Starting phenix.real_space_refine on Thu May 15 15:35:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0d_36761/05_2025/8k0d_36761.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0d_36761/05_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_36761/05_2025/8k0d_36761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0d_36761/05_2025/8k0d_36761.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0d_36761/05_2025/8k0d_36761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0d_36761/05_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-5687/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: 9.93, per 1000 atoms: 0.75 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: 3.08 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: 2.30 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: 4.91 Time building geometry restraints manager: 3.60 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: 18.100 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 35.420 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.100 ------------------------------------------------------------------------------- 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 : 1.603 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: 1.3916 time to fit residues: 249.1245 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 : 1.690 ------------------------------------------------------------------------------- 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 = 61)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.081930 restraints weight = 27507.118| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.67 r_work: 0.3378 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 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 7.63815 ( 1254) SS BOND : bond 0.00343 ( 22) SS BOND : angle 0.85378 ( 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 : 1.442 Fit side-chains REVERT: E 222 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8006 (mmmm) REVERT: F 17 ASP cc_start: 0.8571 (m-30) cc_final: 0.8188 (m-30) REVERT: F 81 GLU cc_start: 0.8666 (pp20) cc_final: 0.8445 (pp20) REVERT: F 169 ASP cc_start: 0.8812 (p0) cc_final: 0.8164 (p0) REVERT: C 99 ARG cc_start: 0.8729 (mtp180) cc_final: 0.8428 (ttp80) REVERT: C 160 ASP cc_start: 0.8808 (m-30) cc_final: 0.8474 (p0) REVERT: D 82 ASP cc_start: 0.8252 (m-30) cc_final: 0.7963 (m-30) outliers start: 17 outliers final: 2 residues processed: 128 average time/residue: 1.3535 time to fit residues: 188.9460 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 : 1.544 ------------------------------------------------------------------------------- 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: 2.9990 chunk 158 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 127 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.116401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.082266 restraints weight = 27605.505| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.58 r_work: 0.3334 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 13646 Z= 0.275 Angle : 0.651 9.390 18604 Z= 0.342 Chirality : 0.048 0.150 2064 Planarity : 0.005 0.052 2380 Dihedral : 5.210 55.838 1854 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.52 % Allowed : 9.46 % Favored : 89.02 % 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: -1.48 (0.20), residues: 1702 helix: -2.37 (0.59), residues: 44 sheet: -1.11 (0.18), residues: 766 loop : -0.63 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 170 HIS 0.006 0.001 HIS B 281 PHE 0.023 0.002 PHE F 83 TYR 0.025 0.002 TYR B 351 ARG 0.004 0.001 ARG A 487 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 426) hydrogen bonds : angle 7.01306 ( 1254) SS BOND : bond 0.00417 ( 22) SS BOND : angle 1.10383 ( 44) covalent geometry : bond 0.00633 (13624) covalent geometry : angle 0.64969 (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 116 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.580 Fit side-chains REVERT: E 74 ASP cc_start: 0.8377 (t70) cc_final: 0.7930 (t0) REVERT: F 81 GLU cc_start: 0.8679 (pp20) cc_final: 0.8433 (pp20) REVERT: F 116 ILE cc_start: 0.8107 (tt) cc_final: 0.7152 (pp) REVERT: F 169 ASP cc_start: 0.8845 (p0) cc_final: 0.8360 (p0) REVERT: A 550 GLN cc_start: 0.8150 (tt0) cc_final: 0.7908 (tt0) REVERT: C 160 ASP cc_start: 0.8792 (m-30) cc_final: 0.8457 (p0) REVERT: D 17 ASP cc_start: 0.8178 (t0) cc_final: 0.7914 (t0) REVERT: D 82 ASP cc_start: 0.8295 (m-30) cc_final: 0.8056 (m-30) REVERT: B 455 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8701 (tt0) outliers start: 23 outliers final: 2 residues processed: 109 average time/residue: 1.3176 time to fit residues: 157.5570 Evaluate side-chains 84 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 THR 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: 0.9990 chunk 101 optimal weight: 0.6980 chunk 120 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 113 optimal weight: 0.7980 chunk 140 optimal weight: 0.0370 chunk 17 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 1 GLN E 114 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 = 0.4098 r_free = 0.4098 target = 0.116703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.082283 restraints weight = 27362.459| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.54 r_work: 0.3376 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13646 Z= 0.175 Angle : 0.598 8.603 18604 Z= 0.312 Chirality : 0.046 0.172 2064 Planarity : 0.005 0.053 2380 Dihedral : 5.074 55.171 1854 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.65 % Allowed : 10.32 % Favored : 88.03 % 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: -2.17 (0.63), residues: 44 sheet: -1.02 (0.18), residues: 776 loop : -0.56 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 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 351 ARG 0.004 0.000 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.03546 ( 426) hydrogen bonds : angle 6.60059 ( 1254) SS BOND : bond 0.00322 ( 22) SS BOND : angle 0.75651 ( 44) covalent geometry : bond 0.00396 (13624) covalent geometry : angle 0.59743 (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 122 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 1.549 Fit side-chains REVERT: E 74 ASP cc_start: 0.8393 (t70) cc_final: 0.7777 (t0) REVERT: F 17 ASP cc_start: 0.8623 (m-30) cc_final: 0.8126 (m-30) REVERT: F 24 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7563 (mpt-90) REVERT: F 81 GLU cc_start: 0.8643 (pp20) cc_final: 0.8395 (pp20) REVERT: F 116 ILE cc_start: 0.8177 (tt) cc_final: 0.7329 (pp) REVERT: F 169 ASP cc_start: 0.8850 (p0) cc_final: 0.8372 (p0) REVERT: A 393 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.8036 (pp20) REVERT: A 550 GLN cc_start: 0.8050 (tt0) cc_final: 0.7813 (tt0) REVERT: C 160 ASP cc_start: 0.8686 (m-30) cc_final: 0.8356 (p0) REVERT: D 17 ASP cc_start: 0.8142 (t0) cc_final: 0.7811 (t0) REVERT: D 197 HIS cc_start: 0.6674 (t-90) cc_final: 0.5718 (t70) outliers start: 25 outliers final: 7 residues processed: 116 average time/residue: 1.2311 time to fit residues: 157.9855 Evaluate side-chains 91 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 ILE 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 C residue 212 CYS Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 84 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 167 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 123 GLN F 136 ASN ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 ASN B 332 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.113967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.079075 restraints weight = 27833.225| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.58 r_work: 0.3310 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 13646 Z= 0.298 Angle : 0.661 12.154 18604 Z= 0.345 Chirality : 0.048 0.169 2064 Planarity : 0.005 0.050 2380 Dihedral : 5.218 54.403 1854 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.38 % Allowed : 10.71 % Favored : 86.90 % 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: -1.31 (0.20), residues: 1702 helix: -2.00 (0.67), residues: 44 sheet: -0.99 (0.18), residues: 768 loop : -0.54 (0.22), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 170 HIS 0.007 0.001 HIS B 281 PHE 0.025 0.002 PHE F 83 TYR 0.027 0.002 TYR B 292 ARG 0.006 0.001 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 426) hydrogen bonds : angle 6.54482 ( 1254) SS BOND : bond 0.00345 ( 22) SS BOND : angle 0.84009 ( 44) covalent geometry : bond 0.00687 (13624) covalent geometry : angle 0.66066 (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: 36 poor density : 90 time to evaluate : 1.617 Fit side-chains REVERT: E 74 ASP cc_start: 0.8547 (t70) cc_final: 0.7936 (t0) REVERT: E 228 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8590 (tm-30) REVERT: F 24 ARG cc_start: 0.7917 (ttm110) cc_final: 0.7508 (mmt90) REVERT: F 81 GLU cc_start: 0.8636 (pp20) cc_final: 0.8237 (pp20) REVERT: F 116 ILE cc_start: 0.8154 (tt) cc_final: 0.7269 (pp) REVERT: F 169 ASP cc_start: 0.8781 (p0) cc_final: 0.8246 (p0) REVERT: A 393 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.7983 (pp20) REVERT: A 519 TRP cc_start: 0.8726 (OUTLIER) cc_final: 0.7024 (t60) REVERT: A 550 GLN cc_start: 0.8124 (tt0) cc_final: 0.7861 (tt0) REVERT: C 160 ASP cc_start: 0.8725 (m-30) cc_final: 0.8410 (p0) REVERT: D 17 ASP cc_start: 0.8243 (t0) cc_final: 0.7862 (t0) REVERT: D 139 TYR cc_start: 0.7655 (t80) cc_final: 0.7269 (t80) REVERT: D 197 HIS cc_start: 0.6725 (t-90) cc_final: 0.5739 (t70) REVERT: B 455 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8754 (tt0) outliers start: 36 outliers final: 12 residues processed: 119 average time/residue: 1.1896 time to fit residues: 156.8124 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 : 1.579 ------------------------------------------------------------------------------- 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 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 519 TRP Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain D residue 5 THR 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 455 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 42 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 chunk 46 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 128 optimal weight: 6.9990 chunk 168 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 0.0070 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 269 ASN B 281 HIS B 332 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.116914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.082604 restraints weight = 27661.910| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.57 r_work: 0.3378 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13646 Z= 0.142 Angle : 0.584 10.188 18604 Z= 0.306 Chirality : 0.046 0.175 2064 Planarity : 0.005 0.048 2380 Dihedral : 5.036 53.150 1854 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.85 % Allowed : 11.44 % Favored : 86.71 % 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: -1.21 (0.20), residues: 1702 helix: -1.78 (0.71), residues: 44 sheet: -0.94 (0.18), residues: 752 loop : -0.48 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 115 HIS 0.004 0.001 HIS A 233 PHE 0.025 0.002 PHE D 138 TYR 0.017 0.001 TYR A 351 ARG 0.008 0.000 ARG F 210 Details of bonding type rmsd hydrogen bonds : bond 0.03183 ( 426) hydrogen bonds : angle 6.21373 ( 1254) SS BOND : bond 0.00376 ( 22) SS BOND : angle 1.22470 ( 44) covalent geometry : bond 0.00321 (13624) covalent geometry : angle 0.58200 (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: 28 poor density : 94 time to evaluate : 1.436 Fit side-chains REVERT: E 74 ASP cc_start: 0.8497 (t70) cc_final: 0.7792 (t0) REVERT: F 17 ASP cc_start: 0.8683 (m-30) cc_final: 0.8165 (m-30) REVERT: F 24 ARG cc_start: 0.7941 (ttm110) cc_final: 0.7503 (mmt90) REVERT: F 70 GLU cc_start: 0.8699 (tp30) cc_final: 0.8388 (tp30) REVERT: F 81 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8324 (pp20) REVERT: F 116 ILE cc_start: 0.8071 (tt) cc_final: 0.7246 (pp) REVERT: F 169 ASP cc_start: 0.8828 (p0) cc_final: 0.8314 (p0) REVERT: A 393 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.7992 (pp20) REVERT: A 455 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8071 (tt0) REVERT: A 550 GLN cc_start: 0.7983 (tt0) cc_final: 0.7689 (tt0) REVERT: C 138 PHE cc_start: 0.8245 (m-80) cc_final: 0.7931 (m-80) REVERT: C 160 ASP cc_start: 0.8702 (m-30) cc_final: 0.8378 (p0) REVERT: C 211 ILE cc_start: 0.8431 (pp) cc_final: 0.7905 (mm) REVERT: D 17 ASP cc_start: 0.8306 (t0) cc_final: 0.7909 (t0) REVERT: D 139 TYR cc_start: 0.7784 (t80) cc_final: 0.7314 (t80) REVERT: D 185 TYR cc_start: 0.7424 (t80) cc_final: 0.7065 (t80) REVERT: D 197 HIS cc_start: 0.6834 (t-90) cc_final: 0.5989 (t70) REVERT: B 334 GLN cc_start: 0.8345 (mt0) cc_final: 0.7700 (tm-30) REVERT: B 455 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8621 (tt0) outliers start: 28 outliers final: 8 residues processed: 115 average time/residue: 1.2800 time to fit residues: 161.5342 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 : 1.537 ------------------------------------------------------------------------------- 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 393 GLU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain D residue 208 PHE 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: 1.9990 chunk 62 optimal weight: 0.0980 chunk 53 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 79 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 326 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.116623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.082459 restraints weight = 27679.103| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.52 r_work: 0.3374 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13646 Z= 0.162 Angle : 0.599 13.855 18604 Z= 0.309 Chirality : 0.046 0.183 2064 Planarity : 0.005 0.048 2380 Dihedral : 4.923 51.373 1854 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.59 % Allowed : 12.24 % Favored : 86.18 % 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: -1.62 (0.73), residues: 44 sheet: -0.82 (0.18), residues: 754 loop : -0.42 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 170 HIS 0.004 0.001 HIS A 233 PHE 0.027 0.002 PHE D 138 TYR 0.015 0.001 TYR B 351 ARG 0.007 0.000 ARG F 141 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 426) hydrogen bonds : angle 6.01713 ( 1254) SS BOND : bond 0.00214 ( 22) SS BOND : angle 1.02811 ( 44) covalent geometry : bond 0.00371 (13624) covalent geometry : angle 0.59750 (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: 24 poor density : 96 time to evaluate : 1.491 Fit side-chains REVERT: E 74 ASP cc_start: 0.8501 (t70) cc_final: 0.7804 (t0) REVERT: E 228 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8490 (tm-30) REVERT: F 17 ASP cc_start: 0.8638 (m-30) cc_final: 0.8140 (m-30) REVERT: F 24 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7564 (mpt-90) REVERT: F 70 GLU cc_start: 0.8699 (tp30) cc_final: 0.8435 (tp30) REVERT: F 81 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8375 (pp20) REVERT: F 116 ILE cc_start: 0.8082 (tt) cc_final: 0.7296 (pp) REVERT: F 169 ASP cc_start: 0.8819 (p0) cc_final: 0.8306 (p0) REVERT: F 191 TYR cc_start: 0.7516 (m-10) cc_final: 0.7016 (m-10) REVERT: A 393 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7697 (pp20) REVERT: A 397 LEU cc_start: 0.9276 (mt) cc_final: 0.9003 (mt) REVERT: A 455 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8056 (tt0) REVERT: A 550 GLN cc_start: 0.7999 (tt0) cc_final: 0.7696 (tt0) REVERT: C 160 ASP cc_start: 0.8692 (m-30) cc_final: 0.8353 (p0) REVERT: D 17 ASP cc_start: 0.8340 (t0) cc_final: 0.7918 (t0) REVERT: D 24 ARG cc_start: 0.8194 (ttm110) cc_final: 0.7892 (tpp80) REVERT: D 139 TYR cc_start: 0.7811 (t80) cc_final: 0.7359 (t80) REVERT: D 197 HIS cc_start: 0.6859 (t-90) cc_final: 0.6044 (t70) REVERT: B 332 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: B 455 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8686 (tt0) outliers start: 24 outliers final: 10 residues processed: 115 average time/residue: 1.2183 time to fit residues: 154.3250 Evaluate side-chains 102 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 393 GLU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain D 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 332 GLN Chi-restraints excluded: chain B residue 440 SER 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: 0.9990 chunk 24 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.116504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.080839 restraints weight = 27732.604| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.75 r_work: 0.3337 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13646 Z= 0.216 Angle : 0.620 12.183 18604 Z= 0.320 Chirality : 0.047 0.186 2064 Planarity : 0.005 0.047 2380 Dihedral : 4.947 50.198 1854 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.26 % Allowed : 12.96 % Favored : 85.78 % 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: -1.08 (0.21), residues: 1702 helix: -1.49 (0.74), residues: 44 sheet: -0.78 (0.19), residues: 750 loop : -0.49 (0.22), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 170 HIS 0.004 0.001 HIS A 233 PHE 0.026 0.002 PHE D 138 TYR 0.017 0.002 TYR A 291 ARG 0.007 0.000 ARG F 141 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 426) hydrogen bonds : angle 6.03037 ( 1254) SS BOND : bond 0.00249 ( 22) SS BOND : angle 1.02295 ( 44) covalent geometry : bond 0.00498 (13624) covalent geometry : angle 0.61859 (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 105 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 1.676 Fit side-chains REVERT: E 74 ASP cc_start: 0.8578 (t70) cc_final: 0.7860 (t0) REVERT: E 228 GLU cc_start: 0.8775 (tm-30) cc_final: 0.8529 (tm-30) REVERT: F 17 ASP cc_start: 0.8661 (m-30) cc_final: 0.8142 (m-30) REVERT: F 81 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8308 (pp20) REVERT: F 116 ILE cc_start: 0.8080 (tt) cc_final: 0.7271 (pp) REVERT: F 169 ASP cc_start: 0.8786 (p0) cc_final: 0.8277 (p0) REVERT: A 393 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.7954 (pp20) REVERT: A 550 GLN cc_start: 0.8081 (tt0) cc_final: 0.7780 (tt0) REVERT: C 3 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8153 (mp10) REVERT: C 160 ASP cc_start: 0.8734 (m-30) cc_final: 0.8443 (p0) REVERT: D 17 ASP cc_start: 0.8415 (t0) cc_final: 0.7918 (t0) REVERT: D 139 TYR cc_start: 0.7792 (t80) cc_final: 0.7439 (t80) REVERT: D 197 HIS cc_start: 0.7047 (t-90) cc_final: 0.6375 (t70) REVERT: D 208 PHE cc_start: 0.5431 (OUTLIER) cc_final: 0.5127 (p90) REVERT: B 332 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: B 455 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8744 (tt0) outliers start: 19 outliers final: 10 residues processed: 101 average time/residue: 1.2847 time to fit residues: 142.7381 Evaluate side-chains 95 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 1.599 ------------------------------------------------------------------------------- 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 140 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 113 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** 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 = 0.4096 r_free = 0.4096 target = 0.116304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.082718 restraints weight = 27260.975| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.60 r_work: 0.3362 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2757 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= 0.191 Angle : 0.616 13.039 18604 Z= 0.317 Chirality : 0.046 0.177 2064 Planarity : 0.005 0.048 2380 Dihedral : 4.938 48.939 1854 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.26 % Allowed : 13.23 % Favored : 85.52 % 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: -1.04 (0.21), residues: 1702 helix: -1.48 (0.73), residues: 44 sheet: -0.77 (0.19), residues: 744 loop : -0.44 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 170 HIS 0.004 0.001 HIS A 233 PHE 0.026 0.002 PHE D 138 TYR 0.020 0.002 TYR A 291 ARG 0.005 0.000 ARG F 141 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 426) hydrogen bonds : angle 5.96594 ( 1254) SS BOND : bond 0.00251 ( 22) SS BOND : angle 0.91953 ( 44) covalent geometry : bond 0.00441 (13624) covalent geometry : angle 0.61503 (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 109 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 1.677 Fit side-chains REVERT: E 74 ASP cc_start: 0.8515 (t70) cc_final: 0.7890 (t0) REVERT: F 17 ASP cc_start: 0.8666 (m-30) cc_final: 0.8160 (m-30) REVERT: F 24 ARG cc_start: 0.7890 (ttm110) cc_final: 0.7541 (mpt-90) REVERT: F 81 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8273 (pp20) REVERT: F 116 ILE cc_start: 0.8156 (tt) cc_final: 0.7340 (pp) REVERT: F 169 ASP cc_start: 0.8748 (p0) cc_final: 0.8211 (p0) REVERT: F 191 TYR cc_start: 0.7582 (m-10) cc_final: 0.7056 (m-80) REVERT: A 393 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8046 (pp20) REVERT: A 550 GLN cc_start: 0.8026 (tt0) cc_final: 0.7724 (tt0) REVERT: C 3 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: C 160 ASP cc_start: 0.8661 (m-30) cc_final: 0.8373 (p0) REVERT: D 17 ASP cc_start: 0.8430 (t0) cc_final: 0.7919 (t0) REVERT: D 24 ARG cc_start: 0.8242 (ttm110) cc_final: 0.7944 (tpp80) REVERT: D 139 TYR cc_start: 0.7738 (t80) cc_final: 0.7335 (t80) REVERT: D 197 HIS cc_start: 0.6939 (t-90) cc_final: 0.6299 (t70) REVERT: D 208 PHE cc_start: 0.5440 (OUTLIER) cc_final: 0.5144 (p90) REVERT: B 455 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8707 (tt0) outliers start: 19 outliers final: 9 residues processed: 106 average time/residue: 1.2273 time to fit residues: 143.9986 Evaluate side-chains 97 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 206 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 393 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 34 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 147 optimal weight: 0.0170 chunk 1 optimal weight: 2.9990 chunk 158 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 0.3980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4101 r_free = 0.4101 target = 0.116939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.082892 restraints weight = 27464.863| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.53 r_work: 0.3389 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13646 Z= 0.149 Angle : 0.602 13.535 18604 Z= 0.310 Chirality : 0.046 0.172 2064 Planarity : 0.004 0.048 2380 Dihedral : 4.855 46.827 1854 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.99 % Allowed : 13.96 % Favored : 85.05 % 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: -0.96 (0.21), residues: 1702 helix: -1.47 (0.73), residues: 44 sheet: -0.70 (0.19), residues: 744 loop : -0.41 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 115 HIS 0.005 0.001 HIS A 233 PHE 0.026 0.002 PHE D 138 TYR 0.021 0.001 TYR A 291 ARG 0.006 0.000 ARG F 141 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 426) hydrogen bonds : angle 5.85723 ( 1254) SS BOND : bond 0.00201 ( 22) SS BOND : angle 0.79332 ( 44) covalent geometry : bond 0.00344 (13624) covalent geometry : angle 0.60170 (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 108 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: F 17 ASP cc_start: 0.8643 (m-30) cc_final: 0.8128 (m-30) REVERT: F 81 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8324 (pp20) REVERT: F 116 ILE cc_start: 0.8123 (tt) cc_final: 0.7299 (pp) REVERT: F 169 ASP cc_start: 0.8725 (p0) cc_final: 0.8166 (p0) REVERT: F 191 TYR cc_start: 0.7586 (m-10) cc_final: 0.7038 (m-80) REVERT: A 393 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8018 (pp20) REVERT: A 550 GLN cc_start: 0.7991 (tt0) cc_final: 0.7664 (tt0) REVERT: C 3 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: C 160 ASP cc_start: 0.8650 (m-30) cc_final: 0.8365 (p0) REVERT: C 211 ILE cc_start: 0.8221 (pp) cc_final: 0.7821 (tt) REVERT: D 17 ASP cc_start: 0.8423 (t0) cc_final: 0.7902 (t0) REVERT: D 24 ARG cc_start: 0.8223 (ttm110) cc_final: 0.8018 (tpp-160) REVERT: D 139 TYR cc_start: 0.7721 (t80) cc_final: 0.7314 (t80) REVERT: D 197 HIS cc_start: 0.6965 (t-90) cc_final: 0.6313 (t70) REVERT: B 332 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.7012 (mp-120) outliers start: 15 outliers final: 7 residues processed: 104 average time/residue: 1.2557 time to fit residues: 144.1949 Evaluate side-chains 98 residues out of total 1512 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 1.467 ------------------------------------------------------------------------------- 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 393 GLU Chi-restraints excluded: chain A residue 538 THR Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 291 TYR Chi-restraints excluded: chain B residue 332 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 89 optimal weight: 0.2980 chunk 98 optimal weight: 7.9990 chunk 139 optimal weight: 0.5980 chunk 137 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4099 r_free = 0.4099 target = 0.116886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.082749 restraints weight = 27436.422| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.54 r_work: 0.3380 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 13646 Z= 0.201 Angle : 0.866 59.192 18604 Z= 0.483 Chirality : 0.046 0.219 2064 Planarity : 0.004 0.048 2380 Dihedral : 4.863 46.809 1854 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 0.93 % Allowed : 14.09 % Favored : 84.99 % Cbeta Deviations : 0.06 % 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: -0.96 (0.21), residues: 1702 helix: -1.47 (0.73), residues: 44 sheet: -0.69 (0.19), residues: 744 loop : -0.41 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 115 HIS 0.004 0.001 HIS A 233 PHE 0.026 0.002 PHE D 138 TYR 0.016 0.001 TYR A 351 ARG 0.005 0.000 ARG F 141 Details of bonding type rmsd hydrogen bonds : bond 0.03012 ( 426) hydrogen bonds : angle 5.85568 ( 1254) SS BOND : bond 0.00193 ( 22) SS BOND : angle 0.74592 ( 44) covalent geometry : bond 0.00429 (13624) covalent geometry : angle 0.86578 (18560) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11013.98 seconds wall clock time: 191 minutes 37.57 seconds (11497.57 seconds total)