Starting phenix.real_space_refine on Fri Jun 5 08:50:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zjy_60160/06_2026/8zjy_60160.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zjy_60160/06_2026/8zjy_60160.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zjy_60160/06_2026/8zjy_60160.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zjy_60160/06_2026/8zjy_60160.map" model { file = "/net/cci-nas-00/data/ceres_data/8zjy_60160/06_2026/8zjy_60160.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zjy_60160/06_2026/8zjy_60160.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 93 5.16 5 C 12052 2.51 5 N 3275 2.21 5 O 3552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18974 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3946 Classifications: {'peptide': 493} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 462} Chain: "B" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3946 Classifications: {'peptide': 493} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 462} Chain: "D" Number of atoms: 1597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1597 Classifications: {'peptide': 204} Link IDs: {'CIS': 8, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 184} Chain: "E" Number of atoms: 3815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3815 Classifications: {'peptide': 482} Link IDs: {'PCIS': 4, 'PTRANS': 22, 'TRANS': 455} Chain: "F" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3832 Classifications: {'peptide': 484} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 457} Chain: "G" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1823 Classifications: {'peptide': 229} Link IDs: {'CIS': 2, 'PTRANS': 12, 'TRANS': 214} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'H6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.96, per 1000 atoms: 0.21 Number of scatterers: 18974 At special positions: 0 Unit cell: (148.919, 178.268, 286.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 93 16.00 P 2 15.00 O 3552 8.00 N 3275 7.00 C 12052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 125 " distance=2.03 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 219 " distance=2.04 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS B 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 125 " distance=2.04 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 219 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 220 " distance=2.04 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 220 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 154 " - pdb=" SG CYS G 210 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 843.7 milliseconds 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4436 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 41 sheets defined 16.2% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 249 through 321 Proline residue: A 261 - end of helix removed outlier: 3.639A pdb=" N TYR A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 301 " --> pdb=" O LEU A 297 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN A 303 " --> pdb=" O LYS A 299 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 removed outlier: 3.981A pdb=" N ALA A 337 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 removed outlier: 4.041A pdb=" N ARG B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 322 Proline residue: B 252 - end of helix Proline residue: B 261 - end of helix removed outlier: 4.009A pdb=" N VAL B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS B 265 " --> pdb=" O PRO B 261 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 322 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 removed outlier: 3.602A pdb=" N ALA B 337 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 31 No H-bonds generated for 'chain 'D' and resid 29 through 31' Processing helix chain 'E' and resid 239 through 242 Processing helix chain 'E' and resid 245 through 320 removed outlier: 3.980A pdb=" N ALA E 250 " --> pdb=" O GLN E 246 " (cutoff:3.500A) Proline residue: E 257 - end of helix removed outlier: 3.571A pdb=" N LEU E 261 " --> pdb=" O PRO E 257 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU E 262 " --> pdb=" O ILE E 258 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU E 263 " --> pdb=" O SER E 259 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER E 303 " --> pdb=" O GLU E 299 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU E 304 " --> pdb=" O GLN E 300 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N MET E 320 " --> pdb=" O LYS E 316 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 332 removed outlier: 3.923A pdb=" N GLU E 331 " --> pdb=" O LEU E 327 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TRP E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 426 through 429 Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.742A pdb=" N TYR F 93 " --> pdb=" O SER F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 238 through 243 removed outlier: 3.517A pdb=" N PHE F 241 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG F 243 " --> pdb=" O PRO F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 321 removed outlier: 3.861A pdb=" N ALA F 250 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA F 251 " --> pdb=" O ARG F 247 " (cutoff:3.500A) Proline residue: F 257 - end of helix removed outlier: 3.830A pdb=" N THR F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE F 317 " --> pdb=" O ARG F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 324 No H-bonds generated for 'chain 'F' and resid 322 through 324' Processing helix chain 'F' and resid 325 through 337 removed outlier: 3.645A pdb=" N TYR F 329 " --> pdb=" O ARG F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 349 removed outlier: 3.505A pdb=" N THR F 348 " --> pdb=" O ASP F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 428 Processing helix chain 'G' and resid 217 through 221 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 3.682A pdb=" N ALA A 143 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.987A pdb=" N ALA A 109 " --> pdb=" O VAL A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.646A pdb=" N LYS A 79 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 153 removed outlier: 3.813A pdb=" N LYS A 190 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 175 through 179 Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327 removed outlier: 3.535A pdb=" N ILE A 497 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 327 removed outlier: 5.143A pdb=" N ASN A 465 " --> pdb=" O HIS A 471 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N HIS A 471 " --> pdb=" O ASN A 465 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 374 through 376 Processing sheet with id=AA9, first strand: chain 'A' and resid 516 through 517 removed outlier: 6.633A pdb=" N PHE B 463 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 474 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 461 " --> pdb=" O THR B 474 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 516 through 517 removed outlier: 6.633A pdb=" N PHE B 463 " --> pdb=" O ILE B 472 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N THR B 474 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 461 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 350 " --> pdb=" O ILE B 497 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 31 through 33 Processing sheet with id=AB3, first strand: chain 'B' and resid 39 through 42 removed outlier: 4.565A pdb=" N VAL B 77 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 150 through 157 removed outlier: 5.809A pdb=" N ARG B 162 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N HIS B 156 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLY B 160 " --> pdb=" O HIS B 156 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N ARG B 162 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE B 209 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLU B 164 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL B 207 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ILE B 166 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR B 205 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ARG B 168 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL B 203 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 175 through 179 Processing sheet with id=AB6, first strand: chain 'B' and resid 374 through 376 removed outlier: 3.684A pdb=" N TRP B 398 " --> pdb=" O MET B 426 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 12 removed outlier: 5.828A pdb=" N PHE D 109 " --> pdb=" O SER D 94 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER D 94 " --> pdb=" O PHE D 109 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LYS D 111 " --> pdb=" O CYS D 92 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N CYS D 92 " --> pdb=" O LYS D 111 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG D 39 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N PHE D 48 " --> pdb=" O ARG D 39 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 19 through 22 Processing sheet with id=AB9, first strand: chain 'D' and resid 128 through 134 removed outlier: 5.983A pdb=" N TYR D 175 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR D 161 " --> pdb=" O LYS D 182 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 128 through 134 removed outlier: 5.983A pdb=" N TYR D 175 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AC3, first strand: chain 'E' and resid 40 through 43 removed outlier: 6.038A pdb=" N SER E 69 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL E 75 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 48 through 53 Processing sheet with id=AC5, first strand: chain 'E' and resid 190 through 191 removed outlier: 5.487A pdb=" N TYR E 202 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY E 161 " --> pdb=" O TYR E 157 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N TYR E 157 " --> pdb=" O GLY E 161 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N HIS E 163 " --> pdb=" O LYS E 155 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE F 237 " --> pdb=" O GLU F 216 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLU F 216 " --> pdb=" O ILE F 237 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.663A pdb=" N TRP E 179 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N VAL F 152 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER E 234 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N VAL F 154 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N SER E 236 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLY F 156 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL F 152 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ARG F 167 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL F 154 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLU F 165 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY F 156 " --> pdb=" O HIS F 163 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR F 202 " --> pdb=" O GLY F 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 343 through 344 removed outlier: 4.263A pdb=" N ILE E 343 " --> pdb=" O CYS E 387 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 354 through 355 removed outlier: 3.503A pdb=" N VAL E 362 " --> pdb=" O LEU E 509 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU E 509 " --> pdb=" O VAL E 362 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 394 through 399 removed outlier: 3.970A pdb=" N ILE E 472 " --> pdb=" O PHE E 486 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR E 484 " --> pdb=" O PHE E 474 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ASN E 476 " --> pdb=" O HIS E 482 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N HIS E 482 " --> pdb=" O ASN E 476 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 450 through 452 removed outlier: 4.127A pdb=" N THR E 450 " --> pdb=" O ALA E 444 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR E 442 " --> pdb=" O LEU E 452 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 32 through 34 removed outlier: 3.625A pdb=" N HIS F 53 " --> pdb=" O LEU F 34 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 42 through 43 removed outlier: 6.977A pdb=" N ALA F 42 " --> pdb=" O ALA F 144 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 48 through 51 removed outlier: 4.770A pdb=" N ALA F 110 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU F 100 " --> pdb=" O ALA F 110 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 75 through 79 removed outlier: 6.426A pdb=" N VAL F 75 " --> pdb=" O SER F 69 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER F 69 " --> pdb=" O VAL F 75 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 338 through 339 removed outlier: 5.196A pdb=" N ASN F 475 " --> pdb=" O HIS F 481 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N HIS F 481 " --> pdb=" O ASN F 475 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 338 through 339 removed outlier: 3.685A pdb=" N THR F 509 " --> pdb=" O GLU F 400 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 353 through 355 Processing sheet with id=AD9, first strand: chain 'F' and resid 383 through 385 removed outlier: 4.635A pdb=" N TYR F 441 " --> pdb=" O LEU F 451 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 3 through 5 removed outlier: 3.763A pdb=" N HIS G 3 " --> pdb=" O SER G 26 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 10 through 14 removed outlier: 5.890A pdb=" N SER G 11 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR G 122 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS G 13 " --> pdb=" O THR G 122 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL G 35 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER G 51 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 10 through 14 removed outlier: 5.890A pdb=" N SER G 11 " --> pdb=" O ILE G 120 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR G 122 " --> pdb=" O SER G 11 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LYS G 13 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 133 through 137 removed outlier: 4.000A pdb=" N LEU G 153 " --> pdb=" O PHE G 137 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N TYR G 191 " --> pdb=" O LYS G 158 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 165 through 170 removed outlier: 3.787A pdb=" N HIS G 208 " --> pdb=" O PHE G 227 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE G 225 " --> pdb=" O CYS G 210 " (cutoff:3.500A) 826 hydrogen bonds defined for protein. 2169 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: 3.69 Time building geometry restraints manager: 2.24 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: 6231 1.34 - 1.46: 4240 1.46 - 1.58: 8805 1.58 - 1.70: 3 1.70 - 1.82: 137 Bond restraints: 19416 Sorted by residual: bond pdb=" O16 H6P F 601 " pdb=" P17 H6P F 601 " ideal model delta sigma weight residual 1.697 1.643 0.054 2.00e-02 2.50e+03 7.29e+00 bond pdb=" O16 H6P F 601 " pdb=" P13 H6P F 601 " ideal model delta sigma weight residual 1.594 1.644 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C28 H6P F 601 " pdb=" O29 H6P F 601 " ideal model delta sigma weight residual 1.442 1.398 0.044 2.00e-02 2.50e+03 4.85e+00 bond pdb=" C31 H6P F 601 " pdb=" O33 H6P F 601 " ideal model delta sigma weight residual 1.440 1.399 0.041 2.00e-02 2.50e+03 4.14e+00 bond pdb=" N MET D 25 " pdb=" CA MET D 25 " ideal model delta sigma weight residual 1.456 1.435 0.021 1.21e-02 6.83e+03 3.01e+00 ... (remaining 19411 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 26015 2.54 - 5.08: 261 5.08 - 7.62: 20 7.62 - 10.16: 8 10.16 - 12.70: 5 Bond angle restraints: 26309 Sorted by residual: angle pdb=" N MET D 25 " pdb=" CA MET D 25 " pdb=" C MET D 25 " ideal model delta sigma weight residual 108.90 96.20 12.70 1.63e+00 3.76e-01 6.07e+01 angle pdb=" C GLY D 43 " pdb=" N ASN D 44 " pdb=" CA ASN D 44 " ideal model delta sigma weight residual 121.70 133.00 -11.30 1.80e+00 3.09e-01 3.94e+01 angle pdb=" C MET D 99 " pdb=" N GLY D 100 " pdb=" CA GLY D 100 " ideal model delta sigma weight residual 121.70 132.35 -10.65 1.80e+00 3.09e-01 3.50e+01 angle pdb=" C ARG F 243 " pdb=" N SER F 244 " pdb=" CA SER F 244 " ideal model delta sigma weight residual 121.70 132.30 -10.60 1.80e+00 3.09e-01 3.46e+01 angle pdb=" C LYS G 171 " pdb=" N LYS G 172 " pdb=" CA LYS G 172 " ideal model delta sigma weight residual 121.70 131.14 -9.44 1.80e+00 3.09e-01 2.75e+01 ... (remaining 26304 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 10388 17.77 - 35.54: 1115 35.54 - 53.31: 186 53.31 - 71.09: 50 71.09 - 88.86: 31 Dihedral angle restraints: 11770 sinusoidal: 4874 harmonic: 6896 Sorted by residual: dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 173.09 -80.09 1 1.00e+01 1.00e-02 7.95e+01 dihedral pdb=" CB CYS A 51 " pdb=" SG CYS A 51 " pdb=" SG CYS A 125 " pdb=" CB CYS A 125 " ideal model delta sinusoidal sigma weight residual 93.00 162.72 -69.72 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CA TYR D 91 " pdb=" C TYR D 91 " pdb=" N CYS D 92 " pdb=" CA CYS D 92 " ideal model delta harmonic sigma weight residual -180.00 -157.13 -22.87 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 11767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2386 0.059 - 0.118: 432 0.118 - 0.177: 54 0.177 - 0.235: 0 0.235 - 0.294: 3 Chirality restraints: 2875 Sorted by residual: chirality pdb=" CA LYS D 26 " pdb=" N LYS D 26 " pdb=" C LYS D 26 " pdb=" CB LYS D 26 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA MET D 25 " pdb=" N MET D 25 " pdb=" C MET D 25 " pdb=" CB MET D 25 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CA ARG E 211 " pdb=" N ARG E 211 " pdb=" C ARG E 211 " pdb=" CB ARG E 211 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2872 not shown) Planarity restraints: 3397 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 260 " 0.037 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO A 261 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 338 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.27e+00 pdb=" N PRO B 339 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 339 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 339 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 260 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO B 261 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.028 5.00e-02 4.00e+02 ... (remaining 3394 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 174 2.56 - 3.14: 15113 3.14 - 3.73: 27512 3.73 - 4.31: 39321 4.31 - 4.90: 68572 Nonbonded interactions: 150692 Sorted by model distance: nonbonded pdb=" O GLU A 119 " pdb=" OH TYR A 123 " model vdw 1.973 3.040 nonbonded pdb=" O ASN D 197 " pdb=" ND2 ASN D 197 " model vdw 2.046 3.120 nonbonded pdb=" O PHE A 480 " pdb=" OG SER A 481 " model vdw 2.083 3.040 nonbonded pdb=" OG1 THR E 348 " pdb=" OE2 GLU E 376 " model vdw 2.096 3.040 nonbonded pdb=" OG1 THR E 232 " pdb=" OD2 ASP F 149 " model vdw 2.097 3.040 ... (remaining 150687 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'E' and (resid 30 through 65 or resid 67 through 151 or resid 154 through \ 157 or resid 159 through 177 or resid 179 through 180 or resid 183 through 188 \ or resid 190 through 215 or resid 217 through 220 or resid 222 through 223 or re \ sid 225 through 246 or resid 248 through 257 or resid 260 through 263 or resid 2 \ 65 through 266 or resid 268 through 271 or resid 273 through 274 or resid 276 th \ rough 277 or resid 282 or resid 286 through 287 or resid 289 or resid 292 throug \ h 293 or resid 300 through 301 or resid 303 or resid 305 or resid 307 through 30 \ 8 or resid 310 through 312 or resid 314 through 315 or resid 317 through 319 or \ resid 322 through 324 or resid 328 through 329 or resid 331 through 333 or resid \ 335 through 346 or resid 348 through 350 or resid 352 through 365 or resid 367 \ through 368 or resid 370 through 378 or resid 380 or resid 382 through 388 or re \ sid 390 or resid 392 through 416 or resid 418 through 419 or resid 421 through 4 \ 30 or resid 432 through 443 or resid 445 through 455 or resid 457 through 458 or \ resid 460 through 462 or resid 464 through 470 or resid 472 through 477 or resi \ d 479 through 483 or resid 485 through 486 or resid 490 through 493 or resid 495 \ through 511)) selection = (chain 'F' and (resid 30 through 65 or resid 67 through 151 or resid 154 through \ 157 or resid 159 through 177 or resid 179 through 180 or resid 183 through 188 \ or resid 190 through 215 or resid 217 through 220 or resid 222 through 223 or re \ sid 225 through 246 or resid 248 through 257 or resid 260 through 263 or resid 2 \ 65 through 266 or resid 268 through 271 or resid 273 through 274 or resid 276 th \ rough 277 or resid 282 or resid 286 through 287 or resid 289 or resid 292 throug \ h 293 or resid 300 through 301 or resid 303 or resid 305 or resid 307 through 30 \ 8 or resid 310 through 312 or resid 314 through 315 or resid 317 through 319 or \ resid 322 through 324 or resid 328 through 329 or resid 331 through 333 or resid \ 335 through 346 or resid 348 through 350 or resid 352 through 365 or resid 367 \ through 368 or resid 370 through 378 or resid 380 or resid 382 through 388 or re \ sid 390 or resid 392 through 416 or resid 418 through 429 or resid 431 through 4 \ 42 or resid 444 through 454 or resid 456 through 457 or resid 459 through 461 or \ resid 463 through 469 or resid 471 through 476 or resid 478 through 482 or resi \ d 484 through 485 or resid 489 through 492 or resid 494 through 510)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.920 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5331 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.635 19431 Z= 0.503 Angle : 0.695 12.701 26337 Z= 0.382 Chirality : 0.047 0.294 2875 Planarity : 0.005 0.067 3397 Dihedral : 15.380 88.857 7292 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.04 % Favored : 92.88 % Rotamer: Outliers : 0.43 % Allowed : 11.54 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.19 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.16), residues: 2373 helix: 2.30 (0.27), residues: 306 sheet: -1.17 (0.18), residues: 813 loop : -2.13 (0.15), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 215 TYR 0.016 0.002 TYR E 134 PHE 0.017 0.001 PHE A 421 TRP 0.022 0.002 TRP F 332 HIS 0.003 0.001 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.21 (19416) covalent geometry : angle 0.69366 / 0.38 (26309) SS BOND : bond 0.00453 / 0.28 ( 14) SS BOND : angle 1.48678 / 0.82 ( 28) hydrogen bonds : bond 0.12950 / 8.98 ( 786) hydrogen bonds : angle 6.32368 / 4.29 ( 2169) Misc. bond : bond 0.63523 / 33.43 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 308 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 VAL cc_start: 0.6966 (t) cc_final: 0.6756 (t) REVERT: B 62 MET cc_start: 0.4289 (mtp) cc_final: 0.3816 (mtp) outliers start: 9 outliers final: 1 residues processed: 315 average time/residue: 0.1460 time to fit residues: 68.5629 Evaluate side-chains 154 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 153 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 442 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 216 optimal weight: 0.0670 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.0050 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 2.9990 overall best weight: 0.7534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN B 303 GLN B 372 GLN D 195 HIS F 114 HIS F 330 ASN G 174 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.106758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.079454 restraints weight = 102327.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.077847 restraints weight = 51703.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.078952 restraints weight = 42463.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.078532 restraints weight = 38851.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.078720 restraints weight = 35862.948| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19431 Z= 0.159 Angle : 0.701 11.262 26337 Z= 0.360 Chirality : 0.047 0.218 2875 Planarity : 0.005 0.053 3397 Dihedral : 5.550 54.999 2629 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 2.64 % Allowed : 14.23 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.19 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.17), residues: 2373 helix: 2.93 (0.27), residues: 310 sheet: -0.79 (0.18), residues: 828 loop : -1.85 (0.16), residues: 1235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 282 TYR 0.018 0.002 TYR E 202 PHE 0.020 0.002 PHE G 160 TRP 0.024 0.002 TRP F 332 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (19416) covalent geometry : angle 0.69998 / 0.36 (26309) SS BOND : bond 0.01015 / 0.62 ( 14) SS BOND : angle 1.39886 / 0.83 ( 28) hydrogen bonds : bond 0.05643 / 3.75 ( 786) hydrogen bonds : angle 5.20025 / 3.53 ( 2169) Misc. bond : bond 0.00067 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 171 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.4678 (OUTLIER) cc_final: 0.4226 (pmm) REVERT: A 202 MET cc_start: 0.6572 (tpp) cc_final: 0.6341 (mmm) REVERT: A 296 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8259 (mm-30) REVERT: B 217 MET cc_start: 0.5498 (mmp) cc_final: 0.4918 (mmp) REVERT: D 132 MET cc_start: 0.6811 (mtm) cc_final: 0.6327 (mtm) REVERT: E 143 VAL cc_start: 0.7049 (OUTLIER) cc_final: 0.5714 (m) REVERT: F 43 MET cc_start: 0.6034 (mmm) cc_final: 0.5138 (tpp) REVERT: G 163 VAL cc_start: 0.8542 (t) cc_final: 0.8266 (t) outliers start: 55 outliers final: 19 residues processed: 212 average time/residue: 0.1267 time to fit residues: 42.2307 Evaluate side-chains 140 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 143 VAL Chi-restraints excluded: chain E residue 237 ILE Chi-restraints excluded: chain E residue 395 HIS Chi-restraints excluded: chain E residue 423 VAL Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 199 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 128 optimal weight: 1.9990 chunk 200 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 GLN B 113 HIS B 303 GLN E 89 GLN F 326 HIS F 374 ASN G 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.094599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.069358 restraints weight = 99358.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.068226 restraints weight = 63403.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.068488 restraints weight = 48745.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.068779 restraints weight = 43229.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.069030 restraints weight = 39442.679| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 19431 Z= 0.183 Angle : 0.692 10.168 26337 Z= 0.359 Chirality : 0.046 0.220 2875 Planarity : 0.005 0.049 3397 Dihedral : 5.257 66.561 2625 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.07 % Rotamer: Outliers : 2.98 % Allowed : 15.82 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.19 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.17), residues: 2373 helix: 3.29 (0.26), residues: 310 sheet: -0.67 (0.18), residues: 841 loop : -1.58 (0.16), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 313 TYR 0.016 0.002 TYR B 387 PHE 0.018 0.002 PHE G 48 TRP 0.027 0.002 TRP E 67 HIS 0.015 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (19416) covalent geometry : angle 0.69018 / 0.36 (26309) SS BOND : bond 0.00576 / 0.34 ( 14) SS BOND : angle 1.78094 / 0.99 ( 28) hydrogen bonds : bond 0.05271 / 3.53 ( 786) hydrogen bonds : angle 5.07925 / 3.46 ( 2169) Misc. bond : bond 0.00231 / 0.12 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 130 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.3717 (OUTLIER) cc_final: 0.2842 (pmm) REVERT: A 116 THR cc_start: 0.7139 (OUTLIER) cc_final: 0.6872 (p) REVERT: A 205 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.8057 (t) REVERT: A 296 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8176 (mm-30) REVERT: A 399 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7886 (t) REVERT: B 66 TRP cc_start: 0.8442 (OUTLIER) cc_final: 0.8013 (m-90) REVERT: B 89 MET cc_start: 0.6688 (tpp) cc_final: 0.6208 (ttm) REVERT: B 104 SER cc_start: 0.9218 (m) cc_final: 0.8437 (p) REVERT: B 241 MET cc_start: 0.6069 (tpt) cc_final: 0.5815 (mmm) REVERT: B 318 LEU cc_start: 0.8125 (tp) cc_final: 0.7876 (tp) REVERT: D 132 MET cc_start: 0.7047 (mtm) cc_final: 0.6679 (mtm) REVERT: F 43 MET cc_start: 0.7051 (mmm) cc_final: 0.5733 (tpp) REVERT: F 174 GLN cc_start: 0.8082 (pm20) cc_final: 0.7724 (pm20) outliers start: 62 outliers final: 28 residues processed: 175 average time/residue: 0.1386 time to fit residues: 38.1916 Evaluate side-chains 140 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 MET Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain B residue 66 TRP Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 166 CYS Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 199 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 24 optimal weight: 9.9990 chunk 210 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 149 optimal weight: 30.0000 chunk 62 optimal weight: 9.9990 chunk 26 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 206 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 HIS F 178 GLN F 326 HIS F 330 ASN G 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.090019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.063842 restraints weight = 96952.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.062962 restraints weight = 53499.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.062880 restraints weight = 53726.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.063185 restraints weight = 47600.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.063690 restraints weight = 38642.724| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.7056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 19431 Z= 0.286 Angle : 0.744 10.371 26337 Z= 0.383 Chirality : 0.048 0.252 2875 Planarity : 0.006 0.082 3397 Dihedral : 5.608 58.082 2625 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.52 % Favored : 94.44 % Rotamer: Outliers : 3.85 % Allowed : 16.20 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.19 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.17), residues: 2373 helix: 3.32 (0.26), residues: 312 sheet: -0.74 (0.18), residues: 838 loop : -1.49 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 105 TYR 0.020 0.002 TYR B 171 PHE 0.023 0.002 PHE G 160 TRP 0.022 0.002 TRP G 196 HIS 0.012 0.002 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.29 (19416) covalent geometry : angle 0.74252 / 0.38 (26309) SS BOND : bond 0.00596 / 0.36 ( 14) SS BOND : angle 1.54533 / 0.89 ( 28) hydrogen bonds : bond 0.05242 / 3.52 ( 786) hydrogen bonds : angle 5.33284 / 3.64 ( 2169) Misc. bond : bond 0.00201 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 93 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.4342 (OUTLIER) cc_final: 0.3623 (pmm) REVERT: A 202 MET cc_start: 0.6719 (tpt) cc_final: 0.6212 (mmm) REVERT: A 399 THR cc_start: 0.8122 (OUTLIER) cc_final: 0.7914 (t) REVERT: D 99 MET cc_start: 0.5288 (mmm) cc_final: 0.4870 (mmp) REVERT: D 132 MET cc_start: 0.7631 (mtm) cc_final: 0.7158 (mtm) REVERT: D 183 TYR cc_start: 0.8099 (m-80) cc_final: 0.7896 (m-10) REVERT: F 242 PHE cc_start: 0.4053 (OUTLIER) cc_final: 0.3293 (m-80) REVERT: G 92 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9016 (mt) outliers start: 80 outliers final: 44 residues processed: 160 average time/residue: 0.1291 time to fit residues: 32.8438 Evaluate side-chains 130 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 82 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 169 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 166 CYS Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 289 GLU Chi-restraints excluded: chain E residue 298 THR Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 220 CYS Chi-restraints excluded: chain F residue 222 ILE Chi-restraints excluded: chain F residue 232 THR Chi-restraints excluded: chain F residue 242 PHE Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 392 SER Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 84 ILE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 194 PHE Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 219 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 106 optimal weight: 0.6980 chunk 216 optimal weight: 0.8980 chunk 161 optimal weight: 40.0000 chunk 171 optimal weight: 0.7980 chunk 201 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 152 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 6 optimal weight: 20.0000 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 HIS F 151 HIS F 326 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.091415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.065702 restraints weight = 95996.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.065239 restraints weight = 53481.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.065003 restraints weight = 51094.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.065347 restraints weight = 46922.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.065938 restraints weight = 39140.359| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.7271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19431 Z= 0.128 Angle : 0.615 9.804 26337 Z= 0.314 Chirality : 0.045 0.199 2875 Planarity : 0.004 0.048 3397 Dihedral : 5.045 59.712 2625 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.21 % Favored : 95.74 % Rotamer: Outliers : 2.84 % Allowed : 18.75 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.19 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.17), residues: 2373 helix: 3.67 (0.26), residues: 308 sheet: -0.54 (0.18), residues: 859 loop : -1.32 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 223 TYR 0.018 0.001 TYR B 387 PHE 0.017 0.001 PHE B 453 TRP 0.026 0.001 TRP F 332 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (19416) covalent geometry : angle 0.61401 / 0.31 (26309) SS BOND : bond 0.00373 / 0.23 ( 14) SS BOND : angle 1.41683 / 0.89 ( 28) hydrogen bonds : bond 0.04644 / 3.14 ( 786) hydrogen bonds : angle 4.92825 / 3.36 ( 2169) Misc. bond : bond 0.00087 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 97 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.4297 (OUTLIER) cc_final: 0.3604 (pmm) REVERT: A 202 MET cc_start: 0.6664 (tpt) cc_final: 0.6454 (mmm) REVERT: A 217 MET cc_start: 0.7183 (tpt) cc_final: 0.6517 (tpt) REVERT: A 296 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8015 (mm-30) REVERT: B 241 MET cc_start: 0.6458 (mmm) cc_final: 0.5746 (mmm) REVERT: B 313 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.8130 (ptpp) REVERT: B 314 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8501 (mp) REVERT: D 99 MET cc_start: 0.4980 (mmm) cc_final: 0.4627 (mmp) REVERT: D 132 MET cc_start: 0.7395 (mtm) cc_final: 0.6836 (mtm) REVERT: E 425 MET cc_start: -0.0911 (tpt) cc_final: -0.2317 (tpt) REVERT: F 162 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7172 (mm) REVERT: F 309 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8726 (pp) REVERT: G 92 ILE cc_start: 0.9260 (OUTLIER) cc_final: 0.8956 (mt) outliers start: 59 outliers final: 25 residues processed: 147 average time/residue: 0.1137 time to fit residues: 27.2881 Evaluate side-chains 116 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 201 HIS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 162 ILE Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 220 CYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 211 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 215 optimal weight: 0.9980 chunk 221 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 146 optimal weight: 1.9990 chunk 213 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 196 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS F 151 HIS G 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.091003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.065311 restraints weight = 95169.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.064608 restraints weight = 51685.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.064385 restraints weight = 55779.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.064730 restraints weight = 46548.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.065010 restraints weight = 38711.766| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.7633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19431 Z= 0.141 Angle : 0.620 9.042 26337 Z= 0.315 Chirality : 0.045 0.208 2875 Planarity : 0.004 0.049 3397 Dihedral : 4.949 59.599 2625 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.36 % Allowed : 19.13 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.19 % Cis-general : 0.49 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.17), residues: 2373 helix: 3.77 (0.26), residues: 308 sheet: -0.39 (0.18), residues: 854 loop : -1.23 (0.17), residues: 1211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 211 TYR 0.017 0.001 TYR A 78 PHE 0.015 0.001 PHE G 160 TRP 0.021 0.001 TRP F 332 HIS 0.008 0.001 HIS E 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (19416) covalent geometry : angle 0.61836 / 0.31 (26309) SS BOND : bond 0.00350 / 0.21 ( 14) SS BOND : angle 1.39665 / 0.81 ( 28) hydrogen bonds : bond 0.04493 / 3.02 ( 786) hydrogen bonds : angle 4.83586 / 3.30 ( 2169) Misc. bond : bond 0.00092 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.4232 (OUTLIER) cc_final: 0.3619 (pmm) REVERT: A 202 MET cc_start: 0.6758 (tpt) cc_final: 0.6401 (mmm) REVERT: A 217 MET cc_start: 0.7220 (tpt) cc_final: 0.6538 (tpt) REVERT: B 241 MET cc_start: 0.6636 (mmm) cc_final: 0.6016 (mmm) REVERT: B 313 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.8029 (ptpp) REVERT: B 314 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8484 (mp) REVERT: D 99 MET cc_start: 0.5313 (mmm) cc_final: 0.5087 (mmp) REVERT: D 132 MET cc_start: 0.7525 (mtm) cc_final: 0.6971 (mtm) REVERT: D 183 TYR cc_start: 0.8105 (m-10) cc_final: 0.7859 (m-10) REVERT: E 58 MET cc_start: 0.8470 (ppp) cc_final: 0.8234 (ppp) REVERT: E 397 TRP cc_start: 0.6829 (p90) cc_final: 0.5950 (p-90) REVERT: E 425 MET cc_start: -0.0993 (tpt) cc_final: -0.2389 (tpt) REVERT: E 434 MET cc_start: 0.7679 (tmm) cc_final: 0.6959 (tpt) REVERT: E 454 LEU cc_start: 0.3983 (OUTLIER) cc_final: 0.3130 (mp) REVERT: E 465 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8935 (tp) REVERT: F 309 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8853 (pp) REVERT: G 92 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.9013 (mt) outliers start: 49 outliers final: 33 residues processed: 134 average time/residue: 0.1247 time to fit residues: 26.9441 Evaluate side-chains 126 residues out of total 2080 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 86 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 313 LYS Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 62 ASP Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 201 HIS Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 454 LEU Chi-restraints excluded: chain E residue 465 LEU Chi-restraints excluded: chain F residue 75 VAL Chi-restraints excluded: chain F residue 152 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 220 CYS Chi-restraints excluded: chain F residue 221 THR Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 484 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 199 VAL Chi-restraints excluded: chain G residue 211 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2333 > 50: distance: 4 - 10: 25.768 distance: 10 - 11: 54.735 distance: 11 - 12: 39.593 distance: 11 - 14: 45.338 distance: 12 - 13: 42.918 distance: 12 - 16: 11.604 distance: 14 - 15: 29.803 distance: 16 - 17: 44.913 distance: 17 - 18: 39.003 distance: 17 - 20: 40.737 distance: 18 - 19: 37.572 distance: 18 - 25: 41.022 distance: 20 - 21: 18.417 distance: 21 - 22: 15.022 distance: 22 - 23: 43.299 distance: 22 - 24: 36.350 distance: 25 - 26: 36.219 distance: 25 - 31: 49.554 distance: 26 - 27: 41.748 distance: 26 - 29: 16.800 distance: 27 - 28: 13.530 distance: 27 - 32: 54.028 distance: 29 - 30: 3.544 distance: 30 - 31: 46.100 distance: 32 - 33: 33.180 distance: 33 - 34: 35.295 distance: 33 - 36: 45.449 distance: 34 - 35: 14.880 distance: 34 - 42: 24.550 distance: 36 - 37: 31.643 distance: 37 - 38: 40.054 distance: 37 - 39: 22.491 distance: 38 - 40: 24.496 distance: 39 - 41: 34.319 distance: 40 - 41: 31.910 distance: 42 - 43: 43.425 distance: 43 - 44: 45.484 distance: 43 - 46: 23.588 distance: 44 - 45: 35.706 distance: 44 - 49: 24.246 distance: 46 - 47: 34.715 distance: 46 - 48: 22.134 distance: 49 - 50: 17.193 distance: 50 - 51: 44.829 distance: 50 - 53: 42.925 distance: 51 - 58: 46.738 distance: 53 - 54: 28.693 distance: 54 - 55: 7.051 distance: 55 - 56: 43.014 distance: 56 - 57: 21.589 distance: 58 - 59: 41.125 distance: 58 - 64: 43.587 distance: 59 - 60: 40.511 distance: 59 - 62: 58.064 distance: 60 - 61: 4.851 distance: 60 - 65: 22.424 distance: 62 - 63: 25.600 distance: 63 - 64: 23.882 distance: 65 - 66: 54.230 distance: 65 - 120: 27.868 distance: 66 - 67: 46.625 distance: 66 - 69: 24.009 distance: 67 - 68: 65.974 distance: 67 - 71: 46.011 distance: 68 - 117: 30.917 distance: 69 - 70: 52.201 distance: 71 - 72: 49.048 distance: 72 - 73: 70.233 distance: 72 - 75: 49.460 distance: 73 - 74: 19.189 distance: 73 - 78: 46.335 distance: 75 - 76: 39.946 distance: 75 - 77: 40.565 distance: 78 - 79: 8.773 distance: 78 - 108: 23.285 distance: 79 - 80: 25.011 distance: 79 - 82: 36.599 distance: 80 - 81: 13.326 distance: 80 - 89: 32.260 distance: 81 - 105: 24.362 distance: 82 - 83: 30.086 distance: 83 - 84: 24.800 distance: 83 - 85: 18.377 distance: 84 - 86: 22.756 distance: 85 - 87: 12.031 distance: 86 - 88: 27.284 distance: 87 - 88: 19.767