Starting phenix.real_space_refine on Sat Feb 17 06:07:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm9_7457/02_2024/6cm9_7457_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm9_7457/02_2024/6cm9_7457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm9_7457/02_2024/6cm9_7457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm9_7457/02_2024/6cm9_7457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm9_7457/02_2024/6cm9_7457_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cm9_7457/02_2024/6cm9_7457_updated.pdb" } resolution = 3.73 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= 0.001 sd= 0.009 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 102 5.16 5 C 11256 2.51 5 N 3014 2.21 5 O 3303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "T ARG 10": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B TYR 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 345": "NH1" <-> "NH2" Residue "H ARG 19": "NH1" <-> "NH2" Residue "H ARG 109": "NH1" <-> "NH2" Residue "H ARG 149": "NH1" <-> "NH2" Residue "M ARG 243": "NH1" <-> "NH2" Residue "M PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 33": "NH1" <-> "NH2" Residue "S TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 17683 Number of models: 1 Model: "" Number of chains: 11 Chain: "L" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 76 Classifications: {'peptide': 10} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "T" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 105 Classifications: {'peptide': 13} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "B" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4513 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 25, 'TRANS': 544} Chain: "C" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1330 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "G" Number of atoms: 4633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4633 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 13, 'TRANS': 571} Chain: "H" Number of atoms: 1312 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1312 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 3, 'TRANS': 159} Chain: "M" Number of atoms: 3362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3362 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Chain: "S" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1197 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 1, 'TRANS': 140} Chain: "N" Number of atoms: 1089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1089 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 118} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.23, per 1000 atoms: 0.52 Number of scatterers: 17683 At special positions: 0 Unit cell: (139.777, 152.581, 130.174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 6 15.00 Mg 2 11.99 O 3303 8.00 N 3014 7.00 C 11256 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: 6.92 Conformation dependent library (CDL) restraints added in 3.5 seconds 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4198 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 14 sheets defined 44.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'B' and resid 15 through 23 Processing helix chain 'B' and resid 27 through 40 removed outlier: 4.420A pdb=" N GLU B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 54 removed outlier: 3.516A pdb=" N PHE B 51 " --> pdb=" O SER B 48 " (cutoff:3.500A) Proline residue: B 52 - end of helix No H-bonds generated for 'chain 'B' and resid 48 through 54' Processing helix chain 'B' and resid 66 through 75 Processing helix chain 'B' and resid 83 through 86 Processing helix chain 'B' and resid 88 through 96 removed outlier: 4.686A pdb=" N GLU B 96 " --> pdb=" O VAL B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 110 Processing helix chain 'B' and resid 121 through 130 removed outlier: 4.130A pdb=" N GLU B 124 " --> pdb=" O TYR B 121 " (cutoff:3.500A) Proline residue: B 125 - end of helix removed outlier: 3.885A pdb=" N LEU B 130 " --> pdb=" O ARG B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 151 removed outlier: 4.187A pdb=" N VAL B 143 " --> pdb=" O LYS B 139 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 159 removed outlier: 3.994A pdb=" N GLU B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'B' and resid 174 through 188 Processing helix chain 'B' and resid 201 through 209 Processing helix chain 'B' and resid 218 through 224 removed outlier: 3.789A pdb=" N LEU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 249 removed outlier: 4.030A pdb=" N ARG B 243 " --> pdb=" O SER B 239 " (cutoff:3.500A) Proline residue: B 246 - end of helix removed outlier: 4.832A pdb=" N SER B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 268 removed outlier: 4.596A pdb=" N GLU B 268 " --> pdb=" O MET B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 283 Processing helix chain 'B' and resid 285 through 293 removed outlier: 4.435A pdb=" N LEU B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N SER B 293 " --> pdb=" O VAL B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 332 through 344 removed outlier: 4.315A pdb=" N GLU B 337 " --> pdb=" O TYR B 333 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU B 339 " --> pdb=" O LYS B 335 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 358 removed outlier: 4.115A pdb=" N ILE B 351 " --> pdb=" O GLN B 348 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N ALA B 352 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 353 " --> pdb=" O ASN B 350 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 388 through 401 removed outlier: 4.304A pdb=" N THR B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 418 removed outlier: 4.364A pdb=" N VAL B 412 " --> pdb=" O GLN B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 442 through 454 removed outlier: 3.920A pdb=" N ALA B 446 " --> pdb=" O PRO B 442 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ALA B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 465 No H-bonds generated for 'chain 'B' and resid 462 through 465' Processing helix chain 'B' and resid 473 through 475 No H-bonds generated for 'chain 'B' and resid 473 through 475' Processing helix chain 'B' and resid 478 through 494 removed outlier: 3.595A pdb=" N VAL B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 510 removed outlier: 3.765A pdb=" N GLN B 504 " --> pdb=" O GLN B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 532 Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 560 through 563 No H-bonds generated for 'chain 'B' and resid 560 through 563' Processing helix chain 'B' and resid 570 through 573 No H-bonds generated for 'chain 'B' and resid 570 through 573' Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 97 through 110 removed outlier: 4.018A pdb=" N ASN C 101 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLU C 102 " --> pdb=" O GLU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 166 through 177 Processing helix chain 'G' and resid 7 through 16 removed outlier: 3.614A pdb=" N THR G 16 " --> pdb=" O ARG G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 39 removed outlier: 4.155A pdb=" N GLU G 25 " --> pdb=" O ALA G 21 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU G 30 " --> pdb=" O MET G 26 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 58 Processing helix chain 'G' and resid 68 through 74 removed outlier: 4.090A pdb=" N LEU G 73 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 92 Processing helix chain 'G' and resid 100 through 110 removed outlier: 4.481A pdb=" N ASN G 105 " --> pdb=" O LEU G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.734A pdb=" N LEU G 126 " --> pdb=" O ALA G 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 137 No H-bonds generated for 'chain 'G' and resid 135 through 137' Processing helix chain 'G' and resid 139 through 142 No H-bonds generated for 'chain 'G' and resid 139 through 142' Processing helix chain 'G' and resid 151 through 167 removed outlier: 3.552A pdb=" N LYS G 155 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS G 156 " --> pdb=" O TYR G 152 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU G 159 " --> pdb=" O LYS G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 188 through 204 Processing helix chain 'G' and resid 209 through 212 No H-bonds generated for 'chain 'G' and resid 209 through 212' Processing helix chain 'G' and resid 216 through 228 Processing helix chain 'G' and resid 243 through 255 removed outlier: 3.626A pdb=" N ARG G 248 " --> pdb=" O PHE G 244 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 266 Processing helix chain 'G' and resid 268 through 274 Processing helix chain 'G' and resid 283 through 298 removed outlier: 3.852A pdb=" N ASP G 298 " --> pdb=" O LEU G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 303 through 317 removed outlier: 3.829A pdb=" N VAL G 307 " --> pdb=" O SER G 303 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU G 308 " --> pdb=" O GLY G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 334 Processing helix chain 'G' and resid 344 through 355 removed outlier: 5.621A pdb=" N SER G 348 " --> pdb=" O ARG G 345 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP G 352 " --> pdb=" O THR G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 372 Processing helix chain 'G' and resid 378 through 390 removed outlier: 3.624A pdb=" N MET G 382 " --> pdb=" O ILE G 378 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS G 383 " --> pdb=" O ARG G 379 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU G 384 " --> pdb=" O GLY G 380 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASP G 390 " --> pdb=" O LEU G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 410 removed outlier: 3.886A pdb=" N PHE G 405 " --> pdb=" O ALA G 401 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS G 410 " --> pdb=" O LEU G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 428 Processing helix chain 'G' and resid 437 through 447 Processing helix chain 'G' and resid 453 through 463 removed outlier: 3.925A pdb=" N ARG G 458 " --> pdb=" O TYR G 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 487 removed outlier: 3.861A pdb=" N TRP G 478 " --> pdb=" O GLN G 474 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASP G 485 " --> pdb=" O GLY G 481 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU G 486 " --> pdb=" O GLU G 482 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 487 " --> pdb=" O TYR G 483 " (cutoff:3.500A) Processing helix chain 'G' and resid 504 through 514 removed outlier: 3.715A pdb=" N LEU G 509 " --> pdb=" O VAL G 505 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 534 removed outlier: 3.613A pdb=" N SER G 534 " --> pdb=" O ILE G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 550 Processing helix chain 'G' and resid 557 through 572 removed outlier: 3.727A pdb=" N VAL G 564 " --> pdb=" O GLN G 560 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU G 569 " --> pdb=" O GLU G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 578 through 580 No H-bonds generated for 'chain 'G' and resid 578 through 580' Processing helix chain 'H' and resid 30 through 37 Processing helix chain 'H' and resid 75 through 80 removed outlier: 3.823A pdb=" N TRP H 78 " --> pdb=" O ARG H 75 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG H 79 " --> pdb=" O PRO H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 110 Processing helix chain 'H' and resid 136 through 143 Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing helix chain 'H' and resid 166 through 175 Processing helix chain 'M' and resid 27 through 41 removed outlier: 3.819A pdb=" N VAL M 30 " --> pdb=" O MET M 27 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU M 31 " --> pdb=" O SER M 28 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N MET M 34 " --> pdb=" O GLU M 31 " (cutoff:3.500A) Proline residue: M 35 - end of helix removed outlier: 3.509A pdb=" N LYS M 40 " --> pdb=" O LEU M 37 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU M 41 " --> pdb=" O MET M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 94 Processing helix chain 'M' and resid 100 through 103 No H-bonds generated for 'chain 'M' and resid 100 through 103' Processing helix chain 'M' and resid 107 through 117 removed outlier: 3.848A pdb=" N TYR M 111 " --> pdb=" O PHE M 107 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU M 112 " --> pdb=" O VAL M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 128 through 133 removed outlier: 4.932A pdb=" N GLU M 133 " --> pdb=" O LYS M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 154 No H-bonds generated for 'chain 'M' and resid 151 through 154' Processing helix chain 'M' and resid 217 through 223 Processing helix chain 'M' and resid 244 through 250 removed outlier: 3.570A pdb=" N ASP M 250 " --> pdb=" O ARG M 246 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 39 removed outlier: 3.833A pdb=" N LYS S 29 " --> pdb=" O ASP S 25 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG S 33 " --> pdb=" O LYS S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 95 removed outlier: 3.520A pdb=" N PHE S 95 " --> pdb=" O LEU S 91 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 104 No H-bonds generated for 'chain 'S' and resid 101 through 104' Processing helix chain 'S' and resid 107 through 117 removed outlier: 3.568A pdb=" N PHE S 112 " --> pdb=" O GLU S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 129 through 140 Processing helix chain 'N' and resid 15 through 22 Processing helix chain 'N' and resid 81 through 93 Processing helix chain 'N' and resid 104 through 118 Processing helix chain 'N' and resid 194 through 198 Processing sheet with id= A, first strand: chain 'C' and resid 19 through 22 removed outlier: 6.451A pdb=" N ILE C 20 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N THR C 64 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N MET C 22 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N TRP C 66 " --> pdb=" O MET C 22 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR C 58 " --> pdb=" O ILE C 61 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 123 through 125 Processing sheet with id= C, first strand: chain 'H' and resid 18 through 22 removed outlier: 3.722A pdb=" N VAL H 68 " --> pdb=" O MET H 22 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL H 65 " --> pdb=" O GLU H 54 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU H 54 " --> pdb=" O VAL H 65 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 91 through 93 removed outlier: 5.898A pdb=" N PHE H 124 " --> pdb=" O VAL H 92 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'M' and resid 49 through 52 removed outlier: 3.605A pdb=" N MET M 58 " --> pdb=" O ALA M 69 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE M 60 " --> pdb=" O LEU M 67 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'M' and resid 406 through 408 removed outlier: 3.542A pdb=" N MET M 265 " --> pdb=" O ILE M 198 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N MET M 200 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLU M 263 " --> pdb=" O MET M 200 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N VAL M 202 " --> pdb=" O GLU M 261 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLU M 261 " --> pdb=" O VAL M 202 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS M 237 " --> pdb=" O SER M 266 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'M' and resid 181 through 183 Processing sheet with id= H, first strand: chain 'M' and resid 253 through 255 removed outlier: 3.710A pdb=" N ILE M 253 " --> pdb=" O LEU M 212 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY M 213 " --> pdb=" O TYR M 394 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR M 394 " --> pdb=" O GLY M 213 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'M' and resid 277 through 280 removed outlier: 3.621A pdb=" N ILE M 291 " --> pdb=" O PHE M 360 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'M' and resid 306 through 308 Processing sheet with id= K, first strand: chain 'M' and resid 310 through 312 removed outlier: 3.733A pdb=" N LYS M 333 " --> pdb=" O VAL M 342 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'M' and resid 5 through 9 removed outlier: 3.574A pdb=" N ILE M 17 " --> pdb=" O VAL M 8 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 49 through 51 Processing sheet with id= N, first strand: chain 'N' and resid 143 through 146 604 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.48 Time building geometry restraints manager: 7.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5201 1.33 - 1.45: 2779 1.45 - 1.57: 9851 1.57 - 1.69: 10 1.69 - 1.81: 166 Bond restraints: 18007 Sorted by residual: bond pdb=" C LEU G 176 " pdb=" N PRO G 177 " ideal model delta sigma weight residual 1.334 1.374 -0.040 8.40e-03 1.42e+04 2.26e+01 bond pdb=" CG1 ILE S 35 " pdb=" CD1 ILE S 35 " ideal model delta sigma weight residual 1.513 1.426 0.087 3.90e-02 6.57e+02 4.98e+00 bond pdb=" CB VAL M 77 " pdb=" CG2 VAL M 77 " ideal model delta sigma weight residual 1.521 1.449 0.072 3.30e-02 9.18e+02 4.71e+00 bond pdb=" CB VAL B 262 " pdb=" CG2 VAL B 262 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.06e+00 bond pdb=" CB VAL M 332 " pdb=" CG2 VAL M 332 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.96e+00 ... (remaining 18002 not shown) Histogram of bond angle deviations from ideal: 97.20 - 104.59: 279 104.59 - 111.98: 8470 111.98 - 119.37: 6776 119.37 - 126.76: 8630 126.76 - 134.15: 213 Bond angle restraints: 24368 Sorted by residual: angle pdb=" N VAL B 47 " pdb=" CA VAL B 47 " pdb=" C VAL B 47 " ideal model delta sigma weight residual 111.91 106.87 5.04 8.90e-01 1.26e+00 3.20e+01 angle pdb=" C LYS H 59 " pdb=" N ASN H 60 " pdb=" CA ASN H 60 " ideal model delta sigma weight residual 121.54 130.83 -9.29 1.91e+00 2.74e-01 2.36e+01 angle pdb=" C ASN M 308 " pdb=" N ASN M 309 " pdb=" CA ASN M 309 " ideal model delta sigma weight residual 121.54 130.49 -8.95 1.91e+00 2.74e-01 2.20e+01 angle pdb=" N GLY N 130 " pdb=" CA GLY N 130 " pdb=" C GLY N 130 " ideal model delta sigma weight residual 112.34 121.54 -9.20 2.04e+00 2.40e-01 2.03e+01 angle pdb=" CA HIS L 166 " pdb=" C HIS L 166 " pdb=" N PRO L 167 " ideal model delta sigma weight residual 118.16 121.24 -3.08 7.00e-01 2.04e+00 1.94e+01 ... (remaining 24363 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.58: 10916 34.58 - 69.16: 70 69.16 - 103.74: 16 103.74 - 138.32: 3 138.32 - 172.91: 3 Dihedral angle restraints: 11008 sinusoidal: 4546 harmonic: 6462 Sorted by residual: dihedral pdb=" O5' GTP H1001 " pdb=" O3A GTP H1001 " pdb=" PA GTP H1001 " pdb=" PB GTP H1001 " ideal model delta sinusoidal sigma weight residual -85.88 87.03 -172.91 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O5' GTP C1001 " pdb=" O3A GTP C1001 " pdb=" PA GTP C1001 " pdb=" PB GTP C1001 " ideal model delta sinusoidal sigma weight residual 274.12 109.86 164.26 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" C8 GTP H1001 " pdb=" C1' GTP H1001 " pdb=" N9 GTP H1001 " pdb=" O4' GTP H1001 " ideal model delta sinusoidal sigma weight residual 104.59 -38.21 142.80 1 2.00e+01 2.50e-03 4.31e+01 ... (remaining 11005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1923 0.057 - 0.114: 716 0.114 - 0.171: 128 0.171 - 0.228: 17 0.228 - 0.285: 6 Chirality restraints: 2790 Sorted by residual: chirality pdb=" CA ASN M 309 " pdb=" N ASN M 309 " pdb=" C ASN M 309 " pdb=" CB ASN M 309 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CB VAL B 47 " pdb=" CA VAL B 47 " pdb=" CG1 VAL B 47 " pdb=" CG2 VAL B 47 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CG LEU B 197 " pdb=" CB LEU B 197 " pdb=" CD1 LEU B 197 " pdb=" CD2 LEU B 197 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2787 not shown) Planarity restraints: 3085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS L 166 " 0.057 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO L 167 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO L 167 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO L 167 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 75 " 0.043 5.00e-02 4.00e+02 6.41e-02 6.58e+00 pdb=" N PRO H 76 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO H 76 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO H 76 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 343 " 0.018 2.00e-02 2.50e+03 1.60e-02 6.44e+00 pdb=" CG TRP M 343 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP M 343 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP M 343 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP M 343 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP M 343 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP M 343 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 343 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 343 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP M 343 " 0.002 2.00e-02 2.50e+03 ... (remaining 3082 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 87 2.51 - 3.10: 12155 3.10 - 3.70: 26933 3.70 - 4.30: 38624 4.30 - 4.90: 63816 Nonbonded interactions: 141615 Sorted by model distance: nonbonded pdb=" O2G GTP H1001 " pdb="MG MG H1002 " model vdw 1.906 2.170 nonbonded pdb=" O1G GTP C1001 " pdb="MG MG C1002 " model vdw 1.933 2.170 nonbonded pdb=" CG2 THR H 31 " pdb="MG MG H1002 " model vdw 2.015 2.590 nonbonded pdb=" O1B GTP C1001 " pdb="MG MG C1002 " model vdw 2.195 2.170 nonbonded pdb=" O2B GTP H1001 " pdb="MG MG H1002 " model vdw 2.209 2.170 ... (remaining 141610 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 'C' and (resid 17 through 179 or resid 1001 through 1002)) 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.490 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 48.290 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.009 0.087 18007 Z= 0.568 Angle : 1.022 10.944 24368 Z= 0.539 Chirality : 0.059 0.285 2790 Planarity : 0.007 0.086 3085 Dihedral : 11.579 172.905 6810 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.26 % Allowed : 2.81 % Favored : 96.94 % 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: -4.83 (0.14), residues: 2170 helix: -3.18 (0.10), residues: 1090 sheet: -4.03 (0.27), residues: 242 loop : -2.66 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP M 343 HIS 0.016 0.003 HIS G 235 PHE 0.029 0.004 PHE M 95 TYR 0.034 0.003 TYR G 290 ARG 0.008 0.001 ARG M 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 561 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 155 LEU cc_start: 0.8426 (tp) cc_final: 0.8129 (tp) REVERT: B 204 ILE cc_start: 0.8980 (mt) cc_final: 0.8745 (mm) REVERT: B 212 ASN cc_start: 0.7890 (m-40) cc_final: 0.7624 (t0) REVERT: G 29 LYS cc_start: 0.8157 (ttmp) cc_final: 0.7900 (tttt) REVERT: G 183 LEU cc_start: 0.7994 (mm) cc_final: 0.7717 (mt) REVERT: G 201 MET cc_start: 0.7703 (mmm) cc_final: 0.7435 (mtp) REVERT: H 114 ASP cc_start: 0.7740 (t70) cc_final: 0.7384 (t0) REVERT: M 28 SER cc_start: 0.7237 (m) cc_final: 0.6634 (p) REVERT: M 58 MET cc_start: 0.8690 (mpp) cc_final: 0.8229 (mtt) REVERT: M 86 LYS cc_start: 0.8346 (tppp) cc_final: 0.7946 (mptt) REVERT: M 264 LEU cc_start: 0.8739 (tp) cc_final: 0.8532 (tp) REVERT: M 298 LYS cc_start: 0.8496 (ptpp) cc_final: 0.8216 (tttm) REVERT: M 324 LYS cc_start: 0.8430 (mttp) cc_final: 0.7761 (tttt) outliers start: 5 outliers final: 4 residues processed: 566 average time/residue: 0.3455 time to fit residues: 280.0671 Evaluate side-chains 328 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 324 time to evaluate : 2.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 378 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN C 86 GLN C 150 HIS C 180 GLN ** G 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 184 ASN G 218 GLN G 273 GLN G 474 GLN H 101 ASN H 128 GLN M 63 ASN M 169 ASN M 239 HIS M 300 GLN M 308 ASN ** M 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 414 GLN ** M 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 419 GLN S 3 HIS S 74 GLN N 73 GLN ** N 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18007 Z= 0.218 Angle : 0.628 8.791 24368 Z= 0.319 Chirality : 0.043 0.179 2790 Planarity : 0.005 0.068 3085 Dihedral : 9.945 171.483 2423 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 2.45 % Allowed : 10.83 % Favored : 86.72 % 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: -3.43 (0.16), residues: 2170 helix: -1.83 (0.14), residues: 1089 sheet: -3.84 (0.29), residues: 239 loop : -2.14 (0.20), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 450 HIS 0.007 0.001 HIS M 313 PHE 0.013 0.002 PHE M 83 TYR 0.017 0.002 TYR G 61 ARG 0.007 0.001 ARG M 211 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 376 time to evaluate : 2.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 58 MET cc_start: 0.8478 (ttp) cc_final: 0.8097 (ttp) REVERT: C 54 GLU cc_start: 0.6239 (mm-30) cc_final: 0.6020 (mp0) REVERT: C 134 MET cc_start: 0.5330 (mpt) cc_final: 0.5111 (mpp) REVERT: G 183 LEU cc_start: 0.7980 (mm) cc_final: 0.7551 (mt) REVERT: G 201 MET cc_start: 0.7668 (mmm) cc_final: 0.7218 (mtp) REVERT: G 212 PHE cc_start: 0.7851 (m-10) cc_final: 0.7323 (m-10) REVERT: G 474 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8543 (mt0) REVERT: H 56 VAL cc_start: 0.8684 (t) cc_final: 0.8437 (m) REVERT: H 59 LYS cc_start: 0.7309 (mmmm) cc_final: 0.7067 (mmmt) REVERT: M 58 MET cc_start: 0.8806 (mpp) cc_final: 0.8296 (mtt) REVERT: M 86 LYS cc_start: 0.8351 (tppp) cc_final: 0.7890 (mptt) REVERT: M 264 LEU cc_start: 0.8916 (tp) cc_final: 0.8625 (tp) REVERT: M 298 LYS cc_start: 0.8301 (ptpp) cc_final: 0.8026 (tttm) REVERT: M 306 THR cc_start: 0.8572 (m) cc_final: 0.8259 (p) REVERT: M 321 ASP cc_start: 0.8593 (p0) cc_final: 0.8294 (p0) REVERT: M 324 LYS cc_start: 0.8264 (mttp) cc_final: 0.7677 (tttt) REVERT: S 13 LYS cc_start: 0.8575 (mmtm) cc_final: 0.8327 (tttt) REVERT: S 100 GLU cc_start: 0.8511 (tp30) cc_final: 0.8258 (tp30) REVERT: S 142 GLN cc_start: 0.6606 (pm20) cc_final: 0.5717 (pm20) REVERT: N 77 ARG cc_start: 0.6285 (ptt180) cc_final: 0.5426 (mtt90) outliers start: 48 outliers final: 30 residues processed: 407 average time/residue: 0.3108 time to fit residues: 188.7988 Evaluate side-chains 346 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 315 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 200 GLU Chi-restraints excluded: chain G residue 208 MET Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 474 GLN Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 322 SER Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain S residue 138 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 54 optimal weight: 5.9990 chunk 197 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 175 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 67 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 ASN C 80 HIS C 180 GLN G 184 ASN G 218 GLN G 474 GLN G 491 GLN H 128 GLN M 63 ASN ** M 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 73 GLN ** N 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18007 Z= 0.276 Angle : 0.628 11.757 24368 Z= 0.313 Chirality : 0.044 0.188 2790 Planarity : 0.005 0.053 3085 Dihedral : 9.664 171.203 2423 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.41 % Favored : 93.55 % Rotamer: Outliers : 3.01 % Allowed : 12.61 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.17), residues: 2170 helix: -1.24 (0.15), residues: 1097 sheet: -3.79 (0.28), residues: 256 loop : -1.78 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 450 HIS 0.007 0.001 HIS M 313 PHE 0.021 0.002 PHE M 107 TYR 0.018 0.002 TYR M 403 ARG 0.004 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 332 time to evaluate : 2.264 Fit side-chains revert: symmetry clash REVERT: B 175 MET cc_start: 0.6840 (tpt) cc_final: 0.6628 (tpt) REVERT: C 26 ASP cc_start: 0.7145 (p0) cc_final: 0.6881 (p0) REVERT: G 183 LEU cc_start: 0.7909 (mm) cc_final: 0.7497 (mt) REVERT: G 201 MET cc_start: 0.7773 (mmm) cc_final: 0.7470 (mtp) REVERT: G 474 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8473 (mt0) REVERT: H 56 VAL cc_start: 0.8649 (t) cc_final: 0.8419 (m) REVERT: M 58 MET cc_start: 0.8852 (mpp) cc_final: 0.8308 (mtt) REVERT: M 86 LYS cc_start: 0.8400 (tppp) cc_final: 0.7960 (mptt) REVERT: M 264 LEU cc_start: 0.8914 (tp) cc_final: 0.8643 (tp) REVERT: M 298 LYS cc_start: 0.8338 (ptpp) cc_final: 0.7942 (ttpp) REVERT: M 306 THR cc_start: 0.8653 (m) cc_final: 0.8347 (p) REVERT: M 321 ASP cc_start: 0.8650 (p0) cc_final: 0.8375 (p0) REVERT: S 100 GLU cc_start: 0.8388 (tp30) cc_final: 0.8136 (tp30) REVERT: S 142 GLN cc_start: 0.6681 (pm20) cc_final: 0.5790 (pm20) REVERT: N 77 ARG cc_start: 0.6256 (ptt180) cc_final: 0.5260 (mtt90) outliers start: 59 outliers final: 43 residues processed: 372 average time/residue: 0.2873 time to fit residues: 163.0491 Evaluate side-chains 336 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 292 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 474 GLN Chi-restraints excluded: chain G residue 502 GLU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 569 LEU Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 362 LEU Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain S residue 138 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 102 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 198 optimal weight: 0.9990 chunk 209 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 187 optimal weight: 0.0370 chunk 56 optimal weight: 1.9990 overall best weight: 0.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS G 119 GLN ** G 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN H 128 GLN M 64 ASN ** M 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18007 Z= 0.192 Angle : 0.580 13.109 24368 Z= 0.285 Chirality : 0.042 0.168 2790 Planarity : 0.004 0.041 3085 Dihedral : 9.405 171.227 2423 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.86 % Allowed : 13.74 % Favored : 83.40 % 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: -2.19 (0.18), residues: 2170 helix: -0.74 (0.15), residues: 1083 sheet: -3.64 (0.28), residues: 256 loop : -1.45 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 450 HIS 0.006 0.001 HIS M 286 PHE 0.019 0.001 PHE M 83 TYR 0.015 0.001 TYR G 61 ARG 0.004 0.000 ARG S 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 324 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6916 (tt0) REVERT: B 175 MET cc_start: 0.7016 (tpp) cc_final: 0.6731 (tpt) REVERT: G 183 LEU cc_start: 0.7833 (mm) cc_final: 0.7629 (mt) REVERT: G 201 MET cc_start: 0.7737 (mmm) cc_final: 0.7457 (mtp) REVERT: G 474 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8453 (mt0) REVERT: H 46 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7556 (mt) REVERT: H 49 ILE cc_start: 0.9056 (mm) cc_final: 0.8761 (mp) REVERT: M 58 MET cc_start: 0.8797 (mpp) cc_final: 0.8312 (mtt) REVERT: M 86 LYS cc_start: 0.8324 (tppp) cc_final: 0.7889 (mptt) REVERT: M 264 LEU cc_start: 0.8916 (tp) cc_final: 0.8676 (tp) REVERT: M 298 LYS cc_start: 0.8265 (ptpp) cc_final: 0.7906 (ttpp) REVERT: M 306 THR cc_start: 0.8682 (m) cc_final: 0.8364 (p) REVERT: M 321 ASP cc_start: 0.8663 (p0) cc_final: 0.8386 (p0) REVERT: S 100 GLU cc_start: 0.8267 (tp30) cc_final: 0.8030 (tp30) REVERT: N 77 ARG cc_start: 0.6153 (ptt180) cc_final: 0.5171 (mtt90) outliers start: 56 outliers final: 41 residues processed: 362 average time/residue: 0.2982 time to fit residues: 162.8533 Evaluate side-chains 339 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 295 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 474 GLN Chi-restraints excluded: chain G residue 502 GLU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 128 GLN Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain S residue 138 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 107 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS G 100 HIS G 119 GLN G 311 ASN ** G 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 474 GLN H 80 HIS H 128 GLN M 64 ASN ** M 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 18007 Z= 0.354 Angle : 0.659 12.785 24368 Z= 0.325 Chirality : 0.045 0.173 2790 Planarity : 0.004 0.052 3085 Dihedral : 9.448 171.705 2423 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 3.32 % Allowed : 14.71 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.18), residues: 2170 helix: -0.63 (0.15), residues: 1077 sheet: -3.69 (0.28), residues: 257 loop : -1.39 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 450 HIS 0.006 0.001 HIS G 163 PHE 0.016 0.002 PHE M 83 TYR 0.023 0.002 TYR B 524 ARG 0.007 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 315 time to evaluate : 2.013 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6917 (tt0) REVERT: B 76 TYR cc_start: 0.7939 (m-80) cc_final: 0.7670 (m-80) REVERT: B 175 MET cc_start: 0.7161 (tpp) cc_final: 0.6859 (tpt) REVERT: G 183 LEU cc_start: 0.7861 (mm) cc_final: 0.7605 (mt) REVERT: G 201 MET cc_start: 0.7890 (mmm) cc_final: 0.7686 (mtp) REVERT: H 46 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7621 (mt) REVERT: H 49 ILE cc_start: 0.9113 (mm) cc_final: 0.8800 (mp) REVERT: M 58 MET cc_start: 0.8885 (mpp) cc_final: 0.8343 (mtt) REVERT: M 86 LYS cc_start: 0.8415 (tppp) cc_final: 0.8020 (mptt) REVERT: M 298 LYS cc_start: 0.8335 (ptpp) cc_final: 0.7978 (ttpp) REVERT: M 321 ASP cc_start: 0.8676 (p0) cc_final: 0.8429 (p0) REVERT: S 108 GLU cc_start: 0.7064 (pt0) cc_final: 0.6674 (tt0) REVERT: N 77 ARG cc_start: 0.6206 (ptt180) cc_final: 0.5227 (mtt90) outliers start: 65 outliers final: 53 residues processed: 362 average time/residue: 0.2976 time to fit residues: 161.8622 Evaluate side-chains 347 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 292 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 98 ASP Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 381 MET Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 502 GLU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 48 THR Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 127 ASP Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain M residue 265 MET Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 119 ILE Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain N residue 20 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 50.0000 chunk 188 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 51 optimal weight: 0.2980 chunk 209 optimal weight: 20.0000 chunk 174 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 69 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 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 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 386 GLN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS C 180 GLN G 443 GLN M 64 ASN ** N 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18007 Z= 0.266 Angle : 0.603 13.160 24368 Z= 0.298 Chirality : 0.043 0.161 2790 Planarity : 0.004 0.044 3085 Dihedral : 9.308 172.524 2423 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.27 % Allowed : 15.83 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.18), residues: 2170 helix: -0.43 (0.16), residues: 1081 sheet: -3.55 (0.29), residues: 256 loop : -1.15 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 450 HIS 0.004 0.001 HIS M 62 PHE 0.020 0.001 PHE M 83 TYR 0.015 0.001 TYR G 290 ARG 0.007 0.000 ARG B 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 313 time to evaluate : 2.169 Fit side-chains revert: symmetry clash REVERT: B 14 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6860 (tt0) REVERT: B 76 TYR cc_start: 0.7858 (m-80) cc_final: 0.7653 (m-80) REVERT: B 175 MET cc_start: 0.7062 (tpp) cc_final: 0.6755 (tpt) REVERT: B 409 GLU cc_start: 0.8382 (tp30) cc_final: 0.8154 (tp30) REVERT: C 26 ASP cc_start: 0.7584 (p0) cc_final: 0.7365 (p0) REVERT: G 201 MET cc_start: 0.7879 (mmm) cc_final: 0.7663 (mtp) REVERT: G 228 MET cc_start: 0.7082 (mmt) cc_final: 0.6857 (mmm) REVERT: G 427 THR cc_start: 0.7351 (p) cc_final: 0.7089 (t) REVERT: H 49 ILE cc_start: 0.9099 (mm) cc_final: 0.8792 (mp) REVERT: M 58 MET cc_start: 0.8844 (mpp) cc_final: 0.8337 (mtt) REVERT: M 86 LYS cc_start: 0.8355 (tppp) cc_final: 0.7886 (mptt) REVERT: M 298 LYS cc_start: 0.8375 (ptpp) cc_final: 0.7995 (ttpp) REVERT: M 306 THR cc_start: 0.8936 (t) cc_final: 0.8472 (p) REVERT: M 321 ASP cc_start: 0.8692 (p0) cc_final: 0.8449 (p0) REVERT: N 77 ARG cc_start: 0.6165 (ptt180) cc_final: 0.5210 (mtt90) outliers start: 64 outliers final: 49 residues processed: 359 average time/residue: 0.3067 time to fit residues: 163.5990 Evaluate side-chains 350 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 300 time to evaluate : 2.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 180 GLN Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 443 GLN Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 95 PHE Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 81 LEU Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 209 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 127 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 GLN G 418 HIS ** G 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 567 ASN M 64 ASN ** N 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 18007 Z= 0.507 Angle : 0.762 12.533 24368 Z= 0.379 Chirality : 0.048 0.171 2790 Planarity : 0.005 0.059 3085 Dihedral : 9.567 173.305 2423 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 3.93 % Allowed : 15.58 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.18), residues: 2170 helix: -0.72 (0.15), residues: 1094 sheet: -3.78 (0.28), residues: 240 loop : -1.48 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 334 HIS 0.008 0.002 HIS G 163 PHE 0.018 0.002 PHE G 79 TYR 0.020 0.002 TYR G 61 ARG 0.005 0.001 ARG C 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 300 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: T 13 MET cc_start: 0.7443 (mmm) cc_final: 0.7015 (tpp) REVERT: B 14 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6887 (tt0) REVERT: B 83 MET cc_start: 0.7809 (mtp) cc_final: 0.7581 (mtt) REVERT: B 212 ASN cc_start: 0.8300 (m110) cc_final: 0.7650 (t0) REVERT: C 26 ASP cc_start: 0.7623 (p0) cc_final: 0.7397 (p0) REVERT: G 427 THR cc_start: 0.7555 (p) cc_final: 0.7178 (t) REVERT: G 443 GLN cc_start: 0.8214 (OUTLIER) cc_final: 0.7704 (tp40) REVERT: G 483 TYR cc_start: 0.8044 (m-80) cc_final: 0.7810 (m-80) REVERT: M 28 SER cc_start: 0.7275 (m) cc_final: 0.7070 (p) REVERT: M 58 MET cc_start: 0.8915 (mpp) cc_final: 0.8321 (mtt) REVERT: M 86 LYS cc_start: 0.8506 (tppp) cc_final: 0.8079 (mptt) REVERT: M 118 MET cc_start: 0.8353 (mtp) cc_final: 0.8141 (mtt) REVERT: M 298 LYS cc_start: 0.8374 (ptpp) cc_final: 0.8058 (ttpt) REVERT: M 306 THR cc_start: 0.8848 (t) cc_final: 0.8554 (p) REVERT: M 321 ASP cc_start: 0.8747 (p0) cc_final: 0.8360 (p0) REVERT: S 108 GLU cc_start: 0.7493 (pt0) cc_final: 0.6923 (tt0) outliers start: 77 outliers final: 59 residues processed: 355 average time/residue: 0.2898 time to fit residues: 156.4218 Evaluate side-chains 350 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 289 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 162 VAL Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 428 THR Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 443 GLN Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 140 THR Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 90 VAL Chi-restraints excluded: chain M residue 95 PHE Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 161 SER Chi-restraints excluded: chain M residue 265 MET Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain N residue 20 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 142 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 164 optimal weight: 6.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 435 ASN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 HIS ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 GLN ** G 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18007 Z= 0.206 Angle : 0.604 13.743 24368 Z= 0.296 Chirality : 0.042 0.168 2790 Planarity : 0.004 0.042 3085 Dihedral : 9.170 173.879 2423 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.17 % Allowed : 16.39 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.18), residues: 2170 helix: -0.23 (0.16), residues: 1084 sheet: -3.44 (0.30), residues: 249 loop : -1.18 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 172 HIS 0.004 0.001 HIS M 62 PHE 0.016 0.001 PHE M 83 TYR 0.014 0.001 TYR S 20 ARG 0.005 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 314 time to evaluate : 2.112 Fit side-chains revert: symmetry clash REVERT: T 13 MET cc_start: 0.7258 (mmm) cc_final: 0.7029 (tpp) REVERT: G 427 THR cc_start: 0.7430 (p) cc_final: 0.7108 (t) REVERT: G 584 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5048 (mmm) REVERT: M 58 MET cc_start: 0.8809 (mpp) cc_final: 0.8385 (mtt) REVERT: M 86 LYS cc_start: 0.8244 (tppp) cc_final: 0.7876 (mptt) REVERT: M 298 LYS cc_start: 0.8352 (ptpp) cc_final: 0.7980 (ttpp) REVERT: M 306 THR cc_start: 0.8868 (t) cc_final: 0.8567 (p) REVERT: M 366 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7058 (mm-30) REVERT: S 79 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8217 (tt) REVERT: S 99 CYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8325 (m) REVERT: S 108 GLU cc_start: 0.7039 (pt0) cc_final: 0.6542 (tt0) outliers start: 62 outliers final: 49 residues processed: 358 average time/residue: 0.3079 time to fit residues: 164.2071 Evaluate side-chains 341 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 289 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 269 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 102 GLU Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 584 MET Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 265 MET Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 127 SER Chi-restraints excluded: chain N residue 20 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 1.9990 chunk 200 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 435 ASN ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 567 ASN M 64 ASN ** N 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 18007 Z= 0.248 Angle : 0.626 13.343 24368 Z= 0.306 Chirality : 0.043 0.164 2790 Planarity : 0.004 0.041 3085 Dihedral : 9.096 173.434 2423 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.81 % Allowed : 17.21 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.18), residues: 2170 helix: -0.18 (0.16), residues: 1088 sheet: -3.39 (0.29), residues: 256 loop : -1.02 (0.23), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 172 HIS 0.004 0.001 HIS M 62 PHE 0.016 0.001 PHE M 83 TYR 0.020 0.002 TYR B 524 ARG 0.005 0.000 ARG B 243 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 294 time to evaluate : 2.098 Fit side-chains revert: symmetry clash REVERT: T 13 MET cc_start: 0.7307 (mmm) cc_final: 0.7089 (tpp) REVERT: G 201 MET cc_start: 0.7961 (mtp) cc_final: 0.7708 (mtp) REVERT: G 427 THR cc_start: 0.7450 (p) cc_final: 0.7099 (t) REVERT: G 584 MET cc_start: 0.6189 (OUTLIER) cc_final: 0.5296 (mmm) REVERT: M 58 MET cc_start: 0.8854 (mpp) cc_final: 0.8357 (mtt) REVERT: M 86 LYS cc_start: 0.8298 (tppp) cc_final: 0.7910 (mptt) REVERT: M 298 LYS cc_start: 0.8369 (ptpp) cc_final: 0.8024 (ttpt) REVERT: M 306 THR cc_start: 0.8849 (t) cc_final: 0.8582 (p) REVERT: M 366 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7109 (mm-30) REVERT: S 108 GLU cc_start: 0.7064 (pt0) cc_final: 0.6599 (tt0) outliers start: 55 outliers final: 48 residues processed: 333 average time/residue: 0.3139 time to fit residues: 157.7269 Evaluate side-chains 341 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 292 time to evaluate : 1.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 143 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain G residue 584 MET Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 265 MET Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 390 ILE Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 198 optimal weight: 1.9990 chunk 172 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN ** N 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 18007 Z= 0.230 Angle : 0.627 13.313 24368 Z= 0.305 Chirality : 0.043 0.168 2790 Planarity : 0.004 0.041 3085 Dihedral : 9.033 174.018 2423 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.45 % Allowed : 17.93 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.18), residues: 2170 helix: -0.10 (0.16), residues: 1082 sheet: -3.29 (0.30), residues: 255 loop : -1.01 (0.23), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 172 HIS 0.004 0.001 HIS M 62 PHE 0.016 0.001 PHE M 83 TYR 0.026 0.002 TYR B 72 ARG 0.005 0.000 ARG B 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4340 Ramachandran restraints generated. 2170 Oldfield, 0 Emsley, 2170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 297 time to evaluate : 2.026 Fit side-chains revert: symmetry clash REVERT: T 13 MET cc_start: 0.7272 (mmm) cc_final: 0.7070 (tpp) REVERT: G 201 MET cc_start: 0.7949 (mtp) cc_final: 0.7681 (mtp) REVERT: G 427 THR cc_start: 0.7376 (p) cc_final: 0.7103 (t) REVERT: H 116 LEU cc_start: 0.8542 (tt) cc_final: 0.8288 (tp) REVERT: M 58 MET cc_start: 0.8838 (mpp) cc_final: 0.8366 (mtt) REVERT: M 86 LYS cc_start: 0.8280 (tppp) cc_final: 0.7868 (mptt) REVERT: M 298 LYS cc_start: 0.8360 (ptpp) cc_final: 0.8013 (ttpt) REVERT: M 306 THR cc_start: 0.8797 (t) cc_final: 0.8532 (p) REVERT: M 366 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7089 (mm-30) outliers start: 48 outliers final: 46 residues processed: 330 average time/residue: 0.2985 time to fit residues: 148.4040 Evaluate side-chains 334 residues out of total 1959 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 288 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 162 THR Chi-restraints excluded: chain B residue 42 THR Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 267 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain B residue 347 SER Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain B residue 489 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain G residue 276 THR Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 321 ASP Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 368 LEU Chi-restraints excluded: chain G residue 372 LEU Chi-restraints excluded: chain G residue 433 VAL Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 506 LEU Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 527 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 102 GLU Chi-restraints excluded: chain H residue 118 ASP Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain M residue 36 ILE Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 88 VAL Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 265 MET Chi-restraints excluded: chain M residue 271 THR Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 310 VAL Chi-restraints excluded: chain M residue 378 VAL Chi-restraints excluded: chain M residue 390 ILE Chi-restraints excluded: chain S residue 99 CYS Chi-restraints excluded: chain S residue 127 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 72 optimal weight: 20.0000 chunk 177 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 166 HIS ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN ** C 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 64 ASN ** N 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.169385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135422 restraints weight = 23468.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.133680 restraints weight = 27140.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.135540 restraints weight = 29539.272| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18007 Z= 0.226 Angle : 0.634 13.220 24368 Z= 0.307 Chirality : 0.043 0.163 2790 Planarity : 0.004 0.041 3085 Dihedral : 8.975 174.259 2423 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.66 % Allowed : 17.88 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 2170 helix: -0.03 (0.16), residues: 1079 sheet: -3.25 (0.30), residues: 255 loop : -1.00 (0.23), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 172 HIS 0.004 0.001 HIS M 62 PHE 0.017 0.001 PHE M 83 TYR 0.031 0.002 TYR B 72 ARG 0.005 0.000 ARG B 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3942.87 seconds wall clock time: 72 minutes 30.13 seconds (4350.13 seconds total)