Starting phenix.real_space_refine on Mon Apr 8 05:24:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vff_31951/04_2024/7vff_31951.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vff_31951/04_2024/7vff_31951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vff_31951/04_2024/7vff_31951.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vff_31951/04_2024/7vff_31951.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vff_31951/04_2024/7vff_31951.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vff_31951/04_2024/7vff_31951.pdb" } resolution = 4.1 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 8043 2.51 5 N 2043 2.21 5 O 2457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 113": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A ASP 333": "OD1" <-> "OD2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B GLU 317": "OE1" <-> "OE2" Residue "B ASP 333": "OD1" <-> "OD2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 165": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C GLU 248": "OE1" <-> "OE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "C GLU 314": "OE1" <-> "OE2" Residue "C GLU 317": "OE1" <-> "OE2" Residue "C ASP 333": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12579 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4193 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Chain: "B" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4193 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Chain: "C" Number of atoms: 4193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4193 Classifications: {'peptide': 527} Link IDs: {'PTRANS': 25, 'TRANS': 501} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ARG A 83 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG A 83 " occ=0.50 residue: pdb=" N ARG B 83 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG B 83 " occ=0.50 residue: pdb=" N ARG C 83 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG C 83 " occ=0.50 Time building chain proxies: 6.56, per 1000 atoms: 0.52 Number of scatterers: 12579 At special positions: 0 Unit cell: (99.68, 104.16, 106.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 2457 8.00 N 2043 7.00 C 8043 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: 4.33 Conformation dependent library (CDL) restraints added in 2.3 seconds 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 33 sheets defined 20.3% alpha, 43.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'A' and resid 89 through 94 Processing helix chain 'A' and resid 112 through 120 Processing helix chain 'A' and resid 122 through 129 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.696A pdb=" N VAL A 164 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 198 through 206 Processing helix chain 'A' and resid 279 through 295 removed outlier: 4.169A pdb=" N ASP A 293 " --> pdb=" O SER A 289 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.865A pdb=" N TRP A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 401 " --> pdb=" O VAL A 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 396 through 401' Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 458 through 469 Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 112 through 120 Processing helix chain 'B' and resid 122 through 129 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.696A pdb=" N VAL B 164 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 198 through 206 Processing helix chain 'B' and resid 279 through 295 removed outlier: 4.170A pdb=" N ASP B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ASP B 294 " --> pdb=" O ARG B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 395 Processing helix chain 'B' and resid 396 through 401 removed outlier: 3.865A pdb=" N TRP B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR B 401 " --> pdb=" O VAL B 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 396 through 401' Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 458 through 469 Processing helix chain 'B' and resid 516 through 521 Processing helix chain 'C' and resid 89 through 94 Processing helix chain 'C' and resid 112 through 120 Processing helix chain 'C' and resid 122 through 129 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.696A pdb=" N VAL C 164 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 198 through 206 Processing helix chain 'C' and resid 279 through 295 removed outlier: 4.169A pdb=" N ASP C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP C 294 " --> pdb=" O ARG C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 395 Processing helix chain 'C' and resid 396 through 401 removed outlier: 3.866A pdb=" N TRP C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR C 401 " --> pdb=" O VAL C 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 396 through 401' Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 458 through 469 Processing helix chain 'C' and resid 516 through 521 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.951A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU A 69 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 40 removed outlier: 3.951A pdb=" N ILE A 215 " --> pdb=" O HIS A 68 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS A 68 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR A 217 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU A 66 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44 removed outlier: 7.157A pdb=" N ASN A 96 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU A 111 " --> pdb=" O ASN A 96 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 98 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU A 109 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE A 100 " --> pdb=" O ILE A 107 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 79 removed outlier: 6.941A pdb=" N VAL A 78 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 139 through 141 removed outlier: 5.729A pdb=" N ARG A 83 " --> pdb=" O ASP A 194 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 236 removed outlier: 4.473A pdb=" N GLN A 522 " --> pdb=" O TYR A 262 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA A 252 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478 removed outlier: 3.857A pdb=" N ARG A 475 " --> pdb=" O VAL A 257 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA A 252 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU A 532 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER A 254 " --> pdb=" O ASN A 530 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN A 522 " --> pdb=" O TYR A 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 247 removed outlier: 6.318A pdb=" N LYS A 502 " --> pdb=" O PHE A 447 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE A 447 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER A 504 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL A 445 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG A 506 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU A 443 " --> pdb=" O ARG A 506 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 508 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE A 447 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL A 451 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 296 through 299 Processing sheet with id=AB1, first strand: chain 'A' and resid 320 through 323 removed outlier: 6.760A pdb=" N ASP A 327 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE A 368 " --> pdb=" O ASP A 327 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR A 329 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY A 370 " --> pdb=" O TYR A 329 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS A 331 " --> pdb=" O GLY A 370 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TYR A 372 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP A 333 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE A 365 " --> pdb=" O HIS A 386 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N HIS A 386 " --> pdb=" O PHE A 365 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA A 367 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE A 384 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR A 369 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG A 378 " --> pdb=" O SER A 373 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 349 through 350 Processing sheet with id=AB3, first strand: chain 'B' and resid 32 through 40 removed outlier: 3.951A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU B 69 " --> pdb=" O ILE B 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 32 through 40 removed outlier: 3.951A pdb=" N ILE B 215 " --> pdb=" O HIS B 68 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N HIS B 68 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N TYR B 217 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N LEU B 66 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 44 removed outlier: 7.157A pdb=" N ASN B 96 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU B 111 " --> pdb=" O ASN B 96 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 98 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU B 109 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE B 100 " --> pdb=" O ILE B 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 78 through 79 removed outlier: 6.942A pdb=" N VAL B 78 " --> pdb=" O ILE B 148 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 139 through 141 removed outlier: 5.729A pdb=" N ARG B 83 " --> pdb=" O ASP B 194 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 227 through 236 removed outlier: 4.473A pdb=" N GLN B 522 " --> pdb=" O TYR B 262 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 252 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 475 through 478 removed outlier: 3.857A pdb=" N ARG B 475 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA B 252 " --> pdb=" O LEU B 532 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N LEU B 532 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER B 254 " --> pdb=" O ASN B 530 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN B 522 " --> pdb=" O TYR B 262 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 243 through 247 removed outlier: 6.317A pdb=" N LYS B 502 " --> pdb=" O PHE B 447 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N PHE B 447 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N SER B 504 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL B 445 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG B 506 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU B 443 " --> pdb=" O ARG B 506 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL B 508 " --> pdb=" O SER B 441 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE B 447 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL B 451 " --> pdb=" O PHE B 447 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 296 through 299 Processing sheet with id=AC3, first strand: chain 'B' and resid 320 through 323 removed outlier: 6.760A pdb=" N ASP B 327 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE B 368 " --> pdb=" O ASP B 327 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR B 329 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY B 370 " --> pdb=" O TYR B 329 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS B 331 " --> pdb=" O GLY B 370 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TYR B 372 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP B 333 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N PHE B 365 " --> pdb=" O HIS B 386 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N HIS B 386 " --> pdb=" O PHE B 365 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ALA B 367 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE B 384 " --> pdb=" O ALA B 367 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N THR B 369 " --> pdb=" O ALA B 382 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 378 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 349 through 350 Processing sheet with id=AC5, first strand: chain 'C' and resid 32 through 40 removed outlier: 3.952A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C 69 " --> pdb=" O ILE C 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 32 through 40 removed outlier: 3.952A pdb=" N ILE C 215 " --> pdb=" O HIS C 68 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N HIS C 68 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N TYR C 217 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N LEU C 66 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 42 through 44 removed outlier: 7.158A pdb=" N ASN C 96 " --> pdb=" O GLU C 111 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU C 111 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 98 " --> pdb=" O GLU C 109 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU C 109 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE C 100 " --> pdb=" O ILE C 107 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.941A pdb=" N VAL C 78 " --> pdb=" O ILE C 148 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 139 through 141 removed outlier: 5.729A pdb=" N ARG C 83 " --> pdb=" O ASP C 194 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 227 through 236 removed outlier: 4.473A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 252 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 475 through 478 removed outlier: 3.857A pdb=" N ARG C 475 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ALA C 252 " --> pdb=" O LEU C 532 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N LEU C 532 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER C 254 " --> pdb=" O ASN C 530 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN C 522 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 243 through 247 removed outlier: 6.318A pdb=" N LYS C 502 " --> pdb=" O PHE C 447 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N PHE C 447 " --> pdb=" O LYS C 502 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N SER C 504 " --> pdb=" O VAL C 445 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL C 445 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG C 506 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU C 443 " --> pdb=" O ARG C 506 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL C 508 " --> pdb=" O SER C 441 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N PHE C 447 " --> pdb=" O VAL C 451 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL C 451 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 296 through 299 Processing sheet with id=AD5, first strand: chain 'C' and resid 320 through 323 removed outlier: 6.760A pdb=" N ASP C 327 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ILE C 368 " --> pdb=" O ASP C 327 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR C 329 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY C 370 " --> pdb=" O TYR C 329 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS C 331 " --> pdb=" O GLY C 370 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TYR C 372 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP C 333 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N HIS C 383 " --> pdb=" O THR C 369 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR C 371 " --> pdb=" O PHE C 381 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE C 381 " --> pdb=" O THR C 371 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER C 373 " --> pdb=" O THR C 379 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N THR C 379 " --> pdb=" O SER C 373 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 349 through 350 515 hydrogen bonds defined for protein. 1365 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: 4.57 Time building geometry restraints manager: 4.75 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: 3989 1.34 - 1.45: 1878 1.45 - 1.57: 6928 1.57 - 1.69: 0 1.69 - 1.80: 60 Bond restraints: 12855 Sorted by residual: bond pdb=" N TYR C 453 " pdb=" CA TYR C 453 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.18e-02 7.18e+03 5.51e+00 bond pdb=" N TYR A 453 " pdb=" CA TYR A 453 " ideal model delta sigma weight residual 1.455 1.483 -0.028 1.18e-02 7.18e+03 5.46e+00 bond pdb=" N TYR B 453 " pdb=" CA TYR B 453 " ideal model delta sigma weight residual 1.455 1.483 -0.027 1.18e-02 7.18e+03 5.39e+00 bond pdb=" N TYR C 359 " pdb=" CA TYR C 359 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.04e+00 bond pdb=" N TYR A 359 " pdb=" CA TYR A 359 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.23e-02 6.61e+03 4.00e+00 ... (remaining 12850 not shown) Histogram of bond angle deviations from ideal: 99.00 - 106.00: 268 106.00 - 113.00: 7078 113.00 - 120.01: 4358 120.01 - 127.01: 5681 127.01 - 134.01: 105 Bond angle restraints: 17490 Sorted by residual: angle pdb=" CA ASP A 333 " pdb=" C ASP A 333 " pdb=" O ASP A 333 " ideal model delta sigma weight residual 121.72 117.99 3.73 1.18e+00 7.18e-01 9.98e+00 angle pdb=" CA ASP B 333 " pdb=" C ASP B 333 " pdb=" O ASP B 333 " ideal model delta sigma weight residual 121.72 118.02 3.70 1.18e+00 7.18e-01 9.84e+00 angle pdb=" CA ASP C 333 " pdb=" C ASP C 333 " pdb=" O ASP C 333 " ideal model delta sigma weight residual 121.72 118.03 3.69 1.18e+00 7.18e-01 9.76e+00 angle pdb=" CA TYR C 359 " pdb=" C TYR C 359 " pdb=" O TYR C 359 " ideal model delta sigma weight residual 120.58 117.66 2.92 1.07e+00 8.73e-01 7.46e+00 angle pdb=" CA TYR B 359 " pdb=" C TYR B 359 " pdb=" O TYR B 359 " ideal model delta sigma weight residual 120.58 117.66 2.92 1.07e+00 8.73e-01 7.45e+00 ... (remaining 17485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 6994 17.48 - 34.96: 600 34.96 - 52.45: 86 52.45 - 69.93: 15 69.93 - 87.41: 24 Dihedral angle restraints: 7719 sinusoidal: 3036 harmonic: 4683 Sorted by residual: dihedral pdb=" CA PRO A 483 " pdb=" C PRO A 483 " pdb=" N LYS A 484 " pdb=" CA LYS A 484 " ideal model delta harmonic sigma weight residual -180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PRO B 483 " pdb=" C PRO B 483 " pdb=" N LYS B 484 " pdb=" CA LYS B 484 " ideal model delta harmonic sigma weight residual 180.00 -158.61 -21.39 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA PRO C 483 " pdb=" C PRO C 483 " pdb=" N LYS C 484 " pdb=" CA LYS C 484 " ideal model delta harmonic sigma weight residual -180.00 -158.65 -21.35 0 5.00e+00 4.00e-02 1.82e+01 ... (remaining 7716 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1262 0.044 - 0.088: 504 0.088 - 0.132: 232 0.132 - 0.176: 12 0.176 - 0.220: 6 Chirality restraints: 2016 Sorted by residual: chirality pdb=" CA TYR C 359 " pdb=" N TYR C 359 " pdb=" C TYR C 359 " pdb=" CB TYR C 359 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA TYR A 359 " pdb=" N TYR A 359 " pdb=" C TYR A 359 " pdb=" CB TYR A 359 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA TYR B 359 " pdb=" N TYR B 359 " pdb=" C TYR B 359 " pdb=" CB TYR B 359 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 2013 not shown) Planarity restraints: 2235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 209 " -0.035 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO B 210 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 209 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 210 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 210 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 210 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 209 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO C 210 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 210 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 210 " 0.029 5.00e-02 4.00e+02 ... (remaining 2232 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4280 2.85 - 3.36: 10495 3.36 - 3.87: 20247 3.87 - 4.39: 22484 4.39 - 4.90: 39944 Nonbonded interactions: 97450 Sorted by model distance: nonbonded pdb=" OG SER C 322 " pdb=" OD1 ASP C 327 " model vdw 2.334 2.440 nonbonded pdb=" OG SER B 322 " pdb=" OD1 ASP B 327 " model vdw 2.334 2.440 nonbonded pdb=" OG SER A 322 " pdb=" OD1 ASP A 327 " model vdw 2.335 2.440 nonbonded pdb=" O PHE B 22 " pdb=" NZ LYS C 172 " model vdw 2.355 2.520 nonbonded pdb=" NE2 HIS A 128 " pdb=" OE1 GLU B 465 " model vdw 2.390 2.520 ... (remaining 97445 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' selection = chain 'C' } 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=0.50 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.060 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 35.090 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 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 0.064 12855 Z= 0.467 Angle : 0.723 8.446 17490 Z= 0.411 Chirality : 0.054 0.220 2016 Planarity : 0.005 0.052 2235 Dihedral : 13.866 87.411 4707 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 0.41 % Allowed : 4.95 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.19), residues: 1569 helix: -1.03 (0.29), residues: 237 sheet: 0.06 (0.22), residues: 462 loop : -0.67 (0.19), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 108 HIS 0.004 0.001 HIS A 97 PHE 0.028 0.003 PHE B 479 TYR 0.023 0.002 TYR C 157 ARG 0.021 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 425 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8844 (tttt) cc_final: 0.8586 (tttp) REVERT: A 208 TYR cc_start: 0.8073 (m-80) cc_final: 0.7810 (m-80) REVERT: A 298 VAL cc_start: 0.8694 (t) cc_final: 0.8002 (m) REVERT: A 380 ILE cc_start: 0.8680 (mm) cc_final: 0.8341 (mt) REVERT: A 392 ASP cc_start: 0.6550 (m-30) cc_final: 0.6300 (m-30) REVERT: A 432 ASP cc_start: 0.8379 (p0) cc_final: 0.8002 (p0) REVERT: A 437 THR cc_start: 0.8048 (m) cc_final: 0.7679 (p) REVERT: A 531 ASP cc_start: 0.6988 (m-30) cc_final: 0.6754 (m-30) REVERT: A 546 ILE cc_start: 0.9068 (mm) cc_final: 0.8825 (tt) REVERT: B 163 ASP cc_start: 0.8358 (m-30) cc_final: 0.8024 (m-30) REVERT: B 173 LEU cc_start: 0.8731 (mp) cc_final: 0.8283 (mt) REVERT: B 178 ILE cc_start: 0.9373 (mm) cc_final: 0.9149 (mm) REVERT: B 208 TYR cc_start: 0.8119 (m-80) cc_final: 0.7888 (m-80) REVERT: B 253 THR cc_start: 0.8778 (p) cc_final: 0.8465 (m) REVERT: B 298 VAL cc_start: 0.8366 (t) cc_final: 0.7621 (m) REVERT: B 380 ILE cc_start: 0.8509 (mm) cc_final: 0.8256 (mt) REVERT: B 392 ASP cc_start: 0.6210 (m-30) cc_final: 0.5901 (m-30) REVERT: C 73 LEU cc_start: 0.8979 (mt) cc_final: 0.8736 (mt) REVERT: C 179 THR cc_start: 0.8959 (m) cc_final: 0.8712 (p) REVERT: C 266 THR cc_start: 0.8078 (p) cc_final: 0.7791 (t) REVERT: C 298 VAL cc_start: 0.8522 (t) cc_final: 0.7705 (m) REVERT: C 380 ILE cc_start: 0.8634 (mm) cc_final: 0.8343 (mt) REVERT: C 392 ASP cc_start: 0.6392 (m-30) cc_final: 0.5765 (m-30) REVERT: C 425 ASP cc_start: 0.8194 (t70) cc_final: 0.7919 (t0) REVERT: C 432 ASP cc_start: 0.8161 (p0) cc_final: 0.7732 (p0) REVERT: C 455 GLU cc_start: 0.7334 (pt0) cc_final: 0.7070 (pt0) REVERT: C 493 THR cc_start: 0.8541 (p) cc_final: 0.8309 (t) outliers start: 6 outliers final: 3 residues processed: 428 average time/residue: 0.2610 time to fit residues: 156.8571 Evaluate side-chains 221 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 218 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 ASN B 97 HIS C 97 HIS C 128 HIS C 480 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12855 Z= 0.190 Angle : 0.519 9.996 17490 Z= 0.282 Chirality : 0.048 0.153 2016 Planarity : 0.004 0.028 2235 Dihedral : 4.581 18.690 1725 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.14 % Allowed : 2.06 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.20), residues: 1569 helix: -0.08 (0.34), residues: 234 sheet: 0.40 (0.23), residues: 474 loop : -0.21 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 108 HIS 0.003 0.001 HIS A 128 PHE 0.015 0.001 PHE A 228 TYR 0.016 0.001 TYR C 208 ARG 0.003 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 286 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8775 (tttt) cc_final: 0.8543 (tttp) REVERT: A 163 ASP cc_start: 0.8241 (m-30) cc_final: 0.7796 (m-30) REVERT: A 208 TYR cc_start: 0.8142 (m-80) cc_final: 0.7751 (m-80) REVERT: A 266 THR cc_start: 0.8409 (p) cc_final: 0.8076 (t) REVERT: A 287 TYR cc_start: 0.8826 (t80) cc_final: 0.8065 (t80) REVERT: A 380 ILE cc_start: 0.8582 (mm) cc_final: 0.8126 (mt) REVERT: B 208 TYR cc_start: 0.8237 (m-80) cc_final: 0.7986 (m-80) REVERT: B 253 THR cc_start: 0.8883 (p) cc_final: 0.8444 (m) REVERT: B 290 ARG cc_start: 0.8624 (mmm160) cc_final: 0.7907 (tpp80) REVERT: B 380 ILE cc_start: 0.8456 (mm) cc_final: 0.8090 (mt) REVERT: B 423 ILE cc_start: 0.8969 (mt) cc_final: 0.8645 (mt) REVERT: B 460 SER cc_start: 0.8928 (p) cc_final: 0.8648 (p) REVERT: C 81 MET cc_start: 0.7706 (mtp) cc_final: 0.7481 (mtp) REVERT: C 179 THR cc_start: 0.8845 (m) cc_final: 0.8527 (p) REVERT: C 218 MET cc_start: 0.7928 (mpp) cc_final: 0.7552 (mpp) REVERT: C 290 ARG cc_start: 0.8614 (mmm160) cc_final: 0.8017 (tpp80) REVERT: C 380 ILE cc_start: 0.8629 (mm) cc_final: 0.8291 (mt) REVERT: C 423 ILE cc_start: 0.9042 (mt) cc_final: 0.8727 (mt) REVERT: C 425 ASP cc_start: 0.8080 (t70) cc_final: 0.7876 (m-30) outliers start: 2 outliers final: 0 residues processed: 286 average time/residue: 0.2223 time to fit residues: 95.8488 Evaluate side-chains 201 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 39 optimal weight: 0.0670 chunk 141 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 HIS ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12855 Z= 0.177 Angle : 0.480 6.934 17490 Z= 0.260 Chirality : 0.047 0.144 2016 Planarity : 0.003 0.028 2235 Dihedral : 4.239 16.087 1725 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.04 % Favored : 97.90 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: 0.06 (0.21), residues: 1569 helix: 0.04 (0.34), residues: 237 sheet: 0.39 (0.22), residues: 507 loop : -0.07 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 108 HIS 0.003 0.001 HIS A 383 PHE 0.018 0.001 PHE C 199 TYR 0.016 0.001 TYR C 208 ARG 0.003 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.8177 (m-30) cc_final: 0.7890 (m-30) REVERT: A 208 TYR cc_start: 0.8186 (m-80) cc_final: 0.7948 (m-80) REVERT: A 266 THR cc_start: 0.8480 (p) cc_final: 0.8152 (t) REVERT: A 287 TYR cc_start: 0.8590 (t80) cc_final: 0.8226 (t80) REVERT: A 380 ILE cc_start: 0.8418 (mm) cc_final: 0.8100 (mt) REVERT: B 208 TYR cc_start: 0.8155 (m-80) cc_final: 0.7798 (m-80) REVERT: B 253 THR cc_start: 0.8842 (p) cc_final: 0.8501 (m) REVERT: B 290 ARG cc_start: 0.8634 (mmm160) cc_final: 0.7901 (tpp80) REVERT: B 380 ILE cc_start: 0.8520 (mm) cc_final: 0.8206 (mt) REVERT: B 460 SER cc_start: 0.9012 (p) cc_final: 0.8725 (p) REVERT: C 120 ILE cc_start: 0.8557 (tp) cc_final: 0.8353 (tp) REVERT: C 218 MET cc_start: 0.7998 (mpp) cc_final: 0.7562 (mpp) REVERT: C 290 ARG cc_start: 0.8623 (mmm160) cc_final: 0.7948 (tpp80) REVERT: C 380 ILE cc_start: 0.8615 (mm) cc_final: 0.8257 (mt) REVERT: C 425 ASP cc_start: 0.8202 (t70) cc_final: 0.7989 (m-30) REVERT: C 512 MET cc_start: 0.7944 (mtp) cc_final: 0.7732 (mtp) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.2181 time to fit residues: 79.3568 Evaluate side-chains 191 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 140 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 6.9990 chunk 150 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 134 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12855 Z= 0.377 Angle : 0.590 8.272 17490 Z= 0.320 Chirality : 0.049 0.177 2016 Planarity : 0.004 0.038 2235 Dihedral : 4.653 17.337 1725 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 0.07 % Allowed : 1.92 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.20), residues: 1569 helix: -0.22 (0.33), residues: 231 sheet: 0.38 (0.23), residues: 465 loop : -0.28 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 108 HIS 0.004 0.001 HIS C 344 PHE 0.019 0.002 PHE C 447 TYR 0.020 0.002 TYR C 89 ARG 0.004 0.001 ARG A 412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 214 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.8186 (m-30) cc_final: 0.7854 (m-30) REVERT: A 266 THR cc_start: 0.8479 (p) cc_final: 0.8200 (t) REVERT: A 380 ILE cc_start: 0.8531 (mm) cc_final: 0.8238 (mt) REVERT: A 432 ASP cc_start: 0.8401 (p0) cc_final: 0.7857 (p0) REVERT: B 208 TYR cc_start: 0.8322 (m-80) cc_final: 0.7954 (m-80) REVERT: B 253 THR cc_start: 0.8944 (p) cc_final: 0.8744 (m) REVERT: B 290 ARG cc_start: 0.8723 (mmm160) cc_final: 0.8172 (tpp80) REVERT: B 380 ILE cc_start: 0.8545 (mm) cc_final: 0.8240 (mt) REVERT: B 460 SER cc_start: 0.9027 (p) cc_final: 0.8631 (p) REVERT: C 380 ILE cc_start: 0.8670 (mm) cc_final: 0.8356 (mt) REVERT: C 512 MET cc_start: 0.7983 (mtp) cc_final: 0.7700 (mtp) outliers start: 1 outliers final: 0 residues processed: 214 average time/residue: 0.2150 time to fit residues: 69.4100 Evaluate side-chains 171 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 125 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 chunk 38 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS ** A 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 HIS ** C 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12855 Z= 0.422 Angle : 0.599 5.952 17490 Z= 0.326 Chirality : 0.049 0.135 2016 Planarity : 0.004 0.040 2235 Dihedral : 4.884 18.721 1725 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.37 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -0.56 (0.20), residues: 1569 helix: -0.39 (0.33), residues: 231 sheet: 0.19 (0.23), residues: 465 loop : -0.63 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 108 HIS 0.004 0.001 HIS C 383 PHE 0.017 0.002 PHE B 447 TYR 0.019 0.002 TYR A 463 ARG 0.004 0.001 ARG C 412 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.8129 (m-30) cc_final: 0.7890 (m-30) REVERT: A 380 ILE cc_start: 0.8551 (mm) cc_final: 0.8274 (mt) REVERT: A 432 ASP cc_start: 0.8459 (p0) cc_final: 0.8099 (p0) REVERT: B 380 ILE cc_start: 0.8550 (mm) cc_final: 0.8282 (mt) REVERT: B 460 SER cc_start: 0.8919 (p) cc_final: 0.8711 (p) REVERT: C 380 ILE cc_start: 0.8645 (mm) cc_final: 0.8362 (mt) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.2447 time to fit residues: 70.9776 Evaluate side-chains 152 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 0.0000 chunk 150 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 12855 Z= 0.166 Angle : 0.476 5.656 17490 Z= 0.258 Chirality : 0.047 0.141 2016 Planarity : 0.004 0.033 2235 Dihedral : 4.395 17.648 1725 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % 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: -0.24 (0.21), residues: 1569 helix: 0.03 (0.35), residues: 231 sheet: 0.39 (0.23), residues: 462 loop : -0.45 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 108 HIS 0.002 0.001 HIS C 386 PHE 0.012 0.001 PHE B 199 TYR 0.012 0.001 TYR B 407 ARG 0.003 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 ASP cc_start: 0.8382 (p0) cc_final: 0.8023 (p0) REVERT: B 460 SER cc_start: 0.8959 (p) cc_final: 0.8748 (p) REVERT: C 128 HIS cc_start: 0.7553 (m-70) cc_final: 0.7285 (m-70) REVERT: C 380 ILE cc_start: 0.8634 (mm) cc_final: 0.8367 (mt) REVERT: C 500 LYS cc_start: 0.6935 (ptpt) cc_final: 0.6624 (pttm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2185 time to fit residues: 72.1761 Evaluate side-chains 170 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 chunk 150 optimal weight: 0.7980 chunk 94 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 93 optimal weight: 0.0010 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS ** B 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 12855 Z= 0.187 Angle : 0.480 5.350 17490 Z= 0.259 Chirality : 0.047 0.140 2016 Planarity : 0.004 0.034 2235 Dihedral : 4.284 16.601 1725 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.21), residues: 1569 helix: 0.05 (0.35), residues: 234 sheet: 0.44 (0.23), residues: 462 loop : -0.33 (0.21), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 108 HIS 0.004 0.001 HIS C 383 PHE 0.015 0.001 PHE A 199 TYR 0.020 0.001 TYR A 287 ARG 0.003 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.452 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 432 ASP cc_start: 0.8448 (p0) cc_final: 0.8121 (p0) REVERT: B 81 MET cc_start: 0.8240 (mmm) cc_final: 0.8024 (mmm) REVERT: C 380 ILE cc_start: 0.8602 (mm) cc_final: 0.8334 (mt) REVERT: C 500 LYS cc_start: 0.6888 (ptpt) cc_final: 0.6361 (ptpp) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2023 time to fit residues: 66.4120 Evaluate side-chains 174 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 60 optimal weight: 0.8980 chunk 89 optimal weight: 0.1980 chunk 45 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 95 optimal weight: 0.0870 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 0.0270 chunk 14 optimal weight: 0.4980 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 12855 Z= 0.117 Angle : 0.460 6.642 17490 Z= 0.245 Chirality : 0.046 0.144 2016 Planarity : 0.004 0.034 2235 Dihedral : 4.018 15.565 1725 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.21), residues: 1569 helix: 0.17 (0.36), residues: 234 sheet: 0.34 (0.23), residues: 471 loop : -0.09 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 108 HIS 0.002 0.000 HIS A 250 PHE 0.014 0.001 PHE A 199 TYR 0.025 0.001 TYR B 453 ARG 0.004 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: A 432 ASP cc_start: 0.8352 (p0) cc_final: 0.8027 (p0) REVERT: B 81 MET cc_start: 0.8216 (mmm) cc_final: 0.7991 (mmm) REVERT: B 171 LEU cc_start: 0.8945 (tp) cc_final: 0.8722 (tp) REVERT: B 290 ARG cc_start: 0.8696 (mmm160) cc_final: 0.8120 (tpp80) REVERT: C 500 LYS cc_start: 0.6785 (ptpt) cc_final: 0.6415 (pttm) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.2071 time to fit residues: 73.8073 Evaluate side-chains 178 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 0.5980 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 92 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12855 Z= 0.154 Angle : 0.472 6.759 17490 Z= 0.251 Chirality : 0.046 0.141 2016 Planarity : 0.004 0.043 2235 Dihedral : 3.968 15.745 1725 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1569 helix: 0.17 (0.36), residues: 234 sheet: 0.53 (0.24), residues: 456 loop : -0.13 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.003 0.001 HIS C 383 PHE 0.017 0.001 PHE B 199 TYR 0.023 0.001 TYR C 287 ARG 0.003 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 1.476 Fit side-chains revert: symmetry clash REVERT: A 171 LEU cc_start: 0.9221 (tp) cc_final: 0.8992 (tp) REVERT: A 432 ASP cc_start: 0.8354 (p0) cc_final: 0.8051 (p0) REVERT: B 287 TYR cc_start: 0.8821 (t80) cc_final: 0.8583 (t80) REVERT: B 290 ARG cc_start: 0.8738 (mmm160) cc_final: 0.8121 (tpp80) REVERT: C 500 LYS cc_start: 0.6763 (ptpt) cc_final: 0.6396 (pttm) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.2020 time to fit residues: 68.1273 Evaluate side-chains 178 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 148 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 143 optimal weight: 7.9990 chunk 123 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 95 optimal weight: 0.0270 chunk 75 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 12855 Z= 0.136 Angle : 0.468 6.314 17490 Z= 0.247 Chirality : 0.046 0.143 2016 Planarity : 0.004 0.044 2235 Dihedral : 3.897 15.681 1725 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.22), residues: 1569 helix: 0.19 (0.36), residues: 234 sheet: 0.41 (0.24), residues: 471 loop : -0.03 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 108 HIS 0.003 0.001 HIS A 250 PHE 0.016 0.001 PHE B 199 TYR 0.021 0.001 TYR C 287 ARG 0.003 0.000 ARG B 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3138 Ramachandran restraints generated. 1569 Oldfield, 0 Emsley, 1569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.9213 (tp) cc_final: 0.9012 (tp) REVERT: A 432 ASP cc_start: 0.8308 (p0) cc_final: 0.7973 (p0) REVERT: B 290 ARG cc_start: 0.8724 (mmm160) cc_final: 0.8041 (tpp80) REVERT: C 500 LYS cc_start: 0.6721 (ptpt) cc_final: 0.6428 (pttm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2034 time to fit residues: 69.0508 Evaluate side-chains 175 residues out of total 1455 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.088647 restraints weight = 23185.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.091508 restraints weight = 13605.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.093493 restraints weight = 9613.054| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3073 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3073 r_free = 0.3073 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 12855 Z= 0.160 Angle : 0.465 6.131 17490 Z= 0.247 Chirality : 0.046 0.141 2016 Planarity : 0.004 0.039 2235 Dihedral : 3.885 15.590 1725 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.87 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.21), residues: 1569 helix: 0.24 (0.36), residues: 234 sheet: 0.56 (0.24), residues: 456 loop : -0.11 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 108 HIS 0.003 0.001 HIS C 383 PHE 0.015 0.001 PHE B 199 TYR 0.021 0.001 TYR C 287 ARG 0.004 0.000 ARG B 234 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2555.06 seconds wall clock time: 47 minutes 47.52 seconds (2867.52 seconds total)