Starting phenix.real_space_refine on Wed Jul 30 18:25:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vff_31951/07_2025/7vff_31951.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vff_31951/07_2025/7vff_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/cci-nas-00/data/ceres_data/7vff_31951/07_2025/7vff_31951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vff_31951/07_2025/7vff_31951.map" model { file = "/net/cci-nas-00/data/ceres_data/7vff_31951/07_2025/7vff_31951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vff_31951/07_2025/7vff_31951.cif" } 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. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12579 Number of models: 1 Model: "" Number of chains: 1 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 Restraints were copied for chains: C, B 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: 8.59, per 1000 atoms: 0.68 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 1.7 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: 1.90 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: 3.72 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: 0.00 - 1.69: 16810 1.69 - 3.38: 632 3.38 - 5.07: 39 5.07 - 6.76: 6 6.76 - 8.45: 3 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 3.040 nonbonded pdb=" OG SER B 322 " pdb=" OD1 ASP B 327 " model vdw 2.334 3.040 nonbonded pdb=" OG SER A 322 " pdb=" OD1 ASP A 327 " model vdw 2.335 3.040 nonbonded pdb=" O PHE B 22 " pdb=" NZ LYS C 172 " model vdw 2.355 3.120 nonbonded pdb=" NE2 HIS A 128 " pdb=" OE1 GLU B 465 " model vdw 2.390 3.120 ... (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 Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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=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: 1.070 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.910 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.690 ------------------------------------------------------------------------------- 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= 0.307 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 Details of bonding type rmsd hydrogen bonds : bond 0.21763 ( 455) hydrogen bonds : angle 7.38313 ( 1365) covalent geometry : bond 0.00715 (12855) covalent geometry : angle 0.72338 (17490) *********************** 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 to be fit. rotamer outliers: 6 poor density : 425 time to evaluate : 1.495 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: 0.2534 time to fit residues: 152.3868 Evaluate side-chains 221 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 218 time to evaluate : 1.659 ------------------------------------------------------------------------------- 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: 0.9990 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 141 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 HIS A 278 GLN A 480 ASN B 97 HIS C 97 HIS C 128 HIS C 480 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.091041 restraints weight = 22261.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.094418 restraints weight = 12675.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.096576 restraints weight = 8619.473| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12855 Z= 0.127 Angle : 0.531 9.927 17490 Z= 0.290 Chirality : 0.049 0.164 2016 Planarity : 0.004 0.031 2235 Dihedral : 4.637 18.897 1725 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.85 % Favored : 98.09 % Rotamer: Outliers : 0.21 % Allowed : 1.86 % 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: -0.07 (0.20), residues: 1569 helix: -0.10 (0.34), residues: 234 sheet: 0.39 (0.23), residues: 474 loop : -0.19 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 108 HIS 0.003 0.001 HIS C 344 PHE 0.014 0.001 PHE A 228 TYR 0.017 0.001 TYR C 208 ARG 0.003 0.000 ARG C 83 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 455) hydrogen bonds : angle 5.64917 ( 1365) covalent geometry : bond 0.00280 (12855) covalent geometry : angle 0.53114 (17490) *********************** 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 296 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 293 time to evaluate : 1.320 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: A 159 LYS cc_start: 0.8856 (tttt) cc_final: 0.8612 (tttp) REVERT: A 163 ASP cc_start: 0.8542 (m-30) cc_final: 0.8092 (m-30) REVERT: A 194 ASP cc_start: 0.8705 (p0) cc_final: 0.8277 (p0) REVERT: A 208 TYR cc_start: 0.8613 (m-80) cc_final: 0.8236 (m-80) REVERT: A 282 ASP cc_start: 0.8613 (m-30) cc_final: 0.8401 (m-30) REVERT: A 287 TYR cc_start: 0.9061 (t80) cc_final: 0.8701 (t80) REVERT: A 298 VAL cc_start: 0.8695 (t) cc_final: 0.8363 (m) REVERT: A 380 ILE cc_start: 0.8652 (mm) cc_final: 0.8307 (mt) REVERT: A 546 ILE cc_start: 0.9226 (mm) cc_final: 0.8917 (tt) REVERT: B 208 TYR cc_start: 0.8856 (m-80) cc_final: 0.8478 (m-80) REVERT: B 380 ILE cc_start: 0.8776 (mm) cc_final: 0.8464 (mt) REVERT: B 424 ASN cc_start: 0.8309 (m-40) cc_final: 0.8053 (t0) REVERT: B 436 LYS cc_start: 0.8720 (tptp) cc_final: 0.8421 (tppp) REVERT: B 460 SER cc_start: 0.9049 (p) cc_final: 0.8759 (p) REVERT: C 73 LEU cc_start: 0.8964 (mt) cc_final: 0.8687 (mt) REVERT: C 81 MET cc_start: 0.8117 (mtp) cc_final: 0.7767 (mtp) REVERT: C 179 THR cc_start: 0.8842 (m) cc_final: 0.8297 (p) REVERT: C 194 ASP cc_start: 0.8517 (p0) cc_final: 0.8030 (p0) REVERT: C 218 MET cc_start: 0.7766 (mpp) cc_final: 0.7422 (mpp) REVERT: C 290 ARG cc_start: 0.9064 (mmm160) cc_final: 0.8477 (tpp80) REVERT: C 298 VAL cc_start: 0.8659 (t) cc_final: 0.8278 (m) REVERT: C 380 ILE cc_start: 0.8956 (mm) cc_final: 0.8690 (mt) REVERT: C 383 HIS cc_start: 0.8329 (t-90) cc_final: 0.8117 (t-170) REVERT: C 424 ASN cc_start: 0.8439 (m-40) cc_final: 0.8168 (t0) outliers start: 3 outliers final: 0 residues processed: 294 average time/residue: 0.2094 time to fit residues: 91.7009 Evaluate side-chains 206 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 86 optimal weight: 0.0010 chunk 142 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.085405 restraints weight = 23369.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.088497 restraints weight = 13327.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.090613 restraints weight = 9189.334| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12855 Z= 0.236 Angle : 0.591 9.136 17490 Z= 0.324 Chirality : 0.049 0.145 2016 Planarity : 0.004 0.037 2235 Dihedral : 4.761 17.459 1725 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % 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: -0.09 (0.21), residues: 1569 helix: -0.28 (0.33), residues: 237 sheet: 0.39 (0.23), residues: 465 loop : -0.15 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 400 HIS 0.004 0.001 HIS A 383 PHE 0.017 0.002 PHE C 447 TYR 0.018 0.002 TYR B 131 ARG 0.004 0.001 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.04756 ( 455) hydrogen bonds : angle 5.48761 ( 1365) covalent geometry : bond 0.00548 (12855) covalent geometry : angle 0.59139 (17490) *********************** 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 221 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 LEU cc_start: 0.9034 (mp) cc_final: 0.8694 (mp) REVERT: A 159 LYS cc_start: 0.8918 (tttt) cc_final: 0.8481 (tttm) REVERT: A 163 ASP cc_start: 0.8688 (m-30) cc_final: 0.8335 (m-30) REVERT: A 194 ASP cc_start: 0.8503 (p0) cc_final: 0.8043 (p0) REVERT: A 208 TYR cc_start: 0.8784 (m-80) cc_final: 0.8444 (m-80) REVERT: A 380 ILE cc_start: 0.8744 (mm) cc_final: 0.8507 (mt) REVERT: A 432 ASP cc_start: 0.8274 (p0) cc_final: 0.7677 (p0) REVERT: B 166 ASP cc_start: 0.8013 (p0) cc_final: 0.7786 (p0) REVERT: B 208 TYR cc_start: 0.8822 (m-80) cc_final: 0.8435 (m-80) REVERT: B 380 ILE cc_start: 0.8871 (mm) cc_final: 0.8660 (mt) REVERT: B 436 LYS cc_start: 0.8813 (tptp) cc_final: 0.8503 (tppp) REVERT: B 463 TYR cc_start: 0.7709 (m-80) cc_final: 0.7481 (m-80) REVERT: B 539 GLN cc_start: 0.8164 (mp10) cc_final: 0.7842 (mp10) REVERT: C 73 LEU cc_start: 0.9000 (mt) cc_final: 0.8692 (mt) REVERT: C 194 ASP cc_start: 0.8450 (p0) cc_final: 0.7912 (p0) REVERT: C 218 MET cc_start: 0.7943 (mpp) cc_final: 0.7584 (mpp) REVERT: C 282 ASP cc_start: 0.8651 (m-30) cc_final: 0.8402 (m-30) REVERT: C 290 ARG cc_start: 0.9099 (mmm160) cc_final: 0.8383 (tpp80) REVERT: C 380 ILE cc_start: 0.9021 (mm) cc_final: 0.8806 (mt) REVERT: C 383 HIS cc_start: 0.8356 (t-90) cc_final: 0.8144 (t-170) REVERT: C 436 LYS cc_start: 0.8644 (tptp) cc_final: 0.8411 (tptp) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2268 time to fit residues: 75.3572 Evaluate side-chains 179 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 10 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 118 optimal weight: 0.4980 chunk 78 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.110159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.088285 restraints weight = 23026.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.091413 restraints weight = 13188.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.093372 restraints weight = 9103.159| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 12855 Z= 0.110 Angle : 0.481 8.050 17490 Z= 0.261 Chirality : 0.047 0.158 2016 Planarity : 0.004 0.032 2235 Dihedral : 4.396 16.705 1725 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.91 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: 0.02 (0.21), residues: 1569 helix: -0.04 (0.35), residues: 234 sheet: 0.38 (0.23), residues: 477 loop : -0.08 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.002 0.001 HIS C 386 PHE 0.010 0.001 PHE C 184 TYR 0.010 0.001 TYR A 89 ARG 0.002 0.000 ARG B 290 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 455) hydrogen bonds : angle 5.16575 ( 1365) covalent geometry : bond 0.00247 (12855) covalent geometry : angle 0.48072 (17490) *********************** 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 238 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 238 time to evaluate : 1.506 Fit side-chains REVERT: A 113 GLU cc_start: 0.7981 (tp30) cc_final: 0.7626 (tm-30) REVERT: A 163 ASP cc_start: 0.8465 (m-30) cc_final: 0.8147 (m-30) REVERT: A 194 ASP cc_start: 0.8432 (p0) cc_final: 0.7987 (p0) REVERT: A 208 TYR cc_start: 0.8801 (m-80) cc_final: 0.8478 (m-10) REVERT: A 218 MET cc_start: 0.7776 (mpp) cc_final: 0.7457 (mpp) REVERT: A 282 ASP cc_start: 0.8680 (m-30) cc_final: 0.8461 (m-30) REVERT: A 287 TYR cc_start: 0.8808 (t80) cc_final: 0.8436 (t80) REVERT: A 380 ILE cc_start: 0.8692 (mm) cc_final: 0.8431 (mt) REVERT: A 432 ASP cc_start: 0.8320 (p0) cc_final: 0.7770 (p0) REVERT: B 166 ASP cc_start: 0.7922 (p0) cc_final: 0.7695 (p0) REVERT: B 194 ASP cc_start: 0.8348 (p0) cc_final: 0.8140 (p0) REVERT: B 208 TYR cc_start: 0.8771 (m-80) cc_final: 0.8344 (m-80) REVERT: B 380 ILE cc_start: 0.8773 (mm) cc_final: 0.8524 (mt) REVERT: B 424 ASN cc_start: 0.8249 (m-40) cc_final: 0.7885 (t0) REVERT: B 436 LYS cc_start: 0.8686 (tptp) cc_final: 0.8421 (tppp) REVERT: B 539 GLN cc_start: 0.8154 (mp10) cc_final: 0.7848 (mp10) REVERT: C 194 ASP cc_start: 0.8340 (p0) cc_final: 0.7819 (p0) REVERT: C 218 MET cc_start: 0.7861 (mpp) cc_final: 0.7459 (mpp) REVERT: C 287 TYR cc_start: 0.8950 (t80) cc_final: 0.8274 (t80) REVERT: C 290 ARG cc_start: 0.9081 (mmm160) cc_final: 0.8328 (tpp80) REVERT: C 321 VAL cc_start: 0.9152 (t) cc_final: 0.8922 (t) REVERT: C 380 ILE cc_start: 0.9010 (mm) cc_final: 0.8783 (mt) outliers start: 0 outliers final: 0 residues processed: 238 average time/residue: 0.2248 time to fit residues: 78.7561 Evaluate side-chains 184 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 0 optimal weight: 9.9990 chunk 105 optimal weight: 0.6980 chunk 138 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 134 optimal weight: 0.4980 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 HIS C 383 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.108880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.086928 restraints weight = 23106.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.089934 restraints weight = 13190.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.092017 restraints weight = 9157.593| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12855 Z= 0.124 Angle : 0.469 5.920 17490 Z= 0.254 Chirality : 0.047 0.145 2016 Planarity : 0.004 0.033 2235 Dihedral : 4.204 15.775 1725 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.29 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1569 helix: 0.05 (0.36), residues: 234 sheet: 0.43 (0.23), residues: 477 loop : 0.04 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 108 HIS 0.003 0.001 HIS A 383 PHE 0.018 0.001 PHE A 199 TYR 0.011 0.001 TYR C 407 ARG 0.005 0.000 ARG C 446 Details of bonding type rmsd hydrogen bonds : bond 0.03345 ( 455) hydrogen bonds : angle 5.02884 ( 1365) covalent geometry : bond 0.00281 (12855) covalent geometry : angle 0.46917 (17490) *********************** 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 225 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 1.348 Fit side-chains REVERT: A 113 GLU cc_start: 0.7852 (tp30) cc_final: 0.7421 (tm-30) REVERT: A 163 ASP cc_start: 0.8468 (m-30) cc_final: 0.8134 (m-30) REVERT: A 208 TYR cc_start: 0.8786 (m-80) cc_final: 0.8471 (m-10) REVERT: A 218 MET cc_start: 0.7798 (mpp) cc_final: 0.7508 (mpp) REVERT: A 282 ASP cc_start: 0.8705 (m-30) cc_final: 0.8481 (m-30) REVERT: A 287 TYR cc_start: 0.8880 (t80) cc_final: 0.8471 (t80) REVERT: A 432 ASP cc_start: 0.8299 (p0) cc_final: 0.7738 (p0) REVERT: A 460 SER cc_start: 0.9195 (t) cc_final: 0.8993 (p) REVERT: B 165 GLU cc_start: 0.8247 (mm-30) cc_final: 0.8030 (tp30) REVERT: B 380 ILE cc_start: 0.8724 (mm) cc_final: 0.8493 (mt) REVERT: B 423 ILE cc_start: 0.9038 (mt) cc_final: 0.8810 (mt) REVERT: B 424 ASN cc_start: 0.8241 (m-40) cc_final: 0.7886 (t0) REVERT: B 436 LYS cc_start: 0.8772 (tptp) cc_final: 0.8409 (tppp) REVERT: B 460 SER cc_start: 0.9090 (p) cc_final: 0.8809 (p) REVERT: C 218 MET cc_start: 0.7860 (mpp) cc_final: 0.7478 (mpp) REVERT: C 287 TYR cc_start: 0.8921 (t80) cc_final: 0.8391 (t80) REVERT: C 290 ARG cc_start: 0.9071 (mmm160) cc_final: 0.8293 (tpp80) REVERT: C 380 ILE cc_start: 0.9012 (mm) cc_final: 0.8800 (mt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.2199 time to fit residues: 74.0266 Evaluate side-chains 179 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 22 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 106 optimal weight: 0.0570 chunk 135 optimal weight: 0.0980 chunk 58 optimal weight: 4.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.107438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.085294 restraints weight = 23534.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.088323 restraints weight = 13406.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.090358 restraints weight = 9272.565| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12855 Z= 0.156 Angle : 0.496 5.260 17490 Z= 0.270 Chirality : 0.047 0.144 2016 Planarity : 0.004 0.034 2235 Dihedral : 4.270 20.246 1725 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % 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: 0.11 (0.21), residues: 1569 helix: 0.05 (0.35), residues: 237 sheet: 0.55 (0.23), residues: 462 loop : -0.08 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 108 HIS 0.002 0.001 HIS A 344 PHE 0.018 0.001 PHE C 199 TYR 0.013 0.001 TYR C 62 ARG 0.004 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.03648 ( 455) hydrogen bonds : angle 5.07921 ( 1365) covalent geometry : bond 0.00363 (12855) covalent geometry : angle 0.49581 (17490) *********************** 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 to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7927 (tp30) cc_final: 0.7431 (tm-30) REVERT: A 208 TYR cc_start: 0.8738 (m-80) cc_final: 0.8520 (m-10) REVERT: A 218 MET cc_start: 0.7826 (mpp) cc_final: 0.7516 (mpp) REVERT: A 282 ASP cc_start: 0.8733 (m-30) cc_final: 0.8516 (m-30) REVERT: A 287 TYR cc_start: 0.8934 (t80) cc_final: 0.8505 (t80) REVERT: A 432 ASP cc_start: 0.8335 (p0) cc_final: 0.7781 (p0) REVERT: B 166 ASP cc_start: 0.7894 (p0) cc_final: 0.7672 (p0) REVERT: B 436 LYS cc_start: 0.8789 (tptp) cc_final: 0.8471 (tppp) REVERT: B 460 SER cc_start: 0.9096 (p) cc_final: 0.8766 (p) REVERT: B 539 GLN cc_start: 0.8311 (mp10) cc_final: 0.7960 (mp10) REVERT: C 218 MET cc_start: 0.7845 (mpp) cc_final: 0.7528 (mpp) REVERT: C 287 TYR cc_start: 0.8980 (t80) cc_final: 0.8304 (t80) REVERT: C 290 ARG cc_start: 0.9096 (mmm160) cc_final: 0.8291 (tpp80) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2248 time to fit residues: 72.5620 Evaluate side-chains 174 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.379 ------------------------------------------------------------------------------- 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: 4.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 100 optimal weight: 0.4980 chunk 128 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 138 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.107227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.085260 restraints weight = 23421.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.088184 restraints weight = 13755.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.090142 restraints weight = 9666.837| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12855 Z= 0.160 Angle : 0.495 5.419 17490 Z= 0.269 Chirality : 0.047 0.149 2016 Planarity : 0.004 0.063 2235 Dihedral : 4.308 19.189 1725 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: 0.09 (0.21), residues: 1569 helix: 0.04 (0.35), residues: 237 sheet: 0.51 (0.23), residues: 462 loop : -0.09 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 108 HIS 0.004 0.001 HIS C 383 PHE 0.013 0.001 PHE B 199 TYR 0.013 0.001 TYR C 453 ARG 0.005 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 455) hydrogen bonds : angle 5.03618 ( 1365) covalent geometry : bond 0.00372 (12855) covalent geometry : angle 0.49513 (17490) *********************** 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 217 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 1.460 Fit side-chains revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7874 (tp30) cc_final: 0.7589 (tm-30) REVERT: A 208 TYR cc_start: 0.8721 (m-80) cc_final: 0.8493 (m-10) REVERT: A 218 MET cc_start: 0.7852 (mpp) cc_final: 0.7544 (mpp) REVERT: A 282 ASP cc_start: 0.8722 (m-30) cc_final: 0.8513 (m-30) REVERT: A 287 TYR cc_start: 0.8894 (t80) cc_final: 0.8523 (t80) REVERT: A 432 ASP cc_start: 0.8376 (p0) cc_final: 0.7859 (p0) REVERT: B 165 GLU cc_start: 0.7975 (tp30) cc_final: 0.7669 (tp30) REVERT: B 436 LYS cc_start: 0.8792 (tptp) cc_final: 0.8438 (tppp) REVERT: B 460 SER cc_start: 0.8984 (p) cc_final: 0.8747 (p) REVERT: B 539 GLN cc_start: 0.8281 (mp10) cc_final: 0.7946 (mp10) REVERT: C 218 MET cc_start: 0.7888 (mpp) cc_final: 0.7560 (mpp) REVERT: C 287 TYR cc_start: 0.8986 (t80) cc_final: 0.8365 (t80) REVERT: C 290 ARG cc_start: 0.9107 (mmm160) cc_final: 0.8259 (tpp80) REVERT: C 500 LYS cc_start: 0.6873 (ptpt) cc_final: 0.6379 (pttm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2156 time to fit residues: 70.6644 Evaluate side-chains 181 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 155 optimal weight: 4.9990 chunk 69 optimal weight: 0.0970 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 0.0470 chunk 112 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 36 optimal weight: 0.2980 chunk 56 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.088989 restraints weight = 23292.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.092125 restraints weight = 13095.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.094273 restraints weight = 8983.146| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 12855 Z= 0.086 Angle : 0.469 5.459 17490 Z= 0.250 Chirality : 0.047 0.156 2016 Planarity : 0.004 0.033 2235 Dihedral : 4.016 19.807 1725 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 0.23 (0.22), residues: 1569 helix: 0.14 (0.35), residues: 234 sheet: 0.44 (0.23), residues: 471 loop : 0.12 (0.22), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 108 HIS 0.002 0.000 HIS C 386 PHE 0.013 0.001 PHE B 199 TYR 0.011 0.001 TYR C 258 ARG 0.004 0.000 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.02861 ( 455) hydrogen bonds : angle 4.87521 ( 1365) covalent geometry : bond 0.00186 (12855) covalent geometry : angle 0.46895 (17490) *********************** 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 237 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 GLU cc_start: 0.7855 (tp30) cc_final: 0.7388 (tm-30) REVERT: A 183 THR cc_start: 0.8887 (m) cc_final: 0.8655 (p) REVERT: A 208 TYR cc_start: 0.8714 (m-80) cc_final: 0.8499 (m-10) REVERT: A 218 MET cc_start: 0.7838 (mpp) cc_final: 0.7502 (mpp) REVERT: A 287 TYR cc_start: 0.8803 (t80) cc_final: 0.8520 (t80) REVERT: A 432 ASP cc_start: 0.8307 (p0) cc_final: 0.7721 (p0) REVERT: A 434 LYS cc_start: 0.9146 (mmmt) cc_final: 0.8832 (mmtp) REVERT: B 165 GLU cc_start: 0.7947 (tp30) cc_final: 0.7538 (tp30) REVERT: B 284 ILE cc_start: 0.9041 (mt) cc_final: 0.8810 (mm) REVERT: B 436 LYS cc_start: 0.8734 (tptp) cc_final: 0.8365 (tppp) REVERT: B 482 THR cc_start: 0.7548 (p) cc_final: 0.7340 (p) REVERT: B 539 GLN cc_start: 0.8213 (mp10) cc_final: 0.7852 (mp10) REVERT: C 218 MET cc_start: 0.7830 (mpp) cc_final: 0.7449 (mpp) REVERT: C 287 TYR cc_start: 0.8794 (t80) cc_final: 0.8451 (t80) REVERT: C 500 LYS cc_start: 0.6791 (ptpt) cc_final: 0.6389 (pttm) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.2079 time to fit residues: 75.7320 Evaluate side-chains 185 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 79 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3276 r_free = 0.3276 target = 0.106372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.084665 restraints weight = 23627.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.087518 restraints weight = 13838.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.089448 restraints weight = 9760.618| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.4633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12855 Z= 0.201 Angle : 0.542 6.196 17490 Z= 0.292 Chirality : 0.047 0.139 2016 Planarity : 0.004 0.035 2235 Dihedral : 4.308 19.534 1725 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 (0.22), residues: 1569 helix: 0.13 (0.36), residues: 237 sheet: 0.49 (0.23), residues: 462 loop : -0.09 (0.22), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 400 HIS 0.004 0.001 HIS B 128 PHE 0.013 0.001 PHE A 447 TYR 0.015 0.002 TYR C 453 ARG 0.004 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 455) hydrogen bonds : angle 5.05449 ( 1365) covalent geometry : bond 0.00469 (12855) covalent geometry : angle 0.54153 (17490) *********************** 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 208 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7726 (tp30) cc_final: 0.7438 (tp30) REVERT: A 218 MET cc_start: 0.7848 (mpp) cc_final: 0.7536 (mpp) REVERT: A 282 ASP cc_start: 0.8706 (m-30) cc_final: 0.8444 (m-30) REVERT: A 424 ASN cc_start: 0.8639 (t0) cc_final: 0.8076 (t0) REVERT: A 432 ASP cc_start: 0.8305 (p0) cc_final: 0.7778 (p0) REVERT: A 434 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8883 (mmtp) REVERT: B 436 LYS cc_start: 0.8791 (tptp) cc_final: 0.8479 (tppp) REVERT: B 460 SER cc_start: 0.8986 (p) cc_final: 0.8758 (p) REVERT: B 539 GLN cc_start: 0.8263 (mp10) cc_final: 0.7896 (mp10) REVERT: C 218 MET cc_start: 0.7913 (mpp) cc_final: 0.7553 (mpp) REVERT: C 282 ASP cc_start: 0.8646 (m-30) cc_final: 0.8359 (m-30) REVERT: C 500 LYS cc_start: 0.6960 (ptpt) cc_final: 0.6287 (ptpp) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.2051 time to fit residues: 65.3724 Evaluate side-chains 171 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 82 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 112 optimal weight: 0.0170 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.108072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.086176 restraints weight = 23417.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.089080 restraints weight = 13728.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.091060 restraints weight = 9682.225| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12855 Z= 0.140 Angle : 0.507 5.410 17490 Z= 0.272 Chirality : 0.047 0.142 2016 Planarity : 0.004 0.032 2235 Dihedral : 4.300 18.697 1725 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.26 % 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: 0.07 (0.22), residues: 1569 helix: 0.25 (0.36), residues: 234 sheet: 0.40 (0.24), residues: 456 loop : -0.10 (0.22), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 108 HIS 0.002 0.001 HIS C 386 PHE 0.013 0.001 PHE B 199 TYR 0.016 0.001 TYR A 287 ARG 0.004 0.000 ARG A 290 Details of bonding type rmsd hydrogen bonds : bond 0.03429 ( 455) hydrogen bonds : angle 4.92134 ( 1365) covalent geometry : bond 0.00325 (12855) covalent geometry : angle 0.50689 (17490) ********************** 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 211 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: A 165 GLU cc_start: 0.7709 (tp30) cc_final: 0.7442 (tp30) REVERT: A 218 MET cc_start: 0.7851 (mpp) cc_final: 0.7539 (mpp) REVERT: A 282 ASP cc_start: 0.8637 (m-30) cc_final: 0.8410 (m-30) REVERT: A 424 ASN cc_start: 0.8568 (t0) cc_final: 0.7921 (t0) REVERT: A 432 ASP cc_start: 0.8325 (p0) cc_final: 0.7799 (p0) REVERT: A 434 LYS cc_start: 0.9186 (mmmt) cc_final: 0.8892 (mmtp) REVERT: B 436 LYS cc_start: 0.8784 (tptp) cc_final: 0.8441 (tppp) REVERT: B 539 GLN cc_start: 0.8238 (mp10) cc_final: 0.7913 (mp10) REVERT: C 218 MET cc_start: 0.7897 (mpp) cc_final: 0.7539 (mpp) REVERT: C 287 TYR cc_start: 0.8918 (t80) cc_final: 0.8338 (t80) REVERT: C 344 HIS cc_start: 0.8964 (t-90) cc_final: 0.8595 (t-170) REVERT: C 500 LYS cc_start: 0.6921 (ptpt) cc_final: 0.6417 (pttm) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2116 time to fit residues: 68.8344 Evaluate side-chains 171 residues out of total 1455 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 145 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 24 optimal weight: 0.5980 chunk 140 optimal weight: 0.0970 chunk 80 optimal weight: 6.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 = 0.3288 r_free = 0.3288 target = 0.107198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.085388 restraints weight = 23506.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.088268 restraints weight = 13777.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.090200 restraints weight = 9706.350| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12855 Z= 0.161 Angle : 0.520 5.460 17490 Z= 0.280 Chirality : 0.047 0.142 2016 Planarity : 0.004 0.033 2235 Dihedral : 4.336 22.698 1725 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.13 % 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: 0.02 (0.22), residues: 1569 helix: 0.24 (0.36), residues: 234 sheet: 0.35 (0.24), residues: 456 loop : -0.14 (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 0.013 0.001 PHE B 199 TYR 0.018 0.001 TYR A 287 ARG 0.006 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 455) hydrogen bonds : angle 4.98246 ( 1365) covalent geometry : bond 0.00375 (12855) covalent geometry : angle 0.51963 (17490) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3933.96 seconds wall clock time: 70 minutes 30.79 seconds (4230.79 seconds total)