Starting phenix.real_space_refine on Sat Jun 29 15:21:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ezx_50090/06_2024/9ezx_50090.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ezx_50090/06_2024/9ezx_50090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ezx_50090/06_2024/9ezx_50090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ezx_50090/06_2024/9ezx_50090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ezx_50090/06_2024/9ezx_50090.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ezx_50090/06_2024/9ezx_50090.pdb" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 48 5.16 5 C 11777 2.51 5 N 3247 2.21 5 O 3513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 18": "OE1" <-> "OE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A ASP 104": "OD1" <-> "OD2" Residue "A GLU 117": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A TYR 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 809": "OE1" <-> "OE2" Residue "A TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 970": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 974": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1085": "OD1" <-> "OD2" Residue "A GLU 1113": "OE1" <-> "OE2" Residue "A PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 23": "OD1" <-> "OD2" Residue "B ASP 104": "OD1" <-> "OD2" Residue "B GLU 117": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 201": "OD1" <-> "OD2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B ASP 672": "OD1" <-> "OD2" Residue "B ASP 772": "OD1" <-> "OD2" Residue "B TYR 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 809": "OE1" <-> "OE2" Residue "B TYR 848": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 946": "OD1" <-> "OD2" Residue "B GLU 968": "OE1" <-> "OE2" Residue "B ASP 1012": "OD1" <-> "OD2" Residue "B TYR 1023": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1082": "OE1" <-> "OE2" Residue "B TYR 1115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1124": "OE1" <-> "OE2" Residue "B PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1146": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 18585 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1152, 9299 Classifications: {'peptide': 1152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 1117} Chain breaks: 5 Chain: "B" Number of atoms: 9286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9286 Classifications: {'peptide': 1150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 34, 'TRANS': 1115} Chain breaks: 6 Time building chain proxies: 14.28, per 1000 atoms: 0.77 Number of scatterers: 18585 At special positions: 0 Unit cell: (143.65, 113.75, 131.95, 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 48 16.00 O 3513 8.00 N 3247 7.00 C 11777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.51 Conformation dependent library (CDL) restraints added in 3.2 seconds 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4390 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 24 sheets defined 60.0% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 20 through 38 Proline residue: A 29 - end of helix Processing helix chain 'A' and resid 54 through 78 Processing helix chain 'A' and resid 94 through 112 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'A' and resid 137 through 144 Processing helix chain 'A' and resid 146 through 157 Processing helix chain 'A' and resid 158 through 161 Processing helix chain 'A' and resid 162 through 178 removed outlier: 3.819A pdb=" N LEU A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG A 177 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N HIS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 209 Processing helix chain 'A' and resid 216 through 227 Processing helix chain 'A' and resid 227 through 234 removed outlier: 4.110A pdb=" N LYS A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE A 232 " --> pdb=" O PRO A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 259 through 264 removed outlier: 4.155A pdb=" N LEU A 264 " --> pdb=" O LEU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 286 removed outlier: 3.553A pdb=" N GLN A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLN A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 307 removed outlier: 4.177A pdb=" N ASP A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.665A pdb=" N LEU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE A 322 " --> pdb=" O ILE A 318 " (cutoff:3.500A) Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 346 through 352 removed outlier: 3.527A pdb=" N ASN A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 435 Processing helix chain 'A' and resid 444 through 460 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'A' and resid 464 through 477 removed outlier: 3.967A pdb=" N ASP A 473 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N THR A 474 " --> pdb=" O GLU A 470 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 498 Processing helix chain 'A' and resid 524 through 535 Processing helix chain 'A' and resid 556 through 565 Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'A' and resid 588 through 593 Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'A' and resid 623 through 630 Processing helix chain 'A' and resid 633 through 635 No H-bonds generated for 'chain 'A' and resid 633 through 635' Processing helix chain 'A' and resid 636 through 656 Processing helix chain 'A' and resid 672 through 674 No H-bonds generated for 'chain 'A' and resid 672 through 674' Processing helix chain 'A' and resid 675 through 694 Processing helix chain 'A' and resid 704 through 711 Processing helix chain 'A' and resid 711 through 723 Processing helix chain 'A' and resid 733 through 737 removed outlier: 3.752A pdb=" N GLY A 737 " --> pdb=" O TYR A 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 733 through 737' Processing helix chain 'A' and resid 747 through 752 Processing helix chain 'A' and resid 789 through 808 Processing helix chain 'A' and resid 811 through 825 Processing helix chain 'A' and resid 827 through 836 Processing helix chain 'A' and resid 838 through 855 removed outlier: 3.710A pdb=" N GLN A 842 " --> pdb=" O THR A 838 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG A 855 " --> pdb=" O GLN A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 856 through 858 No H-bonds generated for 'chain 'A' and resid 856 through 858' Processing helix chain 'A' and resid 873 through 880 removed outlier: 4.470A pdb=" N ILE A 877 " --> pdb=" O GLY A 873 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 removed outlier: 4.014A pdb=" N LEU A 887 " --> pdb=" O ASP A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 902 removed outlier: 4.010A pdb=" N ALA A 902 " --> pdb=" O LYS A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 939 Processing helix chain 'A' and resid 943 through 960 Processing helix chain 'A' and resid 970 through 972 No H-bonds generated for 'chain 'A' and resid 970 through 972' Processing helix chain 'A' and resid 992 through 996 removed outlier: 3.700A pdb=" N PHE A 996 " --> pdb=" O PRO A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1002 No H-bonds generated for 'chain 'A' and resid 1000 through 1002' Processing helix chain 'A' and resid 1014 through 1020 removed outlier: 3.700A pdb=" N GLN A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1032 Processing helix chain 'A' and resid 1045 through 1052 Processing helix chain 'A' and resid 1052 through 1069 removed outlier: 3.728A pdb=" N PHE A1069 " --> pdb=" O VAL A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1081 Processing helix chain 'A' and resid 1114 through 1127 removed outlier: 3.844A pdb=" N GLU A1125 " --> pdb=" O LEU A1121 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1189 Processing helix chain 'B' and resid 4 through 9 removed outlier: 3.518A pdb=" N GLU B 7 " --> pdb=" O SER B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 38 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 54 through 78 Processing helix chain 'B' and resid 94 through 112 Processing helix chain 'B' and resid 121 through 131 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 146 through 157 Processing helix chain 'B' and resid 158 through 161 Processing helix chain 'B' and resid 162 through 178 removed outlier: 3.682A pdb=" N ARG B 177 " --> pdb=" O SER B 173 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 209 Processing helix chain 'B' and resid 217 through 227 Processing helix chain 'B' and resid 227 through 234 removed outlier: 3.978A pdb=" N LYS B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 232 " --> pdb=" O PRO B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 259 through 264 removed outlier: 4.192A pdb=" N LEU B 264 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.580A pdb=" N GLN B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASN B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N GLN B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 Processing helix chain 'B' and resid 312 through 316 Processing helix chain 'B' and resid 318 through 337 removed outlier: 3.752A pdb=" N PHE B 322 " --> pdb=" O ILE B 318 " (cutoff:3.500A) Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 346 through 352 Processing helix chain 'B' and resid 402 through 435 removed outlier: 3.600A pdb=" N GLY B 433 " --> pdb=" O GLU B 429 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 460 Processing helix chain 'B' and resid 461 through 463 No H-bonds generated for 'chain 'B' and resid 461 through 463' Processing helix chain 'B' and resid 464 through 476 removed outlier: 4.137A pdb=" N ASP B 473 " --> pdb=" O TYR B 469 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B 474 " --> pdb=" O GLU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 498 Processing helix chain 'B' and resid 524 through 535 Processing helix chain 'B' and resid 556 through 565 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 572 through 587 Processing helix chain 'B' and resid 604 through 616 Processing helix chain 'B' and resid 623 through 631 Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 636 through 656 Processing helix chain 'B' and resid 672 through 674 No H-bonds generated for 'chain 'B' and resid 672 through 674' Processing helix chain 'B' and resid 675 through 694 Processing helix chain 'B' and resid 704 through 711 Processing helix chain 'B' and resid 711 through 723 Processing helix chain 'B' and resid 733 through 737 removed outlier: 3.818A pdb=" N GLY B 737 " --> pdb=" O TYR B 733 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 733 through 737' Processing helix chain 'B' and resid 747 through 752 Processing helix chain 'B' and resid 789 through 808 Processing helix chain 'B' and resid 811 through 825 Processing helix chain 'B' and resid 827 through 837 removed outlier: 3.843A pdb=" N GLN B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 838 through 855 removed outlier: 3.667A pdb=" N GLN B 842 " --> pdb=" O THR B 838 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ARG B 855 " --> pdb=" O GLN B 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 856 through 858 No H-bonds generated for 'chain 'B' and resid 856 through 858' Processing helix chain 'B' and resid 873 through 880 removed outlier: 4.538A pdb=" N ILE B 877 " --> pdb=" O GLY B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 removed outlier: 3.995A pdb=" N LEU B 887 " --> pdb=" O ASP B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 902 removed outlier: 4.070A pdb=" N ALA B 902 " --> pdb=" O LYS B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 939 Processing helix chain 'B' and resid 943 through 960 Processing helix chain 'B' and resid 970 through 972 No H-bonds generated for 'chain 'B' and resid 970 through 972' Processing helix chain 'B' and resid 992 through 996 removed outlier: 3.705A pdb=" N PHE B 996 " --> pdb=" O PRO B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1002 No H-bonds generated for 'chain 'B' and resid 1000 through 1002' Processing helix chain 'B' and resid 1009 through 1014 removed outlier: 3.526A pdb=" N CYS B1013 " --> pdb=" O SER B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1014 through 1020 removed outlier: 3.693A pdb=" N GLN B1020 " --> pdb=" O ALA B1016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1032 Processing helix chain 'B' and resid 1045 through 1052 Processing helix chain 'B' and resid 1052 through 1068 Processing helix chain 'B' and resid 1077 through 1081 Processing helix chain 'B' and resid 1114 through 1127 Processing helix chain 'B' and resid 1176 through 1189 Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 47 removed outlier: 6.164A pdb=" N ALA A 43 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLY A 541 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU A 45 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR A 89 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ASP A 272 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 91 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU A 88 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU A 242 " --> pdb=" O LEU A 88 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N TYR A 90 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 133 " --> pdb=" O PHE A 241 " (cutoff:3.500A) removed outlier: 8.908A pdb=" N THR A 243 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 113 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 251 through 252 Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 292 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.463A pdb=" N ALA A 341 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ILE A 385 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN A 343 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N SER A 387 " --> pdb=" O ASN A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 601 removed outlier: 6.070A pdb=" N ILE A 774 " --> pdb=" O PHE A 869 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASP A 871 " --> pdb=" O ILE A 774 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N LEU A 776 " --> pdb=" O ASP A 871 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N TYR A 662 " --> pdb=" O SER A 773 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N TYR A 775 " --> pdb=" O TYR A 662 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A 664 " --> pdb=" O TYR A 775 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LYS A 698 " --> pdb=" O VAL A 728 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE A 730 " --> pdb=" O LYS A 698 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 700 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N THR A 732 " --> pdb=" O PHE A 700 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 743 through 745 Processing sheet with id=AA8, first strand: chain 'A' and resid 755 through 757 Processing sheet with id=AA9, first strand: chain 'A' and resid 962 through 963 Processing sheet with id=AB1, first strand: chain 'A' and resid 997 through 998 Processing sheet with id=AB2, first strand: chain 'A' and resid 1072 through 1074 removed outlier: 4.032A pdb=" N ILE A1097 " --> pdb=" O VAL A1088 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1137 through 1138 Processing sheet with id=AB4, first strand: chain 'B' and resid 43 through 47 removed outlier: 6.213A pdb=" N ALA B 43 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLY B 541 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LEU B 45 " --> pdb=" O GLY B 541 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR B 89 " --> pdb=" O ILE B 270 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ASP B 272 " --> pdb=" O TYR B 89 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 91 " --> pdb=" O ASP B 272 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 88 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N LEU B 242 " --> pdb=" O LEU B 88 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N TYR B 90 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 133 " --> pdb=" O PHE B 241 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N THR B 243 " --> pdb=" O VAL B 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AB6, first strand: chain 'B' and resid 251 through 252 Processing sheet with id=AB7, first strand: chain 'B' and resid 291 through 292 Processing sheet with id=AB8, first strand: chain 'B' and resid 341 through 344 removed outlier: 6.350A pdb=" N ALA B 341 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE B 385 " --> pdb=" O ALA B 341 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ASN B 343 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N SER B 387 " --> pdb=" O ASN B 343 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 595 through 601 removed outlier: 6.858A pdb=" N VAL B 595 " --> pdb=" O ILE B 866 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU B 868 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR B 597 " --> pdb=" O LEU B 868 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N VAL B 870 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LYS B 599 " --> pdb=" O VAL B 870 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE B 774 " --> pdb=" O PHE B 869 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ASP B 871 " --> pdb=" O ILE B 774 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU B 776 " --> pdb=" O ASP B 871 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR B 662 " --> pdb=" O SER B 773 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N TYR B 775 " --> pdb=" O TYR B 662 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU B 664 " --> pdb=" O TYR B 775 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N LYS B 698 " --> pdb=" O VAL B 728 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE B 730 " --> pdb=" O LYS B 698 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE B 700 " --> pdb=" O PHE B 730 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N THR B 732 " --> pdb=" O PHE B 700 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 743 through 745 Processing sheet with id=AC2, first strand: chain 'B' and resid 755 through 757 Processing sheet with id=AC3, first strand: chain 'B' and resid 962 through 963 Processing sheet with id=AC4, first strand: chain 'B' and resid 997 through 998 Processing sheet with id=AC5, first strand: chain 'B' and resid 1072 through 1074 removed outlier: 4.034A pdb=" N ILE B1097 " --> pdb=" O VAL B1088 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL B1134 " --> pdb=" O ASP B1100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1137 through 1138 1023 hydrogen bonds defined for protein. 2910 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: 9.89 Time building geometry restraints manager: 8.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3290 1.32 - 1.44: 4975 1.44 - 1.57: 10613 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 18954 Sorted by residual: bond pdb=" N VAL B 153 " pdb=" CA VAL B 153 " ideal model delta sigma weight residual 1.460 1.502 -0.042 1.21e-02 6.83e+03 1.20e+01 bond pdb=" N VAL B 133 " pdb=" CA VAL B 133 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.11e-02 8.12e+03 1.07e+01 bond pdb=" N VAL B 239 " pdb=" CA VAL B 239 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.19e-02 7.06e+03 1.02e+01 bond pdb=" N ARG B 475 " pdb=" CA ARG B 475 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" N THR B 513 " pdb=" CA THR B 513 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.23e-02 6.61e+03 9.94e+00 ... (remaining 18949 not shown) Histogram of bond angle deviations from ideal: 100.49 - 107.31: 479 107.31 - 114.13: 10718 114.13 - 120.95: 9119 120.95 - 127.78: 5135 127.78 - 134.60: 163 Bond angle restraints: 25614 Sorted by residual: angle pdb=" CA VAL B 16 " pdb=" C VAL B 16 " pdb=" N PRO B 17 " ideal model delta sigma weight residual 116.57 121.96 -5.39 9.80e-01 1.04e+00 3.02e+01 angle pdb=" CA VAL B 133 " pdb=" C VAL B 133 " pdb=" O VAL B 133 " ideal model delta sigma weight residual 121.67 116.24 5.43 1.05e+00 9.07e-01 2.67e+01 angle pdb=" CA GLY A 346 " pdb=" C GLY A 346 " pdb=" O GLY A 346 " ideal model delta sigma weight residual 122.24 117.83 4.41 8.70e-01 1.32e+00 2.57e+01 angle pdb=" N GLY B 476 " pdb=" CA GLY B 476 " pdb=" C GLY B 476 " ideal model delta sigma weight residual 115.32 109.19 6.13 1.31e+00 5.83e-01 2.19e+01 angle pdb=" CA LEU B 784 " pdb=" C LEU B 784 " pdb=" O LEU B 784 " ideal model delta sigma weight residual 121.56 116.55 5.01 1.09e+00 8.42e-01 2.12e+01 ... (remaining 25609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 10256 17.97 - 35.95: 873 35.95 - 53.92: 237 53.92 - 71.89: 53 71.89 - 89.86: 25 Dihedral angle restraints: 11444 sinusoidal: 4679 harmonic: 6765 Sorted by residual: dihedral pdb=" CA PHE A 520 " pdb=" C PHE A 520 " pdb=" N LEU A 521 " pdb=" CA LEU A 521 " ideal model delta harmonic sigma weight residual 180.00 158.24 21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA PHE B 520 " pdb=" C PHE B 520 " pdb=" N LEU B 521 " pdb=" CA LEU B 521 " ideal model delta harmonic sigma weight residual 180.00 158.30 21.70 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA LYS A 487 " pdb=" C LYS A 487 " pdb=" N LEU A 488 " pdb=" CA LEU A 488 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 11441 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2415 0.059 - 0.118: 337 0.118 - 0.176: 63 0.176 - 0.235: 7 0.235 - 0.294: 3 Chirality restraints: 2825 Sorted by residual: chirality pdb=" CA LYS B 862 " pdb=" N LYS B 862 " pdb=" C LYS B 862 " pdb=" CB LYS B 862 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA VAL B 16 " pdb=" N VAL B 16 " pdb=" C VAL B 16 " pdb=" CB VAL B 16 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CB VAL B 153 " pdb=" CA VAL B 153 " pdb=" CG1 VAL B 153 " pdb=" CG2 VAL B 153 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.59e+00 ... (remaining 2822 not shown) Planarity restraints: 3324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 315 " -0.049 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR B 315 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR B 315 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 315 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR B 315 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR B 315 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 315 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 315 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 862 " 0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C LYS B 862 " -0.062 2.00e-02 2.50e+03 pdb=" O LYS B 862 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG B 863 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 782 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.19e+00 pdb=" C LEU B 782 " 0.052 2.00e-02 2.50e+03 pdb=" O LEU B 782 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU B 783 " -0.018 2.00e-02 2.50e+03 ... (remaining 3321 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 214 2.64 - 3.20: 17700 3.20 - 3.77: 29256 3.77 - 4.33: 41718 4.33 - 4.90: 68709 Nonbonded interactions: 157597 Sorted by model distance: nonbonded pdb=" O LEU A 488 " pdb=" OG SER A 489 " model vdw 2.072 2.440 nonbonded pdb=" N GLN A 508 " pdb=" OE1 GLN A 508 " model vdw 2.134 2.520 nonbonded pdb=" O ASP A1070 " pdb=" OD1 ASP A1070 " model vdw 2.141 3.040 nonbonded pdb=" OG SER A 839 " pdb=" NH1 ARG A 910 " model vdw 2.210 2.520 nonbonded pdb=" O CYS A1013 " pdb=" OH TYR A1103 " model vdw 2.214 2.440 ... (remaining 157592 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 507 or resid 510 through 1190)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 30.430 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: 39.240 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 58.730 Find NCS groups from input model: 1.250 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 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 : 0.005 0.042 18954 Z= 0.313 Angle : 0.741 7.560 25614 Z= 0.526 Chirality : 0.045 0.294 2825 Planarity : 0.003 0.044 3324 Dihedral : 15.187 89.863 7054 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.03 % Allowed : 10.89 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.18), residues: 2276 helix: 2.45 (0.15), residues: 1165 sheet: -0.06 (0.30), residues: 299 loop : 0.69 (0.24), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 643 HIS 0.011 0.001 HIS A 238 PHE 0.016 0.001 PHE B 195 TYR 0.050 0.001 TYR B 315 ARG 0.005 0.000 ARG B 475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 194 time to evaluate : 2.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8678 (tt) REVERT: A 503 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7926 (tp30) REVERT: A 851 GLN cc_start: 0.8224 (tt0) cc_final: 0.7729 (mm110) REVERT: A 1023 TYR cc_start: 0.8911 (m-80) cc_final: 0.8541 (m-80) REVERT: B 140 GLU cc_start: 0.8057 (tp30) cc_final: 0.7731 (tp30) REVERT: B 168 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7682 (mt-10) REVERT: B 663 MET cc_start: 0.5263 (ttm) cc_final: 0.4809 (ttm) REVERT: B 851 GLN cc_start: 0.7612 (mt0) cc_final: 0.7359 (mm110) outliers start: 21 outliers final: 5 residues processed: 210 average time/residue: 1.4273 time to fit residues: 333.9388 Evaluate side-chains 139 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain B residue 938 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 0.9990 chunk 174 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.0060 chunk 117 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 69 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 208 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 289 GLN A 794 GLN A 822 GLN B 144 GLN B 207 GLN B 449 GLN ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS B1086 ASN B1095 GLN B1188 HIS B1189 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18954 Z= 0.189 Angle : 0.504 11.680 25614 Z= 0.262 Chirality : 0.039 0.235 2825 Planarity : 0.004 0.051 3324 Dihedral : 4.621 50.270 2530 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.57 % Allowed : 12.16 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.18), residues: 2276 helix: 2.68 (0.15), residues: 1186 sheet: 0.09 (0.30), residues: 292 loop : 0.79 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 643 HIS 0.008 0.001 HIS B 935 PHE 0.019 0.001 PHE A 448 TYR 0.012 0.001 TYR A 713 ARG 0.008 0.000 ARG B1177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 2.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7985 (tp30) REVERT: A 663 MET cc_start: 0.5651 (OUTLIER) cc_final: 0.4737 (ttm) REVERT: A 851 GLN cc_start: 0.8247 (tt0) cc_final: 0.7693 (mm110) REVERT: B 140 GLU cc_start: 0.8224 (tp30) cc_final: 0.7901 (tp30) REVERT: B 191 GLN cc_start: 0.8435 (mm110) cc_final: 0.8112 (mm110) REVERT: B 663 MET cc_start: 0.5418 (ttm) cc_final: 0.4914 (ttm) REVERT: B 708 MET cc_start: 0.2814 (ptp) cc_final: 0.2430 (ppp) REVERT: B 851 GLN cc_start: 0.7671 (mt0) cc_final: 0.7362 (mm110) REVERT: B 969 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7904 (mmm160) REVERT: B 1115 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7229 (m-80) REVERT: B 1181 GLN cc_start: 0.9521 (mm110) cc_final: 0.9309 (mm110) outliers start: 32 outliers final: 12 residues processed: 176 average time/residue: 1.1865 time to fit residues: 237.9995 Evaluate side-chains 143 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 1101 SER Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 142 optimal weight: 0.1980 chunk 57 optimal weight: 6.9990 chunk 209 optimal weight: 2.9990 chunk 226 optimal weight: 0.0970 chunk 186 optimal weight: 7.9990 chunk 207 optimal weight: 0.1980 chunk 71 optimal weight: 9.9990 chunk 167 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 805 GLN A 822 GLN B 144 GLN B 794 GLN B 822 GLN ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18954 Z= 0.224 Angle : 0.486 10.849 25614 Z= 0.251 Chirality : 0.038 0.169 2825 Planarity : 0.003 0.032 3324 Dihedral : 4.010 21.140 2517 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.62 % Allowed : 13.39 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.18), residues: 2276 helix: 2.67 (0.15), residues: 1188 sheet: 0.09 (0.30), residues: 291 loop : 0.74 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 643 HIS 0.007 0.001 HIS B 238 PHE 0.016 0.001 PHE A 472 TYR 0.012 0.001 TYR B 713 ARG 0.003 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 2.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 503 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7980 (tp30) REVERT: A 663 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.4828 (ttm) REVERT: A 851 GLN cc_start: 0.8262 (tt0) cc_final: 0.7659 (mm110) REVERT: B 140 GLU cc_start: 0.8275 (tp30) cc_final: 0.7924 (tp30) REVERT: B 191 GLN cc_start: 0.8575 (mm110) cc_final: 0.8285 (mm110) REVERT: B 851 GLN cc_start: 0.7683 (mt0) cc_final: 0.7401 (mm110) REVERT: B 1115 TYR cc_start: 0.7797 (OUTLIER) cc_final: 0.7344 (m-80) REVERT: B 1181 GLN cc_start: 0.9551 (mm110) cc_final: 0.9350 (mm110) REVERT: B 1182 GLU cc_start: 0.9121 (OUTLIER) cc_final: 0.8881 (mp0) outliers start: 33 outliers final: 12 residues processed: 167 average time/residue: 1.2150 time to fit residues: 232.5612 Evaluate side-chains 141 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 475 ARG Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 1101 SER Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 108 optimal weight: 0.0070 chunk 23 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 209 optimal weight: 2.9990 chunk 222 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 496 HIS B 134 HIS B 144 GLN B 805 GLN B 822 GLN ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 18954 Z= 0.384 Angle : 0.547 11.531 25614 Z= 0.282 Chirality : 0.041 0.168 2825 Planarity : 0.004 0.035 3324 Dihedral : 4.250 22.962 2517 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.65 % Allowed : 13.29 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.18), residues: 2276 helix: 2.42 (0.15), residues: 1192 sheet: -0.02 (0.30), residues: 285 loop : 0.56 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 643 HIS 0.007 0.001 HIS B 238 PHE 0.017 0.001 PHE B 557 TYR 0.014 0.002 TYR B 713 ARG 0.004 0.000 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 140 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LYS cc_start: 0.9333 (ttpp) cc_final: 0.9056 (ptpp) REVERT: A 269 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8866 (tt) REVERT: A 503 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.8045 (tp30) REVERT: A 563 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8249 (tpt90) REVERT: A 663 MET cc_start: 0.5579 (OUTLIER) cc_final: 0.4987 (tpt) REVERT: A 851 GLN cc_start: 0.8296 (tt0) cc_final: 0.7680 (mm110) REVERT: B 140 GLU cc_start: 0.8229 (tp30) cc_final: 0.7840 (tp30) REVERT: B 521 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9081 (mp) REVERT: B 563 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8435 (tpt90) REVERT: B 851 GLN cc_start: 0.7683 (mt0) cc_final: 0.7376 (mm110) REVERT: B 1115 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: B 1182 GLU cc_start: 0.9122 (OUTLIER) cc_final: 0.8839 (mp0) outliers start: 54 outliers final: 18 residues processed: 177 average time/residue: 1.2846 time to fit residues: 257.6567 Evaluate side-chains 150 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 1.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1080 ILE Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 0.8980 chunk 126 optimal weight: 0.0980 chunk 3 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN B 144 GLN ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18954 Z= 0.196 Angle : 0.471 11.714 25614 Z= 0.242 Chirality : 0.038 0.167 2825 Planarity : 0.003 0.037 3324 Dihedral : 4.010 21.615 2517 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.31 % Allowed : 14.37 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.18), residues: 2276 helix: 2.59 (0.15), residues: 1199 sheet: -0.01 (0.29), residues: 305 loop : 0.61 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 643 HIS 0.005 0.001 HIS A 935 PHE 0.011 0.001 PHE B 557 TYR 0.011 0.001 TYR A 982 ARG 0.007 0.000 ARG B 969 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 137 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LYS cc_start: 0.9331 (ttpp) cc_final: 0.9079 (ptpp) REVERT: A 503 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8009 (tp30) REVERT: A 563 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.7689 (tpp80) REVERT: A 663 MET cc_start: 0.5301 (OUTLIER) cc_final: 0.4992 (tpt) REVERT: A 851 GLN cc_start: 0.8247 (tt0) cc_final: 0.7619 (mm110) REVERT: B 140 GLU cc_start: 0.8215 (tp30) cc_final: 0.7841 (tp30) REVERT: B 185 LYS cc_start: 0.8938 (mttp) cc_final: 0.8689 (mtmt) REVERT: B 191 GLN cc_start: 0.8692 (mm110) cc_final: 0.8382 (mm110) REVERT: B 663 MET cc_start: 0.5401 (OUTLIER) cc_final: 0.4968 (tpt) REVERT: B 851 GLN cc_start: 0.7688 (mt0) cc_final: 0.7399 (mm110) REVERT: B 1115 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.7380 (m-80) REVERT: B 1182 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8902 (mp0) outliers start: 47 outliers final: 20 residues processed: 174 average time/residue: 1.2069 time to fit residues: 239.9508 Evaluate side-chains 154 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 2.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 966 GLN Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 1080 ILE Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 130 optimal weight: 0.0370 chunk 54 optimal weight: 0.3980 chunk 222 optimal weight: 10.0000 chunk 184 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 18 optimal weight: 0.0170 chunk 73 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 overall best weight: 1.0698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 627 ASN ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18954 Z= 0.252 Angle : 0.493 11.176 25614 Z= 0.252 Chirality : 0.039 0.165 2825 Planarity : 0.003 0.043 3324 Dihedral : 4.020 21.228 2517 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.31 % Allowed : 14.91 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.18), residues: 2276 helix: 2.54 (0.15), residues: 1202 sheet: 0.06 (0.30), residues: 295 loop : 0.54 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 643 HIS 0.005 0.001 HIS A 935 PHE 0.014 0.001 PHE B 557 TYR 0.018 0.001 TYR A 615 ARG 0.011 0.000 ARG A 573 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 140 time to evaluate : 2.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LYS cc_start: 0.9335 (ttpp) cc_final: 0.9080 (ptpp) REVERT: A 503 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.8035 (tp30) REVERT: A 517 LYS cc_start: 0.9110 (tppp) cc_final: 0.8826 (tptp) REVERT: A 563 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8404 (tpt90) REVERT: A 663 MET cc_start: 0.5331 (OUTLIER) cc_final: 0.4916 (tpt) REVERT: A 851 GLN cc_start: 0.8261 (tt0) cc_final: 0.7636 (mm110) REVERT: B 140 GLU cc_start: 0.8177 (tp30) cc_final: 0.7929 (tp30) REVERT: B 185 LYS cc_start: 0.8970 (mttp) cc_final: 0.8695 (mtmt) REVERT: B 191 GLN cc_start: 0.8694 (mm110) cc_final: 0.8367 (mm110) REVERT: B 214 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8179 (tm) REVERT: B 503 GLU cc_start: 0.8313 (tp30) cc_final: 0.8051 (tp30) REVERT: B 648 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5931 (mm) REVERT: B 663 MET cc_start: 0.5474 (OUTLIER) cc_final: 0.4993 (tpt) REVERT: B 851 GLN cc_start: 0.7672 (mt0) cc_final: 0.7379 (mm110) REVERT: B 1115 TYR cc_start: 0.7760 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: B 1182 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8890 (mp0) outliers start: 47 outliers final: 20 residues processed: 177 average time/residue: 1.1583 time to fit residues: 234.5498 Evaluate side-chains 153 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 966 GLN Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 269 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 126 optimal weight: 0.6980 chunk 162 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 187 optimal weight: 9.9990 chunk 124 optimal weight: 0.4980 chunk 221 optimal weight: 6.9990 chunk 138 optimal weight: 2.9990 chunk 135 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A1042 ASN B 144 GLN ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18954 Z= 0.189 Angle : 0.479 11.067 25614 Z= 0.243 Chirality : 0.038 0.163 2825 Planarity : 0.003 0.048 3324 Dihedral : 3.933 20.358 2517 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.16 % Allowed : 15.40 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.18), residues: 2276 helix: 2.63 (0.15), residues: 1201 sheet: 0.09 (0.30), residues: 295 loop : 0.54 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 643 HIS 0.005 0.001 HIS A 935 PHE 0.011 0.001 PHE B 557 TYR 0.016 0.001 TYR A 615 ARG 0.013 0.000 ARG B 573 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 136 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LYS cc_start: 0.9327 (ttpp) cc_final: 0.9067 (ptpp) REVERT: A 503 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8036 (tp30) REVERT: A 517 LYS cc_start: 0.9106 (tppp) cc_final: 0.8823 (tptp) REVERT: A 563 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.7782 (tpp80) REVERT: A 663 MET cc_start: 0.5345 (OUTLIER) cc_final: 0.5088 (tpt) REVERT: A 851 GLN cc_start: 0.8242 (tt0) cc_final: 0.7739 (mm110) REVERT: B 140 GLU cc_start: 0.8208 (tp30) cc_final: 0.7967 (tp30) REVERT: B 185 LYS cc_start: 0.8989 (mttp) cc_final: 0.8726 (mtmt) REVERT: B 191 GLN cc_start: 0.8702 (mm110) cc_final: 0.8364 (mm110) REVERT: B 214 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8172 (tm) REVERT: B 314 ARG cc_start: 0.8924 (ttm-80) cc_final: 0.8717 (ttm110) REVERT: B 503 GLU cc_start: 0.8302 (tp30) cc_final: 0.8021 (tp30) REVERT: B 648 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5912 (mm) REVERT: B 663 MET cc_start: 0.5360 (OUTLIER) cc_final: 0.4952 (tpt) REVERT: B 851 GLN cc_start: 0.7640 (mt0) cc_final: 0.7326 (mm110) REVERT: B 1115 TYR cc_start: 0.7773 (OUTLIER) cc_final: 0.7391 (m-80) REVERT: B 1182 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8895 (mp0) outliers start: 44 outliers final: 18 residues processed: 170 average time/residue: 1.1912 time to fit residues: 231.3572 Evaluate side-chains 153 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 127 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 648 LEU Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 chunk 140 optimal weight: 2.9990 chunk 151 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN B 144 GLN ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 18954 Z= 0.357 Angle : 0.537 10.686 25614 Z= 0.274 Chirality : 0.040 0.164 2825 Planarity : 0.003 0.043 3324 Dihedral : 4.133 22.341 2517 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.75 % Allowed : 15.15 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.18), residues: 2276 helix: 2.44 (0.15), residues: 1205 sheet: 0.16 (0.31), residues: 285 loop : 0.49 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 643 HIS 0.005 0.001 HIS A 935 PHE 0.016 0.001 PHE B 557 TYR 0.016 0.001 TYR A 615 ARG 0.012 0.000 ARG B 573 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 131 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 ASP cc_start: 0.9177 (t0) cc_final: 0.8945 (t0) REVERT: A 214 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8479 (tm) REVERT: A 503 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.8038 (tp30) REVERT: A 563 ARG cc_start: 0.9102 (OUTLIER) cc_final: 0.8216 (tpt90) REVERT: A 663 MET cc_start: 0.5427 (OUTLIER) cc_final: 0.4984 (tpt) REVERT: A 851 GLN cc_start: 0.8261 (tt0) cc_final: 0.7757 (mm110) REVERT: B 140 GLU cc_start: 0.8192 (tp30) cc_final: 0.7818 (tp30) REVERT: B 185 LYS cc_start: 0.9022 (mttp) cc_final: 0.8762 (mtmt) REVERT: B 214 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8205 (tm) REVERT: B 521 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8957 (mp) REVERT: B 663 MET cc_start: 0.5510 (OUTLIER) cc_final: 0.4963 (tpt) REVERT: B 851 GLN cc_start: 0.7683 (mt0) cc_final: 0.7378 (mm110) REVERT: B 966 GLN cc_start: 0.8586 (pm20) cc_final: 0.8232 (pp30) REVERT: B 1115 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7406 (m-80) REVERT: B 1182 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.8892 (mp0) outliers start: 56 outliers final: 24 residues processed: 178 average time/residue: 1.0828 time to fit residues: 223.2169 Evaluate side-chains 151 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 118 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 214 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 966 GLN Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 663 MET Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 193 optimal weight: 0.7980 chunk 206 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 162 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 195 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 486 ASN B 144 GLN ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18954 Z= 0.203 Angle : 0.491 10.899 25614 Z= 0.249 Chirality : 0.038 0.162 2825 Planarity : 0.003 0.036 3324 Dihedral : 3.986 21.679 2517 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.96 % Allowed : 15.94 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.18), residues: 2276 helix: 2.56 (0.15), residues: 1205 sheet: 0.22 (0.31), residues: 288 loop : 0.47 (0.23), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 643 HIS 0.005 0.001 HIS A 935 PHE 0.011 0.001 PHE B 557 TYR 0.016 0.001 TYR B 615 ARG 0.010 0.000 ARG B 573 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LYS cc_start: 0.9319 (ttpp) cc_final: 0.9037 (ptpp) REVERT: A 503 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: A 563 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.7800 (tpp80) REVERT: A 663 MET cc_start: 0.5317 (OUTLIER) cc_final: 0.5092 (tpt) REVERT: A 851 GLN cc_start: 0.8240 (tt0) cc_final: 0.7741 (mm110) REVERT: B 140 GLU cc_start: 0.8192 (tp30) cc_final: 0.7928 (tp30) REVERT: B 185 LYS cc_start: 0.9028 (mttp) cc_final: 0.8763 (mtmt) REVERT: B 191 GLN cc_start: 0.8648 (mm110) cc_final: 0.8324 (mm110) REVERT: B 503 GLU cc_start: 0.8310 (tp30) cc_final: 0.8028 (tp30) REVERT: B 662 TYR cc_start: 0.8520 (t80) cc_final: 0.8320 (t80) REVERT: B 851 GLN cc_start: 0.7650 (mt0) cc_final: 0.7329 (mm110) REVERT: B 966 GLN cc_start: 0.8524 (pm20) cc_final: 0.8208 (pp30) REVERT: B 1007 MET cc_start: 0.8966 (tpp) cc_final: 0.8663 (tpp) REVERT: B 1115 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.7398 (m-80) REVERT: B 1182 GLU cc_start: 0.9132 (OUTLIER) cc_final: 0.8885 (mp0) outliers start: 40 outliers final: 20 residues processed: 160 average time/residue: 1.1769 time to fit residues: 215.4109 Evaluate side-chains 150 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 500 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 563 ARG Chi-restraints excluded: chain A residue 594 VAL Chi-restraints excluded: chain A residue 663 MET Chi-restraints excluded: chain A residue 966 GLN Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 816 GLU Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 0.7980 chunk 218 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 210 optimal weight: 0.6980 chunk 182 optimal weight: 0.0060 chunk 18 optimal weight: 0.1980 chunk 140 optimal weight: 0.1980 chunk 111 optimal weight: 6.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 ASN A 781 GLN B 144 GLN ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 938 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 18954 Z= 0.149 Angle : 0.478 10.779 25614 Z= 0.241 Chirality : 0.037 0.202 2825 Planarity : 0.003 0.035 3324 Dihedral : 3.794 19.558 2517 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.32 % Allowed : 16.53 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.18), residues: 2276 helix: 2.73 (0.15), residues: 1198 sheet: 0.17 (0.30), residues: 304 loop : 0.50 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 643 HIS 0.005 0.001 HIS A 935 PHE 0.011 0.001 PHE A 472 TYR 0.014 0.001 TYR B 615 ARG 0.009 0.000 ARG B 573 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4552 Ramachandran restraints generated. 2276 Oldfield, 0 Emsley, 2276 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 143 time to evaluate : 2.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 185 LYS cc_start: 0.9321 (ttpp) cc_final: 0.9038 (ptpp) REVERT: A 269 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8824 (tt) REVERT: A 503 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8017 (tp30) REVERT: A 851 GLN cc_start: 0.8230 (tt0) cc_final: 0.7602 (mm110) REVERT: B 140 GLU cc_start: 0.8196 (tp30) cc_final: 0.7959 (tp30) REVERT: B 185 LYS cc_start: 0.9023 (mttp) cc_final: 0.8760 (mtmt) REVERT: B 191 GLN cc_start: 0.8566 (mm110) cc_final: 0.8327 (mm110) REVERT: B 503 GLU cc_start: 0.8258 (tp30) cc_final: 0.7965 (tp30) REVERT: B 851 GLN cc_start: 0.7566 (mt0) cc_final: 0.7266 (mm110) REVERT: B 966 GLN cc_start: 0.8484 (pm20) cc_final: 0.8185 (pp30) REVERT: B 1007 MET cc_start: 0.8941 (tpp) cc_final: 0.8626 (tpp) REVERT: B 1115 TYR cc_start: 0.7782 (OUTLIER) cc_final: 0.7450 (m-80) REVERT: B 1182 GLU cc_start: 0.9133 (OUTLIER) cc_final: 0.8892 (mp0) outliers start: 27 outliers final: 13 residues processed: 163 average time/residue: 1.1752 time to fit residues: 220.2158 Evaluate side-chains 141 residues out of total 2039 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 2.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 348 ASN Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 1182 GLU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 144 GLN Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 348 ASN Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 989 LEU Chi-restraints excluded: chain B residue 1115 TYR Chi-restraints excluded: chain B residue 1182 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 2.9990 chunk 194 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 168 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 182 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 187 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN A 781 GLN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 GLN ** B 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 935 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 938 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.133012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.084465 restraints weight = 33568.438| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.77 r_work: 0.3035 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 18954 Z= 0.197 Angle : 0.691 59.200 25614 Z= 0.390 Chirality : 0.041 0.756 2825 Planarity : 0.003 0.083 3324 Dihedral : 3.799 19.384 2517 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.13 % Allowed : 17.17 % Favored : 81.71 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.18), residues: 2276 helix: 2.71 (0.15), residues: 1198 sheet: 0.21 (0.31), residues: 294 loop : 0.47 (0.23), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 643 HIS 0.004 0.001 HIS A 935 PHE 0.011 0.001 PHE B 195 TYR 0.014 0.001 TYR B 615 ARG 0.008 0.000 ARG B 573 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6056.61 seconds wall clock time: 109 minutes 56.46 seconds (6596.46 seconds total)