Starting phenix.real_space_refine on Thu Jul 31 08:53:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0d_36761/07_2025/8k0d_36761.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0d_36761/07_2025/8k0d_36761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k0d_36761/07_2025/8k0d_36761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0d_36761/07_2025/8k0d_36761.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0d_36761/07_2025/8k0d_36761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0d_36761/07_2025/8k0d_36761.cif" } resolution = 2.94 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 8414 2.51 5 N 2222 2.21 5 O 2582 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13282 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1842 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Chain: "F" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "A" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3179 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 377} Chain: "C" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1842 Classifications: {'peptide': 242} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 224} Chain: "D" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1620 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "B" Number of atoms: 3179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3179 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 377} Time building chain proxies: 11.03, per 1000 atoms: 0.83 Number of scatterers: 13282 At special positions: 0 Unit cell: (125.46, 99.22, 214.84, 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 64 16.00 O 2582 8.00 N 2222 7.00 C 8414 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 97 " distance=2.03 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 232 " - pdb=" SG CYS F 213 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 216 " - pdb=" SG CYS A 240 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 395 " distance=2.03 Simple disulfide: pdb=" SG CYS A 387 " - pdb=" SG CYS A 499 " distance=2.03 Simple disulfide: pdb=" SG CYS A 493 " - pdb=" SG CYS A 503 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 574 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 156 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS D 213 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 240 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 395 " distance=2.03 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 499 " distance=2.03 Simple disulfide: pdb=" SG CYS B 493 " - pdb=" SG CYS B 503 " distance=2.03 Simple disulfide: pdb=" SG CYS B 565 " - pdb=" SG CYS B 574 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.7 seconds 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3180 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 37 sheets defined 6.2% alpha, 44.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'E' and resid 88 through 92 removed outlier: 3.662A pdb=" N THR E 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'F' and resid 120 through 127 removed outlier: 3.547A pdb=" N GLY F 127 " --> pdb=" O GLN F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 187 Processing helix chain 'A' and resid 204 through 207 removed outlier: 3.644A pdb=" N LEU A 207 " --> pdb=" O SER A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 207' Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.709A pdb=" N GLN A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 378 through 382 Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'C' and resid 88 through 92 removed outlier: 3.577A pdb=" N THR C 92 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'D' and resid 79 through 83 removed outlier: 4.146A pdb=" N PHE D 83 " --> pdb=" O PRO D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 182 through 187 Processing helix chain 'B' and resid 204 through 207 removed outlier: 3.561A pdb=" N LEU B 207 " --> pdb=" O SER B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 204 through 207' Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.553A pdb=" N GLN B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 382 Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 419 through 421 No H-bonds generated for 'chain 'B' and resid 419 through 421' Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.569A pdb=" N PHE E 80 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 12 removed outlier: 4.647A pdb=" N ARG E 34 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY E 50 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ARG E 39 " --> pdb=" O TRP E 48 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N TRP E 48 " --> pdb=" O ARG E 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.968A pdb=" N VAL E 118 " --> pdb=" O ARG E 99 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR E 101 " --> pdb=" O PHE E 116 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N PHE E 116 " --> pdb=" O TYR E 101 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N TYR E 103 " --> pdb=" O ASN E 114 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ASN E 114 " --> pdb=" O TYR E 103 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 136 through 140 removed outlier: 3.585A pdb=" N VAL E 200 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 167 through 170 Processing sheet with id=AA6, first strand: chain 'E' and resid 185 through 186 removed outlier: 3.535A pdb=" N VAL E 185 " --> pdb=" O SER E 193 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 4 through 7 removed outlier: 5.811A pdb=" N THR F 69 " --> pdb=" O ALA F 25 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.082A pdb=" N GLN F 37 " --> pdb=" O LEU F 46 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU F 46 " --> pdb=" O GLN F 37 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 113 through 117 removed outlier: 3.517A pdb=" N ASN F 136 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL F 132 " --> pdb=" O PHE F 117 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N TYR F 172 " --> pdb=" O ASN F 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 152 through 153 removed outlier: 3.705A pdb=" N LYS F 144 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR F 196 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN F 146 " --> pdb=" O GLU F 194 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS F 206 " --> pdb=" O CYS F 193 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 201 through 202 removed outlier: 5.435A pdb=" N LYS A 560 " --> pdb=" O GLU A 579 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR A 581 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA A 558 " --> pdb=" O TYR A 581 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AB4, first strand: chain 'A' and resid 217 through 218 removed outlier: 6.045A pdb=" N ILE A 237 " --> pdb=" O SER A 245 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER A 245 " --> pdb=" O ILE A 237 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLU A 254 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N MET A 267 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 256 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU A 265 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 279 through 287 removed outlier: 5.460A pdb=" N HIS A 281 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA A 296 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER A 313 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET A 316 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG A 318 " --> pdb=" O HIS A 333 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS A 333 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 340 through 341 removed outlier: 7.308A pdb=" N GLU A 341 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLU A 430 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 340 through 341 removed outlier: 7.308A pdb=" N GLU A 341 " --> pdb=" O PHE A 428 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLU A 430 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 442 through 447 removed outlier: 3.581A pdb=" N SER A 447 " --> pdb=" O GLN A 450 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A 476 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 511 through 515 removed outlier: 6.423A pdb=" N ILE A 520 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AC2, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.630A pdb=" N VAL C 123 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG C 34 " --> pdb=" O ASP C 100 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TRP C 35 " --> pdb=" O TYR C 51 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TYR C 51 " --> pdb=" O TRP C 35 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP C 37 " --> pdb=" O ILE C 49 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.630A pdb=" N VAL C 123 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N CYS C 97 " --> pdb=" O TRP C 119 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TRP C 119 " --> pdb=" O CYS C 97 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ARG C 99 " --> pdb=" O ASP C 117 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.504A pdb=" N GLY C 155 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 136 through 140 removed outlier: 3.504A pdb=" N GLY C 155 " --> pdb=" O LEU C 140 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL C 197 " --> pdb=" O HIS C 180 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS C 180 " --> pdb=" O VAL C 197 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 167 through 170 removed outlier: 3.615A pdb=" N LYS C 225 " --> pdb=" O CYS C 212 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 185 through 186 Processing sheet with id=AC8, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.058A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.536A pdb=" N LEU D 33 " --> pdb=" O SER D 49 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N SER D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 113 through 117 removed outlier: 3.664A pdb=" N SER D 176 " --> pdb=" O CYS D 133 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR D 172 " --> pdb=" O ASN D 137 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 153 through 154 removed outlier: 4.418A pdb=" N TRP D 147 " --> pdb=" O GLN D 154 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 208 " --> pdb=" O TYR D 191 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS D 206 " --> pdb=" O CYS D 193 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 201 through 202 removed outlier: 5.382A pdb=" N LYS B 560 " --> pdb=" O GLU B 579 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N TYR B 581 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 558 " --> pdb=" O TYR B 581 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 201 through 202 Processing sheet with id=AD5, first strand: chain 'B' and resid 217 through 218 removed outlier: 6.488A pdb=" N TYR B 231 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 250 " --> pdb=" O TYR B 231 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS B 233 " --> pdb=" O ARG B 248 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG B 248 " --> pdb=" O HIS B 233 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU B 235 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL B 244 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU B 254 " --> pdb=" O MET B 267 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N MET B 267 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU B 256 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU B 265 " --> pdb=" O LEU B 256 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 279 through 287 removed outlier: 5.589A pdb=" N HIS B 281 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA B 296 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N SER B 313 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET B 316 " --> pdb=" O LEU B 335 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 340 through 341 removed outlier: 7.357A pdb=" N GLU B 341 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU B 430 " --> pdb=" O GLU B 341 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS B 347 " --> pdb=" O PHE B 369 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 340 through 341 removed outlier: 7.357A pdb=" N GLU B 341 " --> pdb=" O PHE B 428 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N GLU B 430 " --> pdb=" O GLU B 341 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 442 through 447 removed outlier: 3.522A pdb=" N ASP B 468 " --> pdb=" O ASN B 478 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 476 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 511 through 515 removed outlier: 6.397A pdb=" N ILE B 520 " --> pdb=" O ILE B 514 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1254 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: 6.25 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4237 1.34 - 1.46: 3144 1.46 - 1.58: 6161 1.58 - 1.70: 0 1.70 - 1.82: 82 Bond restraints: 13624 Sorted by residual: bond pdb=" C LYS A 443 " pdb=" N ILE A 444 " ideal model delta sigma weight residual 1.330 1.309 0.022 1.48e-02 4.57e+03 2.14e+00 bond pdb=" C LYS B 443 " pdb=" N ILE B 444 " ideal model delta sigma weight residual 1.330 1.309 0.021 1.48e-02 4.57e+03 2.08e+00 bond pdb=" CA GLY D 68 " pdb=" C GLY D 68 " ideal model delta sigma weight residual 1.514 1.531 -0.017 1.41e-02 5.03e+03 1.37e+00 bond pdb=" CA SER C 106 " pdb=" C SER C 106 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.19e+00 bond pdb=" CA SER E 106 " pdb=" C SER E 106 " ideal model delta sigma weight residual 1.532 1.522 0.010 9.60e-03 1.09e+04 1.17e+00 ... (remaining 13619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 18257 2.13 - 4.27: 282 4.27 - 6.40: 20 6.40 - 8.54: 0 8.54 - 10.67: 1 Bond angle restraints: 18560 Sorted by residual: angle pdb=" N ARG A 402 " pdb=" CA ARG A 402 " pdb=" C ARG A 402 " ideal model delta sigma weight residual 110.40 99.73 10.67 1.43e+00 4.89e-01 5.57e+01 angle pdb=" N VAL A 484 " pdb=" CA VAL A 484 " pdb=" C VAL A 484 " ideal model delta sigma weight residual 113.71 110.17 3.54 9.50e-01 1.11e+00 1.38e+01 angle pdb=" C TYR F 185 " pdb=" N GLU F 186 " pdb=" CA GLU F 186 " ideal model delta sigma weight residual 122.38 116.69 5.69 1.81e+00 3.05e-01 9.87e+00 angle pdb=" N ILE A 401 " pdb=" CA ILE A 401 " pdb=" C ILE A 401 " ideal model delta sigma weight residual 110.42 113.24 -2.82 9.60e-01 1.09e+00 8.66e+00 angle pdb=" C PHE A 290 " pdb=" N TYR A 291 " pdb=" CA TYR A 291 " ideal model delta sigma weight residual 122.86 118.76 4.10 1.42e+00 4.96e-01 8.35e+00 ... (remaining 18555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7716 17.93 - 35.86: 364 35.86 - 53.79: 61 53.79 - 71.71: 12 71.71 - 89.64: 9 Dihedral angle restraints: 8162 sinusoidal: 3184 harmonic: 4978 Sorted by residual: dihedral pdb=" CB CYS A 387 " pdb=" SG CYS A 387 " pdb=" SG CYS A 499 " pdb=" CB CYS A 499 " ideal model delta sinusoidal sigma weight residual -86.00 -175.64 89.64 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CB CYS A 216 " pdb=" SG CYS A 216 " pdb=" SG CYS A 240 " pdb=" CB CYS A 240 " ideal model delta sinusoidal sigma weight residual 93.00 178.38 -85.38 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS B 216 " pdb=" SG CYS B 216 " pdb=" SG CYS B 240 " pdb=" CB CYS B 240 " ideal model delta sinusoidal sigma weight residual 93.00 174.35 -81.35 1 1.00e+01 1.00e-02 8.16e+01 ... (remaining 8159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1543 0.046 - 0.093: 370 0.093 - 0.139: 149 0.139 - 0.186: 0 0.186 - 0.232: 2 Chirality restraints: 2064 Sorted by residual: chirality pdb=" CB ILE B 408 " pdb=" CA ILE B 408 " pdb=" CG1 ILE B 408 " pdb=" CG2 ILE B 408 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE A 408 " pdb=" CA ILE A 408 " pdb=" CG1 ILE A 408 " pdb=" CG2 ILE A 408 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE B 250 " pdb=" N ILE B 250 " pdb=" C ILE B 250 " pdb=" CB ILE B 250 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 2061 not shown) Planarity restraints: 2380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 291 " -0.018 2.00e-02 2.50e+03 1.63e-02 5.33e+00 pdb=" CG TYR B 291 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR B 291 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 291 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B 291 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR B 291 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR B 291 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 291 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 164 " -0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO E 165 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO E 165 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 165 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 351 " 0.018 2.00e-02 2.50e+03 1.52e-02 4.61e+00 pdb=" CG TYR A 351 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR A 351 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 351 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 351 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 351 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 351 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 351 " 0.001 2.00e-02 2.50e+03 ... (remaining 2377 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 200 2.63 - 3.20: 11875 3.20 - 3.77: 21302 3.77 - 4.33: 30453 4.33 - 4.90: 50325 Nonbonded interactions: 114155 Sorted by model distance: nonbonded pdb=" OG SER B 528 " pdb=" O THR B 531 " model vdw 2.065 3.040 nonbonded pdb=" NH2 ARG F 61 " pdb=" OE2 GLU F 81 " model vdw 2.153 3.120 nonbonded pdb=" O LEU A 202 " pdb=" NH2 ARG B 258 " model vdw 2.177 3.120 nonbonded pdb=" OE1 GLU D 105 " pdb=" OH TYR D 172 " model vdw 2.203 3.040 nonbonded pdb=" OG SER F 7 " pdb=" OG1 THR F 22 " model vdw 2.212 3.040 ... (remaining 114150 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'D' selection = chain 'F' } 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: 282.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 37.160 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 334.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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 : 0.004 0.034 13646 Z= 0.181 Angle : 0.628 10.669 18604 Z= 0.354 Chirality : 0.046 0.232 2064 Planarity : 0.004 0.054 2380 Dihedral : 10.650 84.238 4916 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.58 % Favored : 95.30 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.20), residues: 1702 helix: -2.82 (0.62), residues: 44 sheet: -1.34 (0.19), residues: 696 loop : -0.63 (0.20), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 170 HIS 0.004 0.001 HIS F 197 PHE 0.020 0.002 PHE F 83 TYR 0.039 0.002 TYR B 291 ARG 0.008 0.001 ARG A 402 Details of bonding type rmsd hydrogen bonds : bond 0.26170 ( 426) hydrogen bonds : angle 11.34261 ( 1254) SS BOND : bond 0.00176 ( 22) SS BOND : angle 0.78158 ( 44) covalent geometry : bond 0.00389 (13624) covalent geometry : angle 0.62796 (18560) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: E 30 SER cc_start: 0.7993 (t) cc_final: 0.7790 (t) REVERT: E 213 ASN cc_start: 0.7647 (m110) cc_final: 0.7307 (m-40) REVERT: E 215 ASN cc_start: 0.8023 (t0) cc_final: 0.7640 (t0) REVERT: E 222 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7524 (mmmm) REVERT: F 116 ILE cc_start: 0.8400 (tt) cc_final: 0.7549 (mp) REVERT: F 159 GLN cc_start: 0.8471 (mp10) cc_final: 0.8097 (mp10) REVERT: F 169 ASP cc_start: 0.8672 (p0) cc_final: 0.7843 (p0) REVERT: A 463 MET cc_start: 0.8083 (mmt) cc_final: 0.7858 (mmm) REVERT: C 160 ASP cc_start: 0.8656 (m-30) cc_final: 0.8425 (p0) REVERT: D 82 ASP cc_start: 0.7926 (m-30) cc_final: 0.7624 (m-30) REVERT: D 160 GLU cc_start: 0.8047 (tp30) cc_final: 0.7808 (tp30) REVERT: B 399 MET cc_start: 0.8870 (tpp) cc_final: 0.8584 (tpp) REVERT: B 555 ASP cc_start: 0.8418 (p0) cc_final: 0.7838 (t0) outliers start: 0 outliers final: 1 residues processed: 165 average time/residue: 1.7626 time to fit residues: 317.1767 Evaluate side-chains 104 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 142 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 3.9990 chunk 128 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 9.9990 chunk 154 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN E 213 ASN ** F 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN ** D 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.117746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.081922 restraints weight = 27506.956| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 2.66 r_work: 0.3378 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13646 Z= 0.236 Angle : 0.656 8.001 18604 Z= 0.346 Chirality : 0.048 0.188 2064 Planarity : 0.005 0.054 2380 Dihedral : 6.253 150.796 1857 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.12 % Allowed : 7.08 % Favored : 91.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 1702 helix: -2.63 (0.58), residues: 44 sheet: -1.21 (0.18), residues: 734 loop : -0.67 (0.21), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 170 HIS 0.009 0.001 HIS A 233 PHE 0.024 0.002 PHE F 83 TYR 0.029 0.002 TYR A 351 ARG 0.007 0.001 ARG D 24 Details of bonding type rmsd hydrogen bonds : bond 0.04532 ( 426) hydrogen bonds : angle 7.63816 ( 1254) SS BOND : bond 0.00343 ( 22) SS BOND : angle 0.85377 ( 44) covalent geometry : bond 0.00542 (13624) covalent geometry : angle 0.65499 (18560) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 3.642 Fit side-chains REVERT: E 222 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8005 (mmmm) REVERT: F 17 ASP cc_start: 0.8575 (m-30) cc_final: 0.8189 (m-30) REVERT: F 81 GLU cc_start: 0.8669 (pp20) cc_final: 0.8448 (pp20) REVERT: F 169 ASP cc_start: 0.8814 (p0) cc_final: 0.8168 (p0) REVERT: C 99 ARG cc_start: 0.8730 (mtp180) cc_final: 0.8429 (ttp80) REVERT: C 160 ASP cc_start: 0.8811 (m-30) cc_final: 0.8476 (p0) REVERT: D 82 ASP cc_start: 0.8249 (m-30) cc_final: 0.7961 (m-30) outliers start: 17 outliers final: 2 residues processed: 128 average time/residue: 1.7077 time to fit residues: 237.8579 Evaluate side-chains 94 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain B residue 315 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 110 optimal weight: 3.9990 chunk 158 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 167 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN B 269 ASN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.116811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.083096 restraints weight = 27513.808| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 2.58 r_work: 0.3371 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3251 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13646 Z= 0.224 Angle : 0.625 7.443 18604 Z= 0.328 Chirality : 0.047 0.152 2064 Planarity : 0.005 0.052 2380 Dihedral : 5.134 55.450 1854 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.52 % Allowed : 8.99 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.20), residues: 1702 helix: -2.43 (0.59), residues: 44 sheet: -1.13 (0.18), residues: 774 loop : -0.58 (0.22), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 170 HIS 0.005 0.001 HIS B 281 PHE 0.026 0.002 PHE D 117 TYR 0.024 0.002 TYR B 351 ARG 0.004 0.001 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 426) hydrogen bonds : angle 6.94558 ( 1254) SS BOND : bond 0.00313 ( 22) SS BOND : angle 1.10593 ( 44) covalent geometry : bond 0.00515 (13624) covalent geometry : angle 0.62308 (18560) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 1.407 Fit side-chains REVERT: E 74 ASP cc_start: 0.8314 (t70) cc_final: 0.7889 (t0) REVERT: F 17 ASP cc_start: 0.8609 (m-30) cc_final: 0.8156 (m-30) REVERT: F 81 GLU cc_start: 0.8659 (pp20) cc_final: 0.8417 (pp20) REVERT: F 116 ILE cc_start: 0.8138 (tt) cc_final: 0.7192 (pp) REVERT: F 169 ASP cc_start: 0.8807 (p0) cc_final: 0.8291 (p0) REVERT: A 550 GLN cc_start: 0.8080 (tt0) cc_final: 0.7836 (tt0) REVERT: C 99 ARG cc_start: 0.8694 (mtp180) cc_final: 0.8263 (ttp80) REVERT: C 160 ASP cc_start: 0.8709 (m-30) cc_final: 0.8364 (p0) REVERT: D 17 ASP cc_start: 0.8142 (t0) cc_final: 0.7894 (t0) REVERT: D 82 ASP cc_start: 0.8293 (m-30) cc_final: 0.8072 (m-30) REVERT: B 455 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8644 (tt0) outliers start: 23 outliers final: 2 residues processed: 118 average time/residue: 1.3304 time to fit residues: 172.7975 Evaluate side-chains 90 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 455 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 46 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 120 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 113 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 ASN F 136 ASN F 137 ASN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.114537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.079657 restraints weight = 27331.003| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.60 r_work: 0.3325 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13646 Z= 0.276 Angle : 0.649 9.919 18604 Z= 0.339 Chirality : 0.048 0.165 2064 Planarity : 0.005 0.050 2380 Dihedral : 5.214 55.123 1854 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.18 % Allowed : 9.99 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1702 helix: -2.01 (0.68), residues: 44 sheet: -1.02 (0.18), residues: 768 loop : -0.58 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 170 HIS 0.007 0.001 HIS B 281 PHE 0.023 0.002 PHE D 138 TYR 0.024 0.002 TYR B 292 ARG 0.005 0.001 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.03752 ( 426) hydrogen bonds : angle 6.62407 ( 1254) SS BOND : bond 0.00358 ( 22) SS BOND : angle 0.85640 ( 44) covalent geometry : bond 0.00634 (13624) covalent geometry : angle 0.64887 (18560) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 1.409 Fit side-chains REVERT: E 74 ASP cc_start: 0.8479 (t70) cc_final: 0.7886 (t0) REVERT: F 24 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7417 (ttm110) REVERT: F 70 GLU cc_start: 0.8730 (tp30) cc_final: 0.8462 (tp30) REVERT: F 81 GLU cc_start: 0.8625 (pp20) cc_final: 0.8223 (pp20) REVERT: F 116 ILE cc_start: 0.8148 (tt) cc_final: 0.7243 (pp) REVERT: F 169 ASP cc_start: 0.8792 (p0) cc_final: 0.8318 (p0) REVERT: A 393 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8003 (pp20) REVERT: A 463 MET cc_start: 0.8463 (mmt) cc_final: 0.8161 (mmm) REVERT: A 550 GLN cc_start: 0.8147 (tt0) cc_final: 0.7900 (tt0) REVERT: C 160 ASP cc_start: 0.8730 (m-30) cc_final: 0.8408 (p0) REVERT: D 17 ASP cc_start: 0.8175 (t0) cc_final: 0.7817 (t0) REVERT: D 82 ASP cc_start: 0.8375 (m-30) cc_final: 0.8163 (m-30) REVERT: D 139 TYR cc_start: 0.7801 (t80) cc_final: 0.7180 (t80) REVERT: D 197 HIS cc_start: 0.6813 (t-90) cc_final: 0.5843 (t70) REVERT: B 455 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8721 (tt0) outliers start: 33 outliers final: 10 residues processed: 115 average time/residue: 1.2486 time to fit residues: 159.2953 Evaluate side-chains 93 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 455 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 84 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 167 optimal weight: 0.6980 chunk 160 optimal weight: 0.5980 chunk 17 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 ASN F 123 GLN F 136 ASN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.116709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.083005 restraints weight = 27477.115| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.61 r_work: 0.3365 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13646 Z= 0.175 Angle : 0.587 9.473 18604 Z= 0.307 Chirality : 0.046 0.170 2064 Planarity : 0.005 0.049 2380 Dihedral : 5.054 54.058 1854 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.85 % Allowed : 10.91 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.20), residues: 1702 helix: -1.84 (0.71), residues: 44 sheet: -0.94 (0.18), residues: 758 loop : -0.53 (0.22), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 170 HIS 0.004 0.001 HIS B 281 PHE 0.024 0.002 PHE D 138 TYR 0.020 0.002 TYR A 291 ARG 0.004 0.000 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 426) hydrogen bonds : angle 6.34217 ( 1254) SS BOND : bond 0.00392 ( 22) SS BOND : angle 0.72289 ( 44) covalent geometry : bond 0.00396 (13624) covalent geometry : angle 0.58709 (18560) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 98 time to evaluate : 2.692 Fit side-chains REVERT: E 74 ASP cc_start: 0.8486 (t70) cc_final: 0.7874 (t0) REVERT: F 17 ASP cc_start: 0.8695 (m-30) cc_final: 0.8172 (m-30) REVERT: F 24 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7361 (tpp-160) REVERT: F 70 GLU cc_start: 0.8758 (tp30) cc_final: 0.8479 (tp30) REVERT: F 81 GLU cc_start: 0.8653 (pp20) cc_final: 0.8320 (pp20) REVERT: F 116 ILE cc_start: 0.8127 (tt) cc_final: 0.7267 (pp) REVERT: F 169 ASP cc_start: 0.8806 (p0) cc_final: 0.8263 (p0) REVERT: A 393 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7994 (pp20) REVERT: A 550 GLN cc_start: 0.8008 (tt0) cc_final: 0.7735 (tt0) REVERT: C 160 ASP cc_start: 0.8688 (m-30) cc_final: 0.8374 (p0) REVERT: D 17 ASP cc_start: 0.8276 (t0) cc_final: 0.7885 (t0) REVERT: D 139 TYR cc_start: 0.7878 (t80) cc_final: 0.7299 (t80) REVERT: D 185 TYR cc_start: 0.7549 (t80) cc_final: 0.7273 (t80) REVERT: D 197 HIS cc_start: 0.6812 (t-90) cc_final: 0.5956 (t70) outliers start: 28 outliers final: 3 residues processed: 119 average time/residue: 1.7371 time to fit residues: 229.4261 Evaluate side-chains 86 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 chunk 168 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 136 ASN C 5 GLN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.115265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.080597 restraints weight = 27736.708| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.57 r_work: 0.3335 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13646 Z= 0.237 Angle : 0.625 11.030 18604 Z= 0.327 Chirality : 0.047 0.173 2064 Planarity : 0.005 0.048 2380 Dihedral : 5.096 53.309 1854 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.05 % Allowed : 11.51 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.21), residues: 1702 helix: -1.57 (0.75), residues: 44 sheet: -0.98 (0.18), residues: 772 loop : -0.49 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 48 HIS 0.004 0.001 HIS B 281 PHE 0.025 0.002 PHE D 138 TYR 0.016 0.002 TYR B 351 ARG 0.008 0.001 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03433 ( 426) hydrogen bonds : angle 6.26750 ( 1254) SS BOND : bond 0.00321 ( 22) SS BOND : angle 1.17940 ( 44) covalent geometry : bond 0.00546 (13624) covalent geometry : angle 0.62326 (18560) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 91 time to evaluate : 1.494 Fit side-chains REVERT: E 74 ASP cc_start: 0.8534 (t70) cc_final: 0.7875 (t0) REVERT: F 17 ASP cc_start: 0.8706 (m-30) cc_final: 0.8216 (m-30) REVERT: F 24 ARG cc_start: 0.7896 (ttm110) cc_final: 0.7270 (tpp-160) REVERT: F 70 GLU cc_start: 0.8788 (tp30) cc_final: 0.8457 (tp30) REVERT: F 81 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8252 (pp20) REVERT: F 116 ILE cc_start: 0.8082 (tt) cc_final: 0.7256 (pp) REVERT: F 169 ASP cc_start: 0.8820 (p0) cc_final: 0.8293 (p0) REVERT: A 393 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.7979 (pp20) REVERT: A 455 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: A 463 MET cc_start: 0.8448 (mmt) cc_final: 0.8177 (mmm) REVERT: A 519 TRP cc_start: 0.8696 (OUTLIER) cc_final: 0.6898 (t60) REVERT: A 550 GLN cc_start: 0.8066 (tt0) cc_final: 0.7780 (tt0) REVERT: C 160 ASP cc_start: 0.8730 (m-30) cc_final: 0.8415 (p0) REVERT: D 17 ASP cc_start: 0.8295 (t0) cc_final: 0.7878 (t0) REVERT: D 139 TYR cc_start: 0.7910 (t80) cc_final: 0.7298 (t80) REVERT: D 197 HIS cc_start: 0.6864 (t-90) cc_final: 0.5962 (t70) REVERT: B 455 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8717 (tt0) outliers start: 31 outliers final: 11 residues processed: 114 average time/residue: 1.5835 time to fit residues: 198.4788 Evaluate side-chains 98 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 519 TRP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 455 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 149 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 153 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 57 optimal weight: 0.0050 chunk 121 optimal weight: 20.0000 chunk 151 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.116862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.082705 restraints weight = 27636.105| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.54 r_work: 0.3382 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13646 Z= 0.153 Angle : 0.587 11.536 18604 Z= 0.307 Chirality : 0.046 0.184 2064 Planarity : 0.005 0.047 2380 Dihedral : 4.969 51.508 1854 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.65 % Allowed : 12.37 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.20), residues: 1702 helix: -1.44 (0.78), residues: 44 sheet: -0.82 (0.18), residues: 742 loop : -0.48 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 170 HIS 0.004 0.001 HIS A 233 PHE 0.029 0.002 PHE D 138 TYR 0.015 0.001 TYR A 351 ARG 0.007 0.001 ARG F 141 Details of bonding type rmsd hydrogen bonds : bond 0.03114 ( 426) hydrogen bonds : angle 6.04987 ( 1254) SS BOND : bond 0.00341 ( 22) SS BOND : angle 1.11068 ( 44) covalent geometry : bond 0.00348 (13624) covalent geometry : angle 0.58478 (18560) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 1.403 Fit side-chains REVERT: E 16 GLU cc_start: 0.8436 (mp0) cc_final: 0.7838 (mp0) REVERT: E 74 ASP cc_start: 0.8513 (t70) cc_final: 0.7798 (t0) REVERT: F 17 ASP cc_start: 0.8663 (m-30) cc_final: 0.8127 (m-30) REVERT: F 24 ARG cc_start: 0.7909 (ttm110) cc_final: 0.7285 (tpp-160) REVERT: F 70 GLU cc_start: 0.8727 (tp30) cc_final: 0.8418 (tp30) REVERT: F 81 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8248 (pp20) REVERT: F 116 ILE cc_start: 0.8071 (tt) cc_final: 0.7243 (pp) REVERT: F 169 ASP cc_start: 0.8781 (p0) cc_final: 0.8245 (p0) REVERT: F 191 TYR cc_start: 0.7509 (m-10) cc_final: 0.7006 (m-10) REVERT: A 244 VAL cc_start: 0.8862 (t) cc_final: 0.8660 (m) REVERT: A 393 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.7937 (pp20) REVERT: A 455 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: A 463 MET cc_start: 0.8417 (mmt) cc_final: 0.8182 (mmm) REVERT: A 550 GLN cc_start: 0.7990 (tt0) cc_final: 0.7677 (tt0) REVERT: C 3 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: C 160 ASP cc_start: 0.8640 (m-30) cc_final: 0.8318 (p0) REVERT: C 211 ILE cc_start: 0.8365 (pp) cc_final: 0.8131 (tt) REVERT: D 17 ASP cc_start: 0.8305 (t0) cc_final: 0.7895 (t0) REVERT: D 18 ARG cc_start: 0.8878 (ttp-110) cc_final: 0.8559 (ttt-90) REVERT: D 139 TYR cc_start: 0.7870 (t80) cc_final: 0.7381 (t80) REVERT: D 197 HIS cc_start: 0.6838 (t-90) cc_final: 0.6051 (t70) REVERT: B 455 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8651 (tt0) outliers start: 25 outliers final: 6 residues processed: 113 average time/residue: 1.2015 time to fit residues: 149.7804 Evaluate side-chains 97 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 455 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.116061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.081804 restraints weight = 27572.842| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.55 r_work: 0.3361 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13646 Z= 0.187 Angle : 0.609 12.919 18604 Z= 0.316 Chirality : 0.046 0.184 2064 Planarity : 0.005 0.047 2380 Dihedral : 4.941 50.112 1854 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.12 % Allowed : 13.03 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.21), residues: 1702 helix: -1.40 (0.77), residues: 44 sheet: -0.83 (0.18), residues: 754 loop : -0.42 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 115 HIS 0.004 0.001 HIS A 233 PHE 0.027 0.002 PHE D 138 TYR 0.015 0.001 TYR A 291 ARG 0.007 0.000 ARG F 141 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 426) hydrogen bonds : angle 5.99380 ( 1254) SS BOND : bond 0.00252 ( 22) SS BOND : angle 1.02269 ( 44) covalent geometry : bond 0.00433 (13624) covalent geometry : angle 0.60796 (18560) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 1.429 Fit side-chains REVERT: E 16 GLU cc_start: 0.8530 (mp0) cc_final: 0.7984 (mp0) REVERT: E 74 ASP cc_start: 0.8561 (t70) cc_final: 0.7896 (t0) REVERT: F 17 ASP cc_start: 0.8678 (m-30) cc_final: 0.8183 (m-30) REVERT: F 24 ARG cc_start: 0.7878 (ttm110) cc_final: 0.7410 (tpp-160) REVERT: F 81 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8288 (pp20) REVERT: F 116 ILE cc_start: 0.8040 (tt) cc_final: 0.7248 (pp) REVERT: F 169 ASP cc_start: 0.8775 (p0) cc_final: 0.8243 (p0) REVERT: A 393 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7803 (pp20) REVERT: A 550 GLN cc_start: 0.8032 (tt0) cc_final: 0.7720 (tt0) REVERT: C 3 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8233 (mt0) REVERT: C 138 PHE cc_start: 0.7965 (m-80) cc_final: 0.7539 (m-80) REVERT: C 160 ASP cc_start: 0.8722 (m-30) cc_final: 0.8399 (p0) REVERT: C 211 ILE cc_start: 0.8383 (pp) cc_final: 0.7826 (mm) REVERT: D 17 ASP cc_start: 0.8394 (t0) cc_final: 0.7893 (t0) REVERT: D 24 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.8020 (tpp80) REVERT: D 138 PHE cc_start: 0.8273 (p90) cc_final: 0.7745 (p90) REVERT: D 139 TYR cc_start: 0.7868 (t80) cc_final: 0.7414 (t80) REVERT: D 197 HIS cc_start: 0.6977 (t-90) cc_final: 0.6312 (t70) REVERT: B 455 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8690 (tt0) outliers start: 17 outliers final: 8 residues processed: 103 average time/residue: 1.2727 time to fit residues: 144.1901 Evaluate side-chains 95 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 455 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 140 optimal weight: 1.9990 chunk 147 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 5 GLN B 269 ASN ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.114779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.080220 restraints weight = 27441.465| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.54 r_work: 0.3330 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 13646 Z= 0.241 Angle : 0.647 13.830 18604 Z= 0.333 Chirality : 0.047 0.174 2064 Planarity : 0.005 0.047 2380 Dihedral : 5.028 49.080 1854 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.46 % Allowed : 12.96 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.21), residues: 1702 helix: -1.30 (0.76), residues: 44 sheet: -0.87 (0.18), residues: 768 loop : -0.41 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 119 HIS 0.005 0.001 HIS B 281 PHE 0.027 0.002 PHE D 138 TYR 0.019 0.002 TYR A 291 ARG 0.006 0.001 ARG F 141 Details of bonding type rmsd hydrogen bonds : bond 0.03344 ( 426) hydrogen bonds : angle 6.03994 ( 1254) SS BOND : bond 0.00309 ( 22) SS BOND : angle 1.13931 ( 44) covalent geometry : bond 0.00558 (13624) covalent geometry : angle 0.64551 (18560) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 2.116 Fit side-chains REVERT: E 16 GLU cc_start: 0.8542 (mp0) cc_final: 0.8056 (mp0) REVERT: E 74 ASP cc_start: 0.8585 (t70) cc_final: 0.7875 (t0) REVERT: F 17 ASP cc_start: 0.8691 (m-30) cc_final: 0.8178 (m-30) REVERT: F 24 ARG cc_start: 0.7809 (ttm110) cc_final: 0.7593 (mpt-90) REVERT: F 81 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8296 (pp20) REVERT: F 116 ILE cc_start: 0.8085 (tt) cc_final: 0.7280 (pp) REVERT: F 169 ASP cc_start: 0.8771 (p0) cc_final: 0.8263 (p0) REVERT: A 550 GLN cc_start: 0.8091 (tt0) cc_final: 0.7782 (tt0) REVERT: C 3 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8210 (mt0) REVERT: C 160 ASP cc_start: 0.8726 (m-30) cc_final: 0.8453 (p0) REVERT: C 211 ILE cc_start: 0.8416 (pp) cc_final: 0.7852 (mm) REVERT: D 17 ASP cc_start: 0.8372 (t0) cc_final: 0.7814 (t0) REVERT: D 24 ARG cc_start: 0.8292 (tpp-160) cc_final: 0.7966 (tpp80) REVERT: D 139 TYR cc_start: 0.7851 (t80) cc_final: 0.7508 (t80) REVERT: D 185 TYR cc_start: 0.7366 (t80) cc_final: 0.7003 (t80) REVERT: D 197 HIS cc_start: 0.7065 (t-90) cc_final: 0.6444 (t70) REVERT: D 208 PHE cc_start: 0.5645 (OUTLIER) cc_final: 0.5346 (p90) REVERT: B 332 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.7296 (mp-120) REVERT: B 455 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8753 (tt0) outliers start: 22 outliers final: 10 residues processed: 107 average time/residue: 1.7051 time to fit residues: 203.8530 Evaluate side-chains 96 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 332 GLN Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 455 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 138 optimal weight: 0.7980 chunk 147 optimal weight: 0.0970 chunk 1 optimal weight: 0.0870 chunk 158 optimal weight: 0.2980 chunk 135 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN B 332 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.116415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.080665 restraints weight = 27562.209| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.74 r_work: 0.3333 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 13646 Z= 0.212 Angle : 0.857 59.200 18604 Z= 0.478 Chirality : 0.046 0.305 2064 Planarity : 0.005 0.047 2380 Dihedral : 5.037 49.077 1854 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.12 % Allowed : 13.56 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1702 helix: -1.31 (0.77), residues: 44 sheet: -0.86 (0.18), residues: 756 loop : -0.44 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 170 HIS 0.005 0.001 HIS A 233 PHE 0.027 0.002 PHE D 138 TYR 0.033 0.002 TYR D 185 ARG 0.006 0.000 ARG F 141 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 426) hydrogen bonds : angle 6.05348 ( 1254) SS BOND : bond 0.00304 ( 22) SS BOND : angle 1.08351 ( 44) covalent geometry : bond 0.00487 (13624) covalent geometry : angle 0.85635 (18560) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3404 Ramachandran restraints generated. 1702 Oldfield, 0 Emsley, 1702 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.468 Fit side-chains REVERT: E 74 ASP cc_start: 0.8549 (t70) cc_final: 0.7854 (t0) REVERT: F 17 ASP cc_start: 0.8680 (m-30) cc_final: 0.8161 (m-30) REVERT: F 24 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7581 (mpt-90) REVERT: F 81 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8291 (pp20) REVERT: F 116 ILE cc_start: 0.8108 (tt) cc_final: 0.7299 (pp) REVERT: F 169 ASP cc_start: 0.8766 (p0) cc_final: 0.8256 (p0) REVERT: A 455 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8275 (tt0) REVERT: A 550 GLN cc_start: 0.8079 (tt0) cc_final: 0.7765 (tt0) REVERT: C 3 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8187 (mt0) REVERT: C 160 ASP cc_start: 0.8708 (m-30) cc_final: 0.8436 (p0) REVERT: C 211 ILE cc_start: 0.8384 (pp) cc_final: 0.7821 (mm) REVERT: D 17 ASP cc_start: 0.8360 (t0) cc_final: 0.7806 (t0) REVERT: D 24 ARG cc_start: 0.8249 (tpp-160) cc_final: 0.7949 (tpp80) REVERT: D 139 TYR cc_start: 0.7844 (t80) cc_final: 0.7489 (t80) REVERT: D 197 HIS cc_start: 0.7120 (t-90) cc_final: 0.6378 (t70) REVERT: D 208 PHE cc_start: 0.5636 (OUTLIER) cc_final: 0.5331 (p90) REVERT: B 455 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8750 (tt0) outliers start: 17 outliers final: 10 residues processed: 98 average time/residue: 1.1724 time to fit residues: 127.6449 Evaluate side-chains 94 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 455 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 89 optimal weight: 0.0970 chunk 98 optimal weight: 7.9990 chunk 139 optimal weight: 0.9990 chunk 137 optimal weight: 0.9980 chunk 166 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 159 optimal weight: 3.9990 chunk 119 optimal weight: 0.2980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.116337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.080577 restraints weight = 27595.780| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.78 r_work: 0.3332 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.221 13646 Z= 0.212 Angle : 0.857 59.200 18604 Z= 0.478 Chirality : 0.046 0.305 2064 Planarity : 0.005 0.047 2380 Dihedral : 5.037 49.077 1854 Min Nonbonded Distance : 1.441 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.99 % Allowed : 13.69 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.20), residues: 1702 helix: -1.31 (0.77), residues: 44 sheet: -0.86 (0.18), residues: 756 loop : -0.44 (0.22), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 170 HIS 0.005 0.001 HIS A 233 PHE 0.027 0.002 PHE D 138 TYR 0.033 0.002 TYR D 185 ARG 0.006 0.000 ARG F 141 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 426) hydrogen bonds : angle 6.05348 ( 1254) SS BOND : bond 0.00304 ( 22) SS BOND : angle 1.08351 ( 44) covalent geometry : bond 0.00487 (13624) covalent geometry : angle 0.85635 (18560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12219.57 seconds wall clock time: 218 minutes 47.77 seconds (13127.77 seconds total)