Starting phenix.real_space_refine on Thu Mar 14 23:25:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqe_10549/03_2024/6tqe_10549_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqe_10549/03_2024/6tqe_10549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqe_10549/03_2024/6tqe_10549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqe_10549/03_2024/6tqe_10549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqe_10549/03_2024/6tqe_10549_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tqe_10549/03_2024/6tqe_10549_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 24 5.16 5 C 6478 2.51 5 N 1766 2.21 5 O 1800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 115": "NH1" <-> "NH2" Residue "A ARG 138": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ASP 182": "OD1" <-> "OD2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A ARG 294": "NH1" <-> "NH2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "A ARG 441": "NH1" <-> "NH2" Residue "A ARG 461": "NH1" <-> "NH2" Residue "A GLU 490": "OE1" <-> "OE2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A ARG 628": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "B ARG 115": "NH1" <-> "NH2" Residue "B ARG 138": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B ARG 294": "NH1" <-> "NH2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B ASP 363": "OD1" <-> "OD2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ASP 423": "OD1" <-> "OD2" Residue "B ARG 441": "NH1" <-> "NH2" Residue "B ARG 461": "NH1" <-> "NH2" Residue "B GLU 490": "OE1" <-> "OE2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B ARG 628": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10076 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5006 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 603} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 5006 Classifications: {'peptide': 634} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 30, 'TRANS': 603} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.69, per 1000 atoms: 0.56 Number of scatterers: 10076 At special positions: 0 Unit cell: (82.6537, 82.6537, 147.413, 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 24 16.00 P 6 15.00 Mg 2 11.99 O 1800 8.00 N 1766 7.00 C 6478 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: 3.71 Conformation dependent library (CDL) restraints added in 1.8 seconds 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2348 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 8 sheets defined 43.7% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.17 Creating SS restraints... Processing helix chain 'A' and resid 16 through 19 No H-bonds generated for 'chain 'A' and resid 16 through 19' Processing helix chain 'A' and resid 21 through 43 removed outlier: 4.371A pdb=" N THR A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA A 36 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR A 43 " --> pdb=" O VAL A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 removed outlier: 4.014A pdb=" N ARG A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 54' Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.694A pdb=" N VAL A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 67 through 108 removed outlier: 4.020A pdb=" N VAL A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU A 74 " --> pdb=" O MET A 70 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 75 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 87 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ASP A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET A 95 " --> pdb=" O GLN A 91 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN A 100 " --> pdb=" O TYR A 96 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 101 " --> pdb=" O THR A 97 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 103 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 107 " --> pdb=" O PHE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 121 No H-bonds generated for 'chain 'A' and resid 118 through 121' Processing helix chain 'A' and resid 124 through 127 No H-bonds generated for 'chain 'A' and resid 124 through 127' Processing helix chain 'A' and resid 133 through 139 removed outlier: 3.667A pdb=" N VAL A 139 " --> pdb=" O HIS A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 No H-bonds generated for 'chain 'A' and resid 143 through 146' Processing helix chain 'A' and resid 150 through 165 removed outlier: 4.175A pdb=" N TRP A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS A 159 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN A 163 " --> pdb=" O HIS A 159 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 176 Processing helix chain 'A' and resid 186 through 189 No H-bonds generated for 'chain 'A' and resid 186 through 189' Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.828A pdb=" N GLN A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 221 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N VAL A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 264 removed outlier: 3.854A pdb=" N VAL A 254 " --> pdb=" O MET A 250 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 255 " --> pdb=" O PHE A 251 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 256 " --> pdb=" O TRP A 252 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 260 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 282 removed outlier: 3.861A pdb=" N ARG A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU A 280 " --> pdb=" O SER A 276 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 281 " --> pdb=" O PHE A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 303 removed outlier: 3.815A pdb=" N LEU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP A 295 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 296 " --> pdb=" O ARG A 292 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLU A 298 " --> pdb=" O ARG A 294 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ALA A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 322 removed outlier: 3.605A pdb=" N LEU A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Proline residue: A 319 - end of helix Processing helix chain 'A' and resid 337 through 340 No H-bonds generated for 'chain 'A' and resid 337 through 340' Processing helix chain 'A' and resid 349 through 352 No H-bonds generated for 'chain 'A' and resid 349 through 352' Processing helix chain 'A' and resid 355 through 358 No H-bonds generated for 'chain 'A' and resid 355 through 358' Processing helix chain 'A' and resid 365 through 386 removed outlier: 3.562A pdb=" N SER A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS A 378 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A 383 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N PHE A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ARG A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 4.159A pdb=" N PHE A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 405 removed outlier: 4.303A pdb=" N LEU A 404 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 527 through 532 removed outlier: 3.851A pdb=" N LYS A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N VAL A 532 " --> pdb=" O THR A 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 527 through 532' Processing helix chain 'A' and resid 558 through 565 removed outlier: 3.715A pdb=" N ALA A 562 " --> pdb=" O ARG A 558 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 565 " --> pdb=" O PHE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 596 Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'B' and resid 16 through 19 No H-bonds generated for 'chain 'B' and resid 16 through 19' Processing helix chain 'B' and resid 21 through 43 removed outlier: 4.371A pdb=" N THR B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE B 29 " --> pdb=" O LYS B 25 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER B 30 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N CYS B 33 " --> pdb=" O ILE B 29 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA B 36 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR B 43 " --> pdb=" O VAL B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 removed outlier: 4.015A pdb=" N ARG B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 54' Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.694A pdb=" N VAL B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 67 through 108 removed outlier: 4.020A pdb=" N VAL B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU B 74 " --> pdb=" O MET B 70 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ALA B 81 " --> pdb=" O SER B 77 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 84 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER B 89 " --> pdb=" O ASN B 85 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASP B 94 " --> pdb=" O TYR B 90 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N MET B 95 " --> pdb=" O GLN B 91 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 101 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA B 107 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 121 No H-bonds generated for 'chain 'B' and resid 118 through 121' Processing helix chain 'B' and resid 124 through 127 No H-bonds generated for 'chain 'B' and resid 124 through 127' Processing helix chain 'B' and resid 133 through 139 removed outlier: 3.668A pdb=" N VAL B 139 " --> pdb=" O HIS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 146 No H-bonds generated for 'chain 'B' and resid 143 through 146' Processing helix chain 'B' and resid 150 through 165 removed outlier: 4.176A pdb=" N TRP B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS B 159 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR B 162 " --> pdb=" O THR B 158 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 163 " --> pdb=" O HIS B 159 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP B 164 " --> pdb=" O HIS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 176 Processing helix chain 'B' and resid 186 through 189 No H-bonds generated for 'chain 'B' and resid 186 through 189' Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 216 through 226 removed outlier: 3.827A pdb=" N GLN B 220 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER B 221 " --> pdb=" O GLY B 217 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N VAL B 225 " --> pdb=" O SER B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 264 removed outlier: 3.854A pdb=" N VAL B 254 " --> pdb=" O MET B 250 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 256 " --> pdb=" O TRP B 252 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 260 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 261 " --> pdb=" O TYR B 257 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 263 " --> pdb=" O PHE B 259 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 282 removed outlier: 3.861A pdb=" N ARG B 278 " --> pdb=" O TRP B 274 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLU B 280 " --> pdb=" O SER B 276 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 281 " --> pdb=" O PHE B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 303 removed outlier: 3.816A pdb=" N LEU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP B 295 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 296 " --> pdb=" O ARG B 292 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLU B 298 " --> pdb=" O ARG B 294 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ALA B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B 300 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 322 removed outlier: 3.605A pdb=" N LEU B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 314 " --> pdb=" O GLY B 310 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Proline residue: B 319 - end of helix Processing helix chain 'B' and resid 337 through 340 No H-bonds generated for 'chain 'B' and resid 337 through 340' Processing helix chain 'B' and resid 349 through 352 No H-bonds generated for 'chain 'B' and resid 349 through 352' Processing helix chain 'B' and resid 355 through 358 No H-bonds generated for 'chain 'B' and resid 355 through 358' Processing helix chain 'B' and resid 365 through 386 removed outlier: 3.562A pdb=" N SER B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS B 378 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP B 379 " --> pdb=" O GLY B 375 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 383 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N PHE B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 removed outlier: 4.159A pdb=" N PHE B 394 " --> pdb=" O ALA B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 405 removed outlier: 4.301A pdb=" N LEU B 404 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 405 " --> pdb=" O LEU B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 472 Processing helix chain 'B' and resid 527 through 532 removed outlier: 3.851A pdb=" N LYS B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B 532 " --> pdb=" O THR B 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 527 through 532' Processing helix chain 'B' and resid 558 through 565 removed outlier: 3.716A pdb=" N ALA B 562 " --> pdb=" O ARG B 558 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 565 " --> pdb=" O PHE B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 596 Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing sheet with id= A, first strand: chain 'A' and resid 418 through 421 Processing sheet with id= B, first strand: chain 'A' and resid 427 through 429 Processing sheet with id= C, first strand: chain 'A' and resid 480 through 482 removed outlier: 3.927A pdb=" N VAL A 434 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 443 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N THR A 436 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG A 441 " --> pdb=" O THR A 436 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 627 through 631 removed outlier: 6.925A pdb=" N SER A 455 " --> pdb=" O ASN A 617 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LEU A 619 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 457 " --> pdb=" O LEU A 619 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU A 621 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR A 459 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 602 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ILE A 458 " --> pdb=" O VAL A 602 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER A 604 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL A 605 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 418 through 421 Processing sheet with id= F, first strand: chain 'B' and resid 427 through 429 Processing sheet with id= G, first strand: chain 'B' and resid 480 through 482 removed outlier: 3.927A pdb=" N VAL B 434 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ILE B 443 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N THR B 436 " --> pdb=" O ARG B 441 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ARG B 441 " --> pdb=" O THR B 436 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 627 through 631 removed outlier: 6.925A pdb=" N SER B 455 " --> pdb=" O ASN B 617 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU B 619 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 457 " --> pdb=" O LEU B 619 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N LEU B 621 " --> pdb=" O VAL B 457 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N THR B 459 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL B 602 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ILE B 458 " --> pdb=" O VAL B 602 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N SER B 604 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 605 " --> pdb=" O LEU B 574 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 570 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: 2.51 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3257 1.34 - 1.46: 2248 1.46 - 1.57: 4771 1.57 - 1.69: 10 1.69 - 1.81: 40 Bond restraints: 10326 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.18e+01 bond pdb=" C4 ATP B 701 " pdb=" C5 ATP B 701 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 6.01e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.94e+01 bond pdb=" C5 ATP B 701 " pdb=" C6 ATP B 701 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.93e+01 bond pdb=" C5 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.387 1.339 0.048 1.00e-02 1.00e+04 2.27e+01 ... (remaining 10321 not shown) Histogram of bond angle deviations from ideal: 100.26 - 107.39: 425 107.39 - 114.52: 5953 114.52 - 121.64: 5448 121.64 - 128.77: 2148 128.77 - 135.90: 114 Bond angle restraints: 14088 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 116.60 23.27 1.00e+00 1.00e+00 5.42e+02 angle pdb=" PB ATP B 701 " pdb=" O3B ATP B 701 " pdb=" PG ATP B 701 " ideal model delta sigma weight residual 139.87 116.62 23.25 1.00e+00 1.00e+00 5.41e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 115.99 20.84 1.00e+00 1.00e+00 4.34e+02 angle pdb=" PA ATP B 701 " pdb=" O3A ATP B 701 " pdb=" PB ATP B 701 " ideal model delta sigma weight residual 136.83 116.02 20.81 1.00e+00 1.00e+00 4.33e+02 angle pdb=" C5 ATP B 701 " pdb=" C4 ATP B 701 " pdb=" N3 ATP B 701 " ideal model delta sigma weight residual 126.80 118.05 8.75 1.00e+00 1.00e+00 7.66e+01 ... (remaining 14083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5382 17.47 - 34.95: 552 34.95 - 52.42: 124 52.42 - 69.89: 20 69.89 - 87.37: 8 Dihedral angle restraints: 6086 sinusoidal: 2436 harmonic: 3650 Sorted by residual: dihedral pdb=" CA SER B 13 " pdb=" C SER B 13 " pdb=" N ARG B 14 " pdb=" CA ARG B 14 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA SER A 13 " pdb=" C SER A 13 " pdb=" N ARG A 14 " pdb=" CA ARG A 14 " ideal model delta harmonic sigma weight residual -180.00 -153.72 -26.28 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA PHE A 358 " pdb=" C PHE A 358 " pdb=" N ALA A 359 " pdb=" CA ALA A 359 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 6083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1085 0.054 - 0.108: 417 0.108 - 0.162: 74 0.162 - 0.216: 12 0.216 - 0.270: 4 Chirality restraints: 1592 Sorted by residual: chirality pdb=" CA THR B 318 " pdb=" N THR B 318 " pdb=" C THR B 318 " pdb=" CB THR B 318 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA THR A 318 " pdb=" N THR A 318 " pdb=" C THR A 318 " pdb=" CB THR A 318 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ASN A 183 " pdb=" N ASN A 183 " pdb=" C ASN A 183 " pdb=" CB ASN A 183 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1589 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 436 " 0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO A 437 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 437 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 437 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 436 " -0.034 5.00e-02 4.00e+02 5.12e-02 4.20e+00 pdb=" N PRO B 437 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 437 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 437 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 444 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO B 445 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 445 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 445 " 0.026 5.00e-02 4.00e+02 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 153 2.64 - 3.21: 8524 3.21 - 3.77: 13973 3.77 - 4.34: 18282 4.34 - 4.90: 30181 Nonbonded interactions: 71113 Sorted by model distance: nonbonded pdb=" O2G ATP B 701 " pdb="MG MG B 702 " model vdw 2.077 2.170 nonbonded pdb=" O2G ATP A 701 " pdb="MG MG A 702 " model vdw 2.079 2.170 nonbonded pdb=" O2B ATP A 701 " pdb="MG MG A 702 " model vdw 2.109 2.170 nonbonded pdb=" O2B ATP B 701 " pdb="MG MG B 702 " model vdw 2.109 2.170 nonbonded pdb=" OG1 THR A 467 " pdb="MG MG A 702 " model vdw 2.125 2.170 ... (remaining 71108 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 'A' selection = chain 'B' } 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.130 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.560 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 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 : 0.007 0.082 10326 Z= 0.461 Angle : 1.043 23.271 14088 Z= 0.664 Chirality : 0.057 0.270 1592 Planarity : 0.006 0.051 1786 Dihedral : 14.948 87.368 3738 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 0.76 % Allowed : 10.68 % Favored : 88.56 % 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: -6.13 (0.15), residues: 1264 helix: -4.57 (0.09), residues: 654 sheet: -2.07 (0.42), residues: 120 loop : -3.59 (0.21), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 12 HIS 0.003 0.001 HIS B 615 PHE 0.031 0.002 PHE A 88 TYR 0.014 0.002 TYR B 327 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 5 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8031 (pp) REVERT: A 131 MET cc_start: 0.8590 (mtp) cc_final: 0.8258 (ttm) REVERT: B 5 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8097 (pp) REVERT: B 14 ARG cc_start: 0.7357 (ttp-110) cc_final: 0.7014 (ttp80) outliers start: 8 outliers final: 4 residues processed: 72 average time/residue: 0.2227 time to fit residues: 23.6211 Evaluate side-chains 58 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 52 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 52 optimal weight: 0.0270 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 338 ASN ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 GLN B 163 GLN B 204 ASN B 338 ASN ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 618 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10326 Z= 0.131 Angle : 0.558 7.843 14088 Z= 0.276 Chirality : 0.041 0.166 1592 Planarity : 0.004 0.059 1786 Dihedral : 7.010 73.262 1474 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.28 % Allowed : 3.88 % Favored : 95.84 % 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: -5.10 (0.18), residues: 1264 helix: -3.78 (0.13), residues: 644 sheet: -1.25 (0.46), residues: 106 loop : -3.12 (0.22), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 274 HIS 0.001 0.000 HIS B 378 PHE 0.009 0.001 PHE A 573 TYR 0.009 0.001 TYR A 257 ARG 0.005 0.000 ARG B 613 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 1.155 Fit side-chains REVERT: A 385 ARG cc_start: 0.9021 (ptt90) cc_final: 0.8701 (ptt-90) REVERT: B 14 ARG cc_start: 0.7288 (ttp-110) cc_final: 0.7001 (ttp80) outliers start: 3 outliers final: 1 residues processed: 89 average time/residue: 0.1899 time to fit residues: 25.3933 Evaluate side-chains 58 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 123 optimal weight: 9.9990 chunk 102 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 498 GLN A 515 ASN A 618 GLN B 353 GLN B 498 GLN B 515 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10326 Z= 0.281 Angle : 0.630 7.609 14088 Z= 0.311 Chirality : 0.045 0.166 1592 Planarity : 0.004 0.058 1786 Dihedral : 6.935 74.529 1474 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.19 % Allowed : 3.59 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.58 (0.19), residues: 1264 helix: -3.26 (0.15), residues: 644 sheet: -1.40 (0.45), residues: 120 loop : -2.92 (0.24), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 477 HIS 0.002 0.001 HIS B 402 PHE 0.018 0.002 PHE B 103 TYR 0.011 0.001 TYR B 513 ARG 0.003 0.000 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 1.271 Fit side-chains REVERT: A 385 ARG cc_start: 0.9093 (ptt90) cc_final: 0.8862 (ptt90) REVERT: B 14 ARG cc_start: 0.7356 (ttp-110) cc_final: 0.7044 (ttp80) outliers start: 2 outliers final: 1 residues processed: 73 average time/residue: 0.1979 time to fit residues: 22.1163 Evaluate side-chains 50 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 12 optimal weight: 0.0270 chunk 54 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10326 Z= 0.134 Angle : 0.536 7.538 14088 Z= 0.264 Chirality : 0.041 0.160 1592 Planarity : 0.003 0.054 1786 Dihedral : 6.249 72.858 1474 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.20), residues: 1264 helix: -2.75 (0.17), residues: 628 sheet: -0.80 (0.48), residues: 108 loop : -2.57 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 274 HIS 0.001 0.000 HIS B 159 PHE 0.023 0.001 PHE B 88 TYR 0.009 0.001 TYR B 257 ARG 0.003 0.000 ARG B 613 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 1.248 Fit side-chains REVERT: B 366 ASP cc_start: 0.8233 (m-30) cc_final: 0.8032 (m-30) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1777 time to fit residues: 20.3250 Evaluate side-chains 48 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 618 GLN B 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10326 Z= 0.212 Angle : 0.572 7.422 14088 Z= 0.279 Chirality : 0.043 0.163 1592 Planarity : 0.003 0.054 1786 Dihedral : 6.225 75.161 1474 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.19 % Allowed : 2.55 % Favored : 97.26 % 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: -3.70 (0.21), residues: 1264 helix: -2.57 (0.18), residues: 628 sheet: -1.02 (0.47), residues: 122 loop : -2.47 (0.25), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 274 HIS 0.002 0.000 HIS B 402 PHE 0.015 0.001 PHE B 88 TYR 0.007 0.001 TYR B 513 ARG 0.006 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 366 ASP cc_start: 0.8268 (m-30) cc_final: 0.8054 (m-30) outliers start: 2 outliers final: 0 residues processed: 70 average time/residue: 0.1743 time to fit residues: 19.6397 Evaluate side-chains 49 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 0.0870 chunk 10 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 overall best weight: 5.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN B 498 GLN ** B 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 10326 Z= 0.422 Angle : 0.727 7.677 14088 Z= 0.357 Chirality : 0.050 0.174 1592 Planarity : 0.004 0.056 1786 Dihedral : 7.025 83.310 1474 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 0.19 % Allowed : 3.50 % Favored : 96.31 % 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: -3.86 (0.21), residues: 1264 helix: -2.69 (0.17), residues: 648 sheet: -1.07 (0.49), residues: 120 loop : -2.55 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 477 HIS 0.004 0.001 HIS A 402 PHE 0.018 0.002 PHE B 88 TYR 0.020 0.002 TYR A 257 ARG 0.006 0.001 ARG B 400 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ARG cc_start: 0.7346 (ttp-110) cc_final: 0.7035 (ttp80) REVERT: B 14 ARG cc_start: 0.7386 (ttp-110) cc_final: 0.7067 (ttp80) outliers start: 2 outliers final: 0 residues processed: 68 average time/residue: 0.1876 time to fit residues: 19.5371 Evaluate side-chains 48 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10326 Z= 0.256 Angle : 0.623 7.527 14088 Z= 0.303 Chirality : 0.045 0.167 1592 Planarity : 0.004 0.056 1786 Dihedral : 6.709 83.481 1474 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 0.19 % Allowed : 1.70 % Favored : 98.11 % 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: -3.67 (0.22), residues: 1264 helix: -2.55 (0.18), residues: 652 sheet: -0.93 (0.49), residues: 120 loop : -2.44 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 477 HIS 0.002 0.001 HIS B 402 PHE 0.012 0.001 PHE B 573 TYR 0.012 0.001 TYR A 257 ARG 0.003 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 1.259 Fit side-chains REVERT: A 14 ARG cc_start: 0.7418 (ttp-110) cc_final: 0.7102 (ttp80) REVERT: B 14 ARG cc_start: 0.7445 (ttp-110) cc_final: 0.7123 (ttp80) outliers start: 2 outliers final: 0 residues processed: 70 average time/residue: 0.2057 time to fit residues: 21.9073 Evaluate side-chains 48 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 48 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 0.0270 chunk 23 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10326 Z= 0.178 Angle : 0.576 7.570 14088 Z= 0.279 Chirality : 0.043 0.165 1592 Planarity : 0.004 0.058 1786 Dihedral : 6.291 80.351 1474 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.09 % Allowed : 0.28 % Favored : 99.62 % 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: -3.41 (0.22), residues: 1264 helix: -2.30 (0.19), residues: 640 sheet: -0.79 (0.49), residues: 122 loop : -2.40 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 274 HIS 0.001 0.000 HIS A 402 PHE 0.011 0.001 PHE B 573 TYR 0.010 0.001 TYR B 90 ARG 0.013 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 1.121 Fit side-chains REVERT: A 129 SER cc_start: 0.9087 (m) cc_final: 0.8231 (p) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.1707 time to fit residues: 19.0938 Evaluate side-chains 50 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10326 Z= 0.265 Angle : 0.623 7.605 14088 Z= 0.302 Chirality : 0.045 0.169 1592 Planarity : 0.004 0.059 1786 Dihedral : 6.411 80.441 1474 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.19 % Allowed : 0.66 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.22), residues: 1264 helix: -2.22 (0.19), residues: 640 sheet: -0.70 (0.50), residues: 120 loop : -2.29 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 274 HIS 0.002 0.001 HIS B 402 PHE 0.012 0.001 PHE A 573 TYR 0.010 0.001 TYR B 90 ARG 0.012 0.000 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 64 time to evaluate : 1.216 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 66 average time/residue: 0.1730 time to fit residues: 18.2639 Evaluate side-chains 45 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 9.9990 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10326 Z= 0.315 Angle : 0.659 7.692 14088 Z= 0.322 Chirality : 0.047 0.171 1592 Planarity : 0.004 0.065 1786 Dihedral : 6.661 82.535 1474 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.19 % Allowed : 0.47 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.22), residues: 1264 helix: -2.25 (0.19), residues: 640 sheet: -0.79 (0.51), residues: 120 loop : -2.29 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 274 HIS 0.003 0.001 HIS B 402 PHE 0.034 0.002 PHE B 88 TYR 0.009 0.001 TYR A 257 ARG 0.011 0.000 ARG B 115 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2528 Ramachandran restraints generated. 1264 Oldfield, 0 Emsley, 1264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 1.126 Fit side-chains REVERT: A 14 ARG cc_start: 0.7425 (ttp-110) cc_final: 0.7093 (ttp80) REVERT: B 14 ARG cc_start: 0.7422 (ttp-110) cc_final: 0.7098 (ttp80) outliers start: 2 outliers final: 0 residues processed: 67 average time/residue: 0.1908 time to fit residues: 19.9867 Evaluate side-chains 50 residues out of total 1060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.0010 chunk 92 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 87 optimal weight: 20.0000 chunk 5 optimal weight: 0.7980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN A 353 GLN ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN ** B 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.077758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.065595 restraints weight = 24246.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.066564 restraints weight = 16683.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.067323 restraints weight = 12648.043| |-----------------------------------------------------------------------------| r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10326 Z= 0.129 Angle : 0.554 7.611 14088 Z= 0.266 Chirality : 0.041 0.157 1592 Planarity : 0.003 0.055 1786 Dihedral : 5.858 77.690 1474 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.19 % Allowed : 0.47 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.22), residues: 1264 helix: -2.01 (0.19), residues: 638 sheet: -0.16 (0.54), residues: 108 loop : -2.22 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 47 HIS 0.002 0.000 HIS A 160 PHE 0.026 0.001 PHE B 88 TYR 0.008 0.001 TYR B 257 ARG 0.012 0.000 ARG B 115 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1750.30 seconds wall clock time: 32 minutes 25.15 seconds (1945.15 seconds total)