64 PHE 0.020 0.001 PHE F 245 TYR 0.020 0.001 TYR B 186 ARG 0.008 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 279 time to evaluate : 2.370 Fit side-chains REVERT: A 318 MET cc_start: 0.7673 (tpt) cc_final: 0.7222 (tpp) REVERT: A 322 ASN cc_start: 0.8054 (m-40) cc_final: 0.7496 (m-40) REVERT: B 83 ASP cc_start: 0.7520 (p0) cc_final: 0.7304 (p0) REVERT: C 99 ASP cc_start: 0.7302 (m-30) cc_final: 0.7064 (m-30) REVERT: F 70 MSE cc_start: 0.3547 (ppp) cc_final: 0.3207 (ppp) REVERT: F 199 MSE cc_start: 0.5979 (mtt) cc_final: 0.2201 (tpt) REVERT: G 113 GLU cc_start: 0.7455 (tp30) cc_final: 0.6870 (tt0) REVERT: H 20 LYS cc_start: 0.8402 (pttm) cc_final: 0.8141 (ptpp) REVERT: H 101 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8319 (pp) REVERT: H 228 ARG cc_start: 0.7738 (ttm-80) cc_final: 0.7330 (ttm-80) REVERT: H 247 GLN cc_start: 0.7804 (OUTLIER) cc_final: 0.7584 (mp10) outliers start: 46 outliers final: 36 residues processed: 307 average time/residue: 0.3101 time to fit residues: 149.8890 Evaluate side-chains 302 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 264 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 159 ASN Chi-restraints excluded: chain H residue 247 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 219 optimal weight: 2.9990 chunk 230 optimal weight: 0.5980 chunk 210 optimal weight: 0.0370 chunk 224 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 176 optimal weight: 20.0000 chunk 68 optimal weight: 1.9990 chunk 202 optimal weight: 7.9990 chunk 212 optimal weight: 0.7980 chunk 223 optimal weight: 1.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 224 GLN H 64 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 20988 Z= 0.203 Angle : 0.530 9.151 28554 Z= 0.269 Chirality : 0.040 0.222 3326 Planarity : 0.003 0.048 3476 Dihedral : 13.575 150.902 3198 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.09 % Allowed : 16.20 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.17), residues: 2458 helix: 1.47 (0.16), residues: 1142 sheet: -0.66 (0.23), residues: 500 loop : -0.67 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 327 HIS 0.011 0.001 HIS H 64 PHE 0.021 0.001 PHE F 245 TYR 0.019 0.001 TYR B 186 ARG 0.009 0.000 ARG B 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 265 time to evaluate : 2.182 Fit side-chains REVERT: A 318 MET cc_start: 0.7681 (tpt) cc_final: 0.7239 (tpp) REVERT: A 322 ASN cc_start: 0.8069 (m-40) cc_final: 0.7535 (m-40) REVERT: B 83 ASP cc_start: 0.7514 (p0) cc_final: 0.7260 (p0) REVERT: C 52 TYR cc_start: 0.8400 (t80) cc_final: 0.8117 (t80) REVERT: C 99 ASP cc_start: 0.7316 (m-30) cc_final: 0.7075 (m-30) REVERT: F 199 MSE cc_start: 0.5935 (mtt) cc_final: 0.2213 (tpt) REVERT: G 113 GLU cc_start: 0.7459 (tp30) cc_final: 0.6882 (tt0) REVERT: H 20 LYS cc_start: 0.8413 (pttm) cc_final: 0.8131 (ptpp) REVERT: H 101 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8280 (pp) REVERT: H 214 ASP cc_start: 0.7907 (m-30) cc_final: 0.7551 (m-30) REVERT: H 228 ARG cc_start: 0.7729 (ttm-80) cc_final: 0.7307 (ttm-80) REVERT: H 247 GLN cc_start: 0.7772 (OUTLIER) cc_final: 0.7531 (mp10) outliers start: 46 outliers final: 39 residues processed: 292 average time/residue: 0.3143 time to fit residues: 143.6817 Evaluate side-chains 303 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 262 time to evaluate : 2.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 159 ASN Chi-restraints excluded: chain H residue 247 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 147 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 144 optimal weight: 0.4980 chunk 112 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 249 optimal weight: 6.9990 chunk 229 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** B 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 224 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20988 Z= 0.180 Angle : 0.526 9.279 28554 Z= 0.267 Chirality : 0.039 0.209 3326 Planarity : 0.003 0.049 3476 Dihedral : 13.535 149.538 3198 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.00 % Allowed : 16.33 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.17), residues: 2458 helix: 1.49 (0.16), residues: 1142 sheet: -0.63 (0.23), residues: 511 loop : -0.63 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 327 HIS 0.005 0.001 HIS H 64 PHE 0.021 0.001 PHE F 245 TYR 0.021 0.001 TYR D 64 ARG 0.009 0.000 ARG B 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4916 Ramachandran restraints generated. 2458 Oldfield, 0 Emsley, 2458 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 274 time to evaluate : 2.418 Fit side-chains revert: symmetry clash REVERT: A 318 MET cc_start: 0.7668 (tpt) cc_final: 0.7230 (tpp) REVERT: A 322 ASN cc_start: 0.8057 (m-40) cc_final: 0.7504 (m-40) REVERT: B 83 ASP cc_start: 0.7650 (p0) cc_final: 0.7358 (p0) REVERT: C 99 ASP cc_start: 0.7307 (m-30) cc_final: 0.7067 (m-30) REVERT: F 70 MSE cc_start: 0.4424 (ppp) cc_final: 0.3791 (ppp) REVERT: F 197 LEU cc_start: 0.5257 (tp) cc_final: 0.4805 (tp) REVERT: F 199 MSE cc_start: 0.5958 (mtt) cc_final: 0.2236 (tpt) REVERT: G 113 GLU cc_start: 0.7407 (tp30) cc_final: 0.6852 (tt0) REVERT: H 20 LYS cc_start: 0.8393 (pttm) cc_final: 0.8098 (ptpp) REVERT: H 101 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8256 (pp) REVERT: H 214 ASP cc_start: 0.7891 (m-30) cc_final: 0.7510 (m-30) REVERT: H 228 ARG cc_start: 0.7714 (ttm-80) cc_final: 0.7302 (ttm-80) outliers start: 44 outliers final: 40 residues processed: 301 average time/residue: 0.3098 time to fit residues: 146.4758 Evaluate side-chains 306 residues out of total 2204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 265 time to evaluate : 2.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 452 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 73 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 223 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 235 CYS Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 99 ASP Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 146 THR Chi-restraints excluded: chain D residue 171 ASN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain E residue 93 HIS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 104 ASN Chi-restraints excluded: chain E residue 111 GLU Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 259 TRP Chi-restraints excluded: chain F residue 100 ILE Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 229 LEU Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 121 ILE Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 118 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 250 random chunks: chunk 157 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 182 optimal weight: 10.0000 chunk 29 optimal weight: 0.0010 chunk 55 optimal weight: 0.4980 chunk 198 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 203 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN E 224 GLN H 64 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.153235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.117314 restraints weight = 30054.015| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 2.56 r_work: 0.3316 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 20988 Z= 0.158 Angle : 0.522 10.403 28554 Z= 0.264 Chirality : 0.039 0.218 3326 Planarity : 0.003 0.049 3476 Dihedral : 13.487 148.963 3198 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.04 % Allowed : 16.15 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.18), residues: 2458 helix: 1.55 (0.16), residues: 1140 sheet: -0.56 (0.23), residues: 509 loop : -0.64 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 327 HIS 0.011 0.001 HIS H 64 PHE 0.021 0.001 PHE F 245 TYR 0.020 0.001 TYR B 186 ARG 0.008 0.000 ARG B 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4522.56 seconds wall clock time: 83 minutes 19.48 seconds (4999.48 seconds total)