Starting phenix.real_space_refine on Mon May 19 17:49:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bo8_7120/05_2025/6bo8_7120.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bo8_7120/05_2025/6bo8_7120.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6bo8_7120/05_2025/6bo8_7120.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bo8_7120/05_2025/6bo8_7120.map" model { file = "/net/cci-nas-00/data/ceres_data/6bo8_7120/05_2025/6bo8_7120.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bo8_7120/05_2025/6bo8_7120.cif" } resolution = 3.6 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= 0.001 sd= 0.010 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 156 5.16 5 C 12304 2.51 5 N 3220 2.21 5 O 3368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 19048 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 593, 4762 Classifications: {'peptide': 593} Link IDs: {'PTRANS': 26, 'TRANS': 566} Chain breaks: 1 Restraints were copied for chains: C, B, D Time building chain proxies: 10.38, per 1000 atoms: 0.54 Number of scatterers: 19048 At special positions: 0 Unit cell: (136.22, 136.22, 125.44, 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 156 16.00 O 3368 8.00 N 3220 7.00 C 12304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.81 Conformation dependent library (CDL) restraints added in 2.3 seconds 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 62.6% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 29 through 47 removed outlier: 4.014A pdb=" N ARG A 33 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP A 45 " --> pdb=" O GLN A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 55 removed outlier: 3.569A pdb=" N ASP A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 81 through 89 Processing helix chain 'A' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU A 100 " --> pdb=" O MET A 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.646A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.755A pdb=" N CYS A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 184 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.528A pdb=" N LEU A 205 " --> pdb=" O HIS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 222 removed outlier: 4.024A pdb=" N GLN A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN A 217 " --> pdb=" O CYS A 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A 221 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 250 removed outlier: 3.686A pdb=" N GLY A 248 " --> pdb=" O PHE A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.638A pdb=" N HIS A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 262 " --> pdb=" O HIS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.546A pdb=" N LEU A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 removed outlier: 3.797A pdb=" N LEU A 308 " --> pdb=" O ARG A 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP A 309 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 323 removed outlier: 3.530A pdb=" N GLU A 315 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 346 Processing helix chain 'A' and resid 380 through 403 removed outlier: 3.557A pdb=" N ILE A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 445 Processing helix chain 'A' and resid 450 through 464 removed outlier: 3.774A pdb=" N MET A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL A 459 " --> pdb=" O SER A 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 460 " --> pdb=" O PHE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 472 removed outlier: 3.685A pdb=" N ARG A 470 " --> pdb=" O TYR A 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY A 471 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 487 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL A 499 " --> pdb=" O TRP A 495 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER A 506 " --> pdb=" O LEU A 502 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 510 " --> pdb=" O SER A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 524 removed outlier: 4.189A pdb=" N PHE A 523 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR A 524 " --> pdb=" O GLY A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 525 through 538 removed outlier: 3.803A pdb=" N PHE A 531 " --> pdb=" O PRO A 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU A 535 " --> pdb=" O PHE A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 568 removed outlier: 4.009A pdb=" N SER A 556 " --> pdb=" O PRO A 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE A 557 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 560 " --> pdb=" O SER A 556 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 587 Processing helix chain 'A' and resid 588 through 606 removed outlier: 3.559A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 47 removed outlier: 4.013A pdb=" N ARG B 33 " --> pdb=" O TRP B 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TRP B 45 " --> pdb=" O GLN B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.569A pdb=" N ASP B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 66 Processing helix chain 'B' and resid 81 through 89 Processing helix chain 'B' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU B 100 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.647A pdb=" N VAL B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 139 Processing helix chain 'B' and resid 165 through 173 removed outlier: 3.754A pdb=" N CYS B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 184 Processing helix chain 'B' and resid 198 through 205 removed outlier: 3.528A pdb=" N LEU B 205 " --> pdb=" O HIS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 222 removed outlier: 4.023A pdb=" N GLN B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 217 " --> pdb=" O CYS B 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 221 " --> pdb=" O ASN B 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 250 removed outlier: 3.687A pdb=" N GLY B 248 " --> pdb=" O PHE B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 264 removed outlier: 3.636A pdb=" N HIS B 258 " --> pdb=" O VAL B 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 262 " --> pdb=" O HIS B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 299 removed outlier: 3.546A pdb=" N LEU B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 309 removed outlier: 3.797A pdb=" N LEU B 308 " --> pdb=" O ARG B 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 309 " --> pdb=" O GLN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 323 removed outlier: 3.531A pdb=" N GLU B 315 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 346 Processing helix chain 'B' and resid 380 through 403 removed outlier: 3.556A pdb=" N ILE B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR B 392 " --> pdb=" O GLY B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 445 Processing helix chain 'B' and resid 450 through 464 removed outlier: 3.774A pdb=" N MET B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL B 459 " --> pdb=" O SER B 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 460 " --> pdb=" O PHE B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 472 removed outlier: 3.684A pdb=" N ARG B 470 " --> pdb=" O TYR B 467 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY B 471 " --> pdb=" O PHE B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 487 Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'B' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL B 499 " --> pdb=" O TRP B 495 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL B 500 " --> pdb=" O LEU B 496 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 524 removed outlier: 4.190A pdb=" N PHE B 523 " --> pdb=" O LEU B 520 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 520 through 524' Processing helix chain 'B' and resid 525 through 538 removed outlier: 3.802A pdb=" N PHE B 531 " --> pdb=" O PRO B 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU B 535 " --> pdb=" O PHE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 568 removed outlier: 4.010A pdb=" N SER B 556 " --> pdb=" O PRO B 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE B 557 " --> pdb=" O PHE B 553 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 560 " --> pdb=" O SER B 556 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 587 Processing helix chain 'B' and resid 588 through 606 removed outlier: 3.560A pdb=" N LEU B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 47 removed outlier: 4.014A pdb=" N ARG C 33 " --> pdb=" O TRP C 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP C 45 " --> pdb=" O GLN C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 55 removed outlier: 3.570A pdb=" N ASP C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLU C 100 " --> pdb=" O MET C 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.646A pdb=" N VAL C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 165 through 173 removed outlier: 3.755A pdb=" N CYS C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 184 Processing helix chain 'C' and resid 198 through 205 removed outlier: 3.527A pdb=" N LEU C 205 " --> pdb=" O HIS C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 222 removed outlier: 4.023A pdb=" N GLN C 214 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N MET C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 217 " --> pdb=" O CYS C 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER C 221 " --> pdb=" O ASN C 217 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C 222 " --> pdb=" O LEU C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 250 removed outlier: 3.688A pdb=" N GLY C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 removed outlier: 3.638A pdb=" N HIS C 258 " --> pdb=" O VAL C 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS C 262 " --> pdb=" O HIS C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 299 removed outlier: 3.546A pdb=" N LEU C 295 " --> pdb=" O SER C 291 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 removed outlier: 3.796A pdb=" N LEU C 308 " --> pdb=" O ARG C 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP C 309 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 323 removed outlier: 3.530A pdb=" N GLU C 315 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU C 316 " --> pdb=" O PRO C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 346 Processing helix chain 'C' and resid 380 through 403 removed outlier: 3.556A pdb=" N ILE C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 392 " --> pdb=" O GLY C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 445 Processing helix chain 'C' and resid 450 through 464 removed outlier: 3.774A pdb=" N MET C 454 " --> pdb=" O GLU C 450 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 460 " --> pdb=" O PHE C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 472 removed outlier: 3.684A pdb=" N ARG C 470 " --> pdb=" O TYR C 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY C 471 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 487 Processing helix chain 'C' and resid 489 through 492 Processing helix chain 'C' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL C 499 " --> pdb=" O TRP C 495 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL C 500 " --> pdb=" O LEU C 496 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER C 506 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 524 removed outlier: 4.189A pdb=" N PHE C 523 " --> pdb=" O LEU C 520 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR C 524 " --> pdb=" O GLY C 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 520 through 524' Processing helix chain 'C' and resid 525 through 538 removed outlier: 3.802A pdb=" N PHE C 531 " --> pdb=" O PRO C 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU C 535 " --> pdb=" O PHE C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 552 through 568 removed outlier: 4.009A pdb=" N SER C 556 " --> pdb=" O PRO C 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE C 557 " --> pdb=" O PHE C 553 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA C 560 " --> pdb=" O SER C 556 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU C 568 " --> pdb=" O ILE C 564 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 587 Processing helix chain 'C' and resid 588 through 606 removed outlier: 3.559A pdb=" N LEU C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 47 removed outlier: 4.014A pdb=" N ARG D 33 " --> pdb=" O TRP D 29 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN D 40 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TRP D 45 " --> pdb=" O GLN D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 55 removed outlier: 3.569A pdb=" N ASP D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 66 Processing helix chain 'D' and resid 81 through 89 Processing helix chain 'D' and resid 91 through 102 removed outlier: 3.553A pdb=" N VAL D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLU D 100 " --> pdb=" O MET D 96 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA D 101 " --> pdb=" O VAL D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.646A pdb=" N VAL D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 165 through 173 removed outlier: 3.754A pdb=" N CYS D 172 " --> pdb=" O SER D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 184 Processing helix chain 'D' and resid 198 through 205 removed outlier: 3.528A pdb=" N LEU D 205 " --> pdb=" O HIS D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 222 removed outlier: 4.024A pdb=" N GLN D 214 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TYR D 216 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN D 217 " --> pdb=" O CYS D 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D 221 " --> pdb=" O ASN D 217 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR D 222 " --> pdb=" O LEU D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 250 removed outlier: 3.687A pdb=" N GLY D 248 " --> pdb=" O PHE D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 264 removed outlier: 3.637A pdb=" N HIS D 258 " --> pdb=" O VAL D 254 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS D 262 " --> pdb=" O HIS D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 299 removed outlier: 3.547A pdb=" N LEU D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D 297 " --> pdb=" O LEU D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 309 removed outlier: 3.796A pdb=" N LEU D 308 " --> pdb=" O ARG D 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 309 " --> pdb=" O GLN D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 323 removed outlier: 3.530A pdb=" N GLU D 315 " --> pdb=" O THR D 311 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU D 316 " --> pdb=" O PRO D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 346 Processing helix chain 'D' and resid 380 through 403 removed outlier: 3.557A pdb=" N ILE D 384 " --> pdb=" O PRO D 380 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 445 Processing helix chain 'D' and resid 450 through 464 removed outlier: 3.775A pdb=" N MET D 454 " --> pdb=" O GLU D 450 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 459 " --> pdb=" O SER D 455 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU D 460 " --> pdb=" O PHE D 456 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 472 removed outlier: 3.684A pdb=" N ARG D 470 " --> pdb=" O TYR D 467 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY D 471 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 487 Processing helix chain 'D' and resid 489 through 492 Processing helix chain 'D' and resid 493 through 512 removed outlier: 3.861A pdb=" N VAL D 499 " --> pdb=" O TRP D 495 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL D 500 " --> pdb=" O LEU D 496 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER D 506 " --> pdb=" O LEU D 502 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 510 " --> pdb=" O SER D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 524 removed outlier: 4.189A pdb=" N PHE D 523 " --> pdb=" O LEU D 520 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR D 524 " --> pdb=" O GLY D 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 520 through 524' Processing helix chain 'D' and resid 525 through 538 removed outlier: 3.802A pdb=" N PHE D 531 " --> pdb=" O PRO D 527 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU D 535 " --> pdb=" O PHE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 552 through 568 removed outlier: 4.009A pdb=" N SER D 556 " --> pdb=" O PRO D 552 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE D 557 " --> pdb=" O PHE D 553 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 560 " --> pdb=" O SER D 556 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 568 " --> pdb=" O ILE D 564 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 587 Processing helix chain 'D' and resid 588 through 606 removed outlier: 3.560A pdb=" N LEU D 592 " --> pdb=" O GLU D 588 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR A 276 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR B 276 " --> pdb=" O VAL B 633 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR C 276 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 269 through 270 removed outlier: 3.526A pdb=" N THR D 276 " --> pdb=" O VAL D 633 " (cutoff:3.500A) 884 hydrogen bonds defined for protein. 2532 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: 4.87 Time building geometry restraints manager: 5.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5464 1.33 - 1.45: 3323 1.45 - 1.57: 10433 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 19484 Sorted by residual: bond pdb=" CA VAL C 452 " pdb=" CB VAL C 452 " ideal model delta sigma weight residual 1.534 1.550 -0.015 6.80e-03 2.16e+04 4.97e+00 bond pdb=" CA VAL A 452 " pdb=" CB VAL A 452 " ideal model delta sigma weight residual 1.534 1.550 -0.015 6.80e-03 2.16e+04 4.93e+00 bond pdb=" CA VAL D 452 " pdb=" CB VAL D 452 " ideal model delta sigma weight residual 1.534 1.549 -0.015 6.80e-03 2.16e+04 4.69e+00 bond pdb=" CA HIS C 265 " pdb=" CB HIS C 265 " ideal model delta sigma weight residual 1.522 1.494 0.027 1.27e-02 6.20e+03 4.63e+00 bond pdb=" CA VAL B 452 " pdb=" CB VAL B 452 " ideal model delta sigma weight residual 1.534 1.549 -0.015 6.80e-03 2.16e+04 4.63e+00 ... (remaining 19479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 25946 3.67 - 7.33: 434 7.33 - 11.00: 56 11.00 - 14.66: 0 14.66 - 18.33: 4 Bond angle restraints: 26440 Sorted by residual: angle pdb=" N LEU D 352 " pdb=" CA LEU D 352 " pdb=" C LEU D 352 " ideal model delta sigma weight residual 110.91 118.03 -7.12 1.17e+00 7.31e-01 3.70e+01 angle pdb=" N LEU A 352 " pdb=" CA LEU A 352 " pdb=" C LEU A 352 " ideal model delta sigma weight residual 110.91 118.03 -7.12 1.17e+00 7.31e-01 3.70e+01 angle pdb=" N LEU C 352 " pdb=" CA LEU C 352 " pdb=" C LEU C 352 " ideal model delta sigma weight residual 110.91 118.00 -7.09 1.17e+00 7.31e-01 3.67e+01 angle pdb=" N LEU B 352 " pdb=" CA LEU B 352 " pdb=" C LEU B 352 " ideal model delta sigma weight residual 110.91 117.99 -7.08 1.17e+00 7.31e-01 3.67e+01 angle pdb=" N SER D 112 " pdb=" CA SER D 112 " pdb=" C SER D 112 " ideal model delta sigma weight residual 108.79 117.52 -8.73 1.53e+00 4.27e-01 3.26e+01 ... (remaining 26435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.42: 10858 15.42 - 30.85: 657 30.85 - 46.27: 157 46.27 - 61.69: 4 61.69 - 77.11: 12 Dihedral angle restraints: 11688 sinusoidal: 4728 harmonic: 6960 Sorted by residual: dihedral pdb=" CA ASP B 223 " pdb=" C ASP B 223 " pdb=" N ARG B 224 " pdb=" CA ARG B 224 " ideal model delta harmonic sigma weight residual -180.00 -149.04 -30.96 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA ASP A 223 " pdb=" C ASP A 223 " pdb=" N ARG A 224 " pdb=" CA ARG A 224 " ideal model delta harmonic sigma weight residual -180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA ASP D 223 " pdb=" C ASP D 223 " pdb=" N ARG D 224 " pdb=" CA ARG D 224 " ideal model delta harmonic sigma weight residual -180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 11685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2014 0.051 - 0.103: 827 0.103 - 0.154: 141 0.154 - 0.205: 19 0.205 - 0.256: 11 Chirality restraints: 3012 Sorted by residual: chirality pdb=" CA THR A 311 " pdb=" N THR A 311 " pdb=" C THR A 311 " pdb=" CB THR A 311 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.26 2.00e-01 2.50e+01 1.64e+00 chirality pdb=" CA THR B 311 " pdb=" N THR B 311 " pdb=" C THR B 311 " pdb=" CB THR B 311 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA THR D 311 " pdb=" N THR D 311 " pdb=" C THR D 311 " pdb=" CB THR D 311 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 3009 not shown) Planarity restraints: 3336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP D 223 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.62e+00 pdb=" C ASP D 223 " -0.045 2.00e-02 2.50e+03 pdb=" O ASP D 223 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG D 224 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 223 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.61e+00 pdb=" C ASP C 223 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP C 223 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG C 224 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 223 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C ASP A 223 " 0.044 2.00e-02 2.50e+03 pdb=" O ASP A 223 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 224 " -0.015 2.00e-02 2.50e+03 ... (remaining 3333 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5470 2.81 - 3.33: 19064 3.33 - 3.85: 31397 3.85 - 4.38: 37260 4.38 - 4.90: 60177 Nonbonded interactions: 153368 Sorted by model distance: nonbonded pdb=" OH TYR B 161 " pdb=" OD2 ASP B 193 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR A 161 " pdb=" OD2 ASP A 193 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR D 161 " pdb=" OD2 ASP D 193 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR C 161 " pdb=" OD2 ASP C 193 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR D 339 " pdb=" O THR D 392 " model vdw 2.310 3.040 ... (remaining 153363 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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 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: 0.450 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: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 39.450 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6099 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 : 0.008 0.065 19484 Z= 0.368 Angle : 1.192 18.330 26440 Z= 0.668 Chirality : 0.055 0.256 3012 Planarity : 0.007 0.049 3336 Dihedral : 10.831 77.114 7184 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % Rotamer: Outliers : 0.97 % Allowed : 2.13 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.49 (0.14), residues: 2356 helix: -2.68 (0.10), residues: 1344 sheet: -5.00 (0.44), residues: 56 loop : -3.13 (0.18), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP D 629 HIS 0.017 0.003 HIS A 522 PHE 0.029 0.003 PHE D 169 TYR 0.026 0.003 TYR C 547 ARG 0.007 0.001 ARG A 305 Details of bonding type rmsd hydrogen bonds : bond 0.28238 ( 884) hydrogen bonds : angle 8.55933 ( 2532) covalent geometry : bond 0.00754 (19484) covalent geometry : angle 1.19203 (26440) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 759 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 CYS cc_start: 0.7568 (m) cc_final: 0.6918 (p) REVERT: A 183 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7377 (mm) REVERT: A 246 LEU cc_start: 0.6794 (tp) cc_final: 0.6588 (tp) REVERT: A 252 ASN cc_start: 0.6715 (t0) cc_final: 0.6322 (t0) REVERT: A 262 LYS cc_start: 0.8358 (tptp) cc_final: 0.7767 (mttt) REVERT: A 382 ASP cc_start: 0.7143 (m-30) cc_final: 0.6723 (m-30) REVERT: A 383 ASP cc_start: 0.8301 (m-30) cc_final: 0.7916 (t0) REVERT: A 435 MET cc_start: 0.6735 (mmt) cc_final: 0.6409 (mmt) REVERT: A 464 ASN cc_start: 0.6570 (t160) cc_final: 0.6253 (m-40) REVERT: A 487 PHE cc_start: 0.7586 (m-80) cc_final: 0.7338 (m-10) REVERT: A 527 PRO cc_start: 0.8595 (Cg_exo) cc_final: 0.8103 (Cg_endo) REVERT: A 550 ASP cc_start: 0.8049 (t0) cc_final: 0.7022 (p0) REVERT: A 580 ASP cc_start: 0.6486 (t0) cc_final: 0.6159 (m-30) REVERT: A 590 ASP cc_start: 0.7360 (m-30) cc_final: 0.6874 (t0) REVERT: A 628 ARG cc_start: 0.8060 (mtm-85) cc_final: 0.7817 (mtp-110) REVERT: A 630 PHE cc_start: 0.6910 (m-80) cc_final: 0.6499 (m-80) REVERT: B 40 GLN cc_start: 0.7590 (tt0) cc_final: 0.7276 (tt0) REVERT: B 78 MET cc_start: 0.7142 (pmt) cc_final: 0.6848 (pmm) REVERT: B 80 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8255 (mt-10) REVERT: B 97 VAL cc_start: 0.8799 (t) cc_final: 0.8574 (t) REVERT: B 106 VAL cc_start: 0.8541 (t) cc_final: 0.8317 (p) REVERT: B 176 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7981 (mp0) REVERT: B 183 ILE cc_start: 0.7977 (OUTLIER) cc_final: 0.7285 (mm) REVERT: B 235 VAL cc_start: 0.7909 (t) cc_final: 0.7603 (m) REVERT: B 252 ASN cc_start: 0.6490 (t0) cc_final: 0.6118 (t0) REVERT: B 262 LYS cc_start: 0.8342 (tptp) cc_final: 0.7816 (mttt) REVERT: B 328 TYR cc_start: 0.6103 (m-10) cc_final: 0.5805 (m-10) REVERT: B 332 LEU cc_start: 0.6211 (tp) cc_final: 0.5993 (mt) REVERT: B 435 MET cc_start: 0.6695 (mmt) cc_final: 0.6441 (mmt) REVERT: B 450 GLU cc_start: 0.6692 (pt0) cc_final: 0.6366 (pt0) REVERT: B 527 PRO cc_start: 0.8627 (Cg_exo) cc_final: 0.8212 (Cg_endo) REVERT: B 550 ASP cc_start: 0.7753 (t0) cc_final: 0.6641 (p0) REVERT: B 588 GLU cc_start: 0.7042 (pt0) cc_final: 0.6836 (pt0) REVERT: B 590 ASP cc_start: 0.6970 (m-30) cc_final: 0.6519 (t0) REVERT: B 628 ARG cc_start: 0.7917 (mtm-85) cc_final: 0.7660 (mtp-110) REVERT: B 630 PHE cc_start: 0.6582 (m-80) cc_final: 0.6141 (m-80) REVERT: C 40 GLN cc_start: 0.7669 (tt0) cc_final: 0.7412 (tt0) REVERT: C 78 MET cc_start: 0.7233 (pmt) cc_final: 0.6951 (pmm) REVERT: C 80 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8118 (mt-10) REVERT: C 97 VAL cc_start: 0.8824 (t) cc_final: 0.8596 (t) REVERT: C 160 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7906 (pp) REVERT: C 176 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8041 (mp0) REVERT: C 183 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7759 (mp) REVERT: C 202 ILE cc_start: 0.8042 (mm) cc_final: 0.7798 (mm) REVERT: C 214 GLN cc_start: 0.7430 (tt0) cc_final: 0.7115 (tm-30) REVERT: C 217 ASN cc_start: 0.7381 (m-40) cc_final: 0.6998 (m-40) REVERT: C 235 VAL cc_start: 0.8006 (t) cc_final: 0.7606 (m) REVERT: C 252 ASN cc_start: 0.6847 (t0) cc_final: 0.6589 (t0) REVERT: C 262 LYS cc_start: 0.8013 (tptp) cc_final: 0.7402 (mttt) REVERT: C 331 MET cc_start: 0.6016 (tmm) cc_final: 0.5798 (tmm) REVERT: C 435 MET cc_start: 0.6241 (mmt) cc_final: 0.5944 (mmt) REVERT: C 467 TYR cc_start: 0.7290 (t80) cc_final: 0.7081 (t80) REVERT: C 474 MET cc_start: 0.6346 (mmm) cc_final: 0.5995 (ptt) REVERT: C 482 ILE cc_start: 0.6419 (mm) cc_final: 0.6081 (mt) REVERT: C 550 ASP cc_start: 0.7377 (t0) cc_final: 0.6600 (p0) REVERT: C 565 ILE cc_start: 0.7459 (tp) cc_final: 0.7019 (mm) REVERT: C 580 ASP cc_start: 0.6441 (t0) cc_final: 0.5967 (m-30) REVERT: C 583 TRP cc_start: 0.6997 (t60) cc_final: 0.6172 (t60) REVERT: C 591 GLU cc_start: 0.6536 (tt0) cc_final: 0.6220 (tp30) REVERT: C 630 PHE cc_start: 0.6519 (m-80) cc_final: 0.6299 (m-80) REVERT: D 44 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7305 (mp) REVERT: D 78 MET cc_start: 0.7339 (pmt) cc_final: 0.7104 (pmm) REVERT: D 157 CYS cc_start: 0.7881 (m) cc_final: 0.7281 (p) REVERT: D 183 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7650 (mm) REVERT: D 214 GLN cc_start: 0.7416 (tt0) cc_final: 0.7033 (tm-30) REVERT: D 252 ASN cc_start: 0.6554 (t0) cc_final: 0.6155 (t0) REVERT: D 262 LYS cc_start: 0.8305 (tptp) cc_final: 0.7648 (mttt) REVERT: D 265 HIS cc_start: 0.6581 (t70) cc_final: 0.6369 (t70) REVERT: D 328 TYR cc_start: 0.6045 (m-10) cc_final: 0.5785 (m-10) REVERT: D 384 ILE cc_start: 0.7764 (mt) cc_final: 0.7527 (mp) REVERT: D 464 ASN cc_start: 0.6722 (t160) cc_final: 0.6374 (t0) REVERT: D 487 PHE cc_start: 0.7493 (m-80) cc_final: 0.7250 (m-10) REVERT: D 550 ASP cc_start: 0.7811 (t0) cc_final: 0.7168 (p0) REVERT: D 580 ASP cc_start: 0.6471 (t0) cc_final: 0.6163 (m-30) REVERT: D 590 ASP cc_start: 0.7208 (m-30) cc_final: 0.6883 (t0) REVERT: D 634 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8279 (mm-30) outliers start: 20 outliers final: 0 residues processed: 769 average time/residue: 0.3118 time to fit residues: 354.3575 Evaluate side-chains 472 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 466 time to evaluate : 1.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 183 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 184 optimal weight: 0.0060 chunk 71 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 214 optimal weight: 1.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS B 165 HIS ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 GLN C 165 HIS C 265 HIS C 267 GLN C 464 ASN C 522 HIS ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 GLN D 165 HIS ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN D 522 HIS D 548 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.157986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.127840 restraints weight = 28520.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.130961 restraints weight = 15163.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132890 restraints weight = 10347.674| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19484 Z= 0.165 Angle : 0.757 12.158 26440 Z= 0.380 Chirality : 0.043 0.208 3012 Planarity : 0.005 0.043 3336 Dihedral : 6.079 38.616 2608 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.51 % Favored : 90.32 % Rotamer: Outliers : 2.81 % Allowed : 12.55 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.16), residues: 2356 helix: -0.47 (0.13), residues: 1356 sheet: -4.36 (0.48), residues: 56 loop : -2.67 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 629 HIS 0.007 0.001 HIS B 258 PHE 0.018 0.002 PHE B 478 TYR 0.015 0.002 TYR C 526 ARG 0.005 0.001 ARG C 594 Details of bonding type rmsd hydrogen bonds : bond 0.04657 ( 884) hydrogen bonds : angle 4.45550 ( 2532) covalent geometry : bond 0.00370 (19484) covalent geometry : angle 0.75681 (26440) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 516 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ASN cc_start: 0.7802 (m-40) cc_final: 0.7470 (m-40) REVERT: A 302 ARG cc_start: 0.7354 (tpp-160) cc_final: 0.7142 (tpp-160) REVERT: A 435 MET cc_start: 0.7603 (mmt) cc_final: 0.7232 (mmt) REVERT: A 464 ASN cc_start: 0.8336 (t160) cc_final: 0.8056 (t0) REVERT: A 531 PHE cc_start: 0.8445 (t80) cc_final: 0.8075 (t80) REVERT: A 550 ASP cc_start: 0.7846 (t0) cc_final: 0.7410 (p0) REVERT: A 580 ASP cc_start: 0.7937 (t0) cc_final: 0.7594 (m-30) REVERT: A 603 MET cc_start: 0.7290 (ttm) cc_final: 0.7062 (ttm) REVERT: B 435 MET cc_start: 0.7318 (mmt) cc_final: 0.6882 (mmt) REVERT: B 502 LEU cc_start: 0.8963 (mm) cc_final: 0.8609 (mt) REVERT: B 528 MET cc_start: 0.8273 (tmm) cc_final: 0.7875 (tmm) REVERT: B 570 MET cc_start: 0.7856 (mtt) cc_final: 0.7637 (mtp) REVERT: B 580 ASP cc_start: 0.7853 (t0) cc_final: 0.7614 (m-30) REVERT: C 250 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7082 (tm-30) REVERT: C 467 TYR cc_start: 0.8536 (t80) cc_final: 0.8283 (t80) REVERT: C 540 ILE cc_start: 0.8397 (mm) cc_final: 0.8168 (mt) REVERT: C 565 ILE cc_start: 0.9186 (tp) cc_final: 0.8696 (mm) REVERT: C 580 ASP cc_start: 0.8049 (t0) cc_final: 0.7578 (m-30) REVERT: D 158 ASN cc_start: 0.7899 (m-40) cc_final: 0.7557 (m-40) REVERT: D 244 PHE cc_start: 0.8516 (t80) cc_final: 0.8309 (t80) outliers start: 58 outliers final: 30 residues processed: 557 average time/residue: 0.2761 time to fit residues: 239.5927 Evaluate side-chains 411 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 381 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 24 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 194 optimal weight: 0.4980 chunk 128 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 37 optimal weight: 0.4980 chunk 203 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 154 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 267 GLN A 546 ASN B 118 GLN ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN B 522 HIS ** B 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118839 restraints weight = 28594.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.121684 restraints weight = 16052.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.123524 restraints weight = 11224.557| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 19484 Z= 0.223 Angle : 0.792 12.697 26440 Z= 0.390 Chirality : 0.045 0.213 3012 Planarity : 0.005 0.051 3336 Dihedral : 5.464 28.331 2596 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.47 % Favored : 90.41 % Rotamer: Outliers : 4.75 % Allowed : 15.36 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.17), residues: 2356 helix: 0.12 (0.14), residues: 1376 sheet: -3.92 (0.51), residues: 56 loop : -2.80 (0.20), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 321 HIS 0.017 0.001 HIS C 265 PHE 0.018 0.002 PHE B 478 TYR 0.022 0.002 TYR B 324 ARG 0.004 0.001 ARG A 323 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 884) hydrogen bonds : angle 4.33176 ( 2532) covalent geometry : bond 0.00524 (19484) covalent geometry : angle 0.79245 (26440) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 430 time to evaluate : 2.033 Fit side-chains revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7231 (mm-30) REVERT: A 90 ASP cc_start: 0.6314 (t0) cc_final: 0.6107 (t0) REVERT: A 158 ASN cc_start: 0.7917 (m-40) cc_final: 0.7715 (m-40) REVERT: A 182 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8615 (mp) REVERT: A 202 ILE cc_start: 0.9153 (mm) cc_final: 0.8897 (mm) REVERT: A 345 MET cc_start: 0.8429 (mmm) cc_final: 0.8174 (mmt) REVERT: A 464 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8512 (t0) REVERT: A 550 ASP cc_start: 0.7851 (t0) cc_final: 0.7320 (p0) REVERT: A 580 ASP cc_start: 0.8117 (t0) cc_final: 0.7520 (m-30) REVERT: B 96 MET cc_start: 0.7820 (mmm) cc_final: 0.7512 (mmm) REVERT: B 435 MET cc_start: 0.7757 (mmt) cc_final: 0.7353 (mmt) REVERT: B 464 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8263 (t0) REVERT: B 502 LEU cc_start: 0.8954 (mm) cc_final: 0.8664 (mt) REVERT: B 528 MET cc_start: 0.8174 (tmm) cc_final: 0.7797 (tmm) REVERT: B 540 ILE cc_start: 0.8910 (mm) cc_final: 0.8604 (mt) REVERT: B 550 ASP cc_start: 0.7741 (t0) cc_final: 0.7083 (p0) REVERT: B 580 ASP cc_start: 0.7972 (t0) cc_final: 0.7477 (m-30) REVERT: C 80 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6947 (mp0) REVERT: C 345 MET cc_start: 0.7889 (mmm) cc_final: 0.7602 (mmt) REVERT: C 565 ILE cc_start: 0.9349 (tp) cc_final: 0.8854 (mm) REVERT: C 580 ASP cc_start: 0.8048 (t0) cc_final: 0.7451 (m-30) REVERT: D 118 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7077 (tt0) REVERT: D 158 ASN cc_start: 0.7845 (m-40) cc_final: 0.7615 (m-40) outliers start: 98 outliers final: 53 residues processed: 486 average time/residue: 0.2713 time to fit residues: 208.0016 Evaluate side-chains 418 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 361 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 297 ILE Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain B residue 538 LEU Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 451 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 604 LEU Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 297 ILE Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 378 MET Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 79 optimal weight: 3.9990 chunk 191 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 158 optimal weight: 0.0070 chunk 138 optimal weight: 0.3980 chunk 104 optimal weight: 0.8980 chunk 175 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 126 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN A 265 HIS B 265 HIS B 267 GLN B 464 ASN B 546 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 357 ASN C 548 ASN ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 GLN D 464 ASN D 546 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.153788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.124723 restraints weight = 28333.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.127668 restraints weight = 15598.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129509 restraints weight = 10763.151| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.4962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19484 Z= 0.126 Angle : 0.691 11.903 26440 Z= 0.339 Chirality : 0.041 0.198 3012 Planarity : 0.004 0.047 3336 Dihedral : 5.149 29.858 2596 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 4.17 % Allowed : 17.20 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.18), residues: 2356 helix: 0.51 (0.14), residues: 1372 sheet: -3.57 (0.55), residues: 56 loop : -2.59 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 321 HIS 0.004 0.001 HIS A 582 PHE 0.017 0.001 PHE B 244 TYR 0.026 0.001 TYR D 324 ARG 0.004 0.000 ARG B 140 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 884) hydrogen bonds : angle 3.95259 ( 2532) covalent geometry : bond 0.00269 (19484) covalent geometry : angle 0.69090 (26440) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 422 time to evaluate : 2.126 Fit side-chains REVERT: A 80 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7283 (mm-30) REVERT: A 83 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8354 (tt) REVERT: A 96 MET cc_start: 0.7459 (mmm) cc_final: 0.7204 (mmm) REVERT: A 158 ASN cc_start: 0.7783 (m-40) cc_final: 0.7533 (m-40) REVERT: A 352 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7227 (tp) REVERT: A 464 ASN cc_start: 0.8546 (OUTLIER) cc_final: 0.8345 (t0) REVERT: A 550 ASP cc_start: 0.7855 (t0) cc_final: 0.7260 (p0) REVERT: B 96 MET cc_start: 0.7822 (mmm) cc_final: 0.7547 (mmm) REVERT: B 100 GLU cc_start: 0.7297 (mp0) cc_final: 0.7095 (pm20) REVERT: B 118 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6723 (tt0) REVERT: B 435 MET cc_start: 0.7572 (mmt) cc_final: 0.7251 (mmt) REVERT: B 464 ASN cc_start: 0.8105 (OUTLIER) cc_final: 0.7813 (t0) REVERT: B 502 LEU cc_start: 0.8884 (mm) cc_final: 0.8672 (mt) REVERT: B 528 MET cc_start: 0.8120 (tmm) cc_final: 0.7809 (tmm) REVERT: B 540 ILE cc_start: 0.8886 (mm) cc_final: 0.8637 (mt) REVERT: B 550 ASP cc_start: 0.7717 (t0) cc_final: 0.7160 (p0) REVERT: B 580 ASP cc_start: 0.7843 (t0) cc_final: 0.7422 (m-30) REVERT: C 80 GLU cc_start: 0.6840 (mt-10) cc_final: 0.6603 (mt-10) REVERT: C 96 MET cc_start: 0.7686 (mmm) cc_final: 0.7319 (mmm) REVERT: C 118 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6922 (tt0) REVERT: C 345 MET cc_start: 0.7786 (mmm) cc_final: 0.7572 (mmt) REVERT: C 565 ILE cc_start: 0.9183 (tp) cc_final: 0.8717 (mm) REVERT: D 158 ASN cc_start: 0.7643 (m-40) cc_final: 0.7413 (m-40) outliers start: 86 outliers final: 37 residues processed: 474 average time/residue: 0.2703 time to fit residues: 202.3953 Evaluate side-chains 412 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 369 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 217 ASN Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 464 ASN Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 118 GLN Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 567 THR Chi-restraints excluded: chain C residue 631 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 549 VAL Chi-restraints excluded: chain D residue 631 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 122 optimal weight: 30.0000 chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 153 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 183 optimal weight: 6.9990 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 267 GLN A 546 ASN B 265 HIS ** B 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 464 ASN ** B 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 HIS C 464 ASN ** C 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 464 ASN ** D 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.149587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.120142 restraints weight = 28555.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.123061 restraints weight = 15837.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.124785 restraints weight = 10995.029| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19484 Z= 0.164 Angle : 0.713 12.674 26440 Z= 0.350 Chirality : 0.042 0.224 3012 Planarity : 0.004 0.051 3336 Dihedral : 5.035 28.536 2596 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 4.89 % Allowed : 17.39 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.18), residues: 2356 helix: 0.74 (0.14), residues: 1368 sheet: -3.29 (0.56), residues: 56 loop : -2.46 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 462 HIS 0.006 0.001 HIS A 265 PHE 0.016 0.002 PHE B 244 TYR 0.024 0.002 TYR D 324 ARG 0.005 0.000 ARG D 305 Details of bonding type rmsd hydrogen bonds : bond 0.03555 ( 884) hydrogen bonds : angle 3.95036 ( 2532) covalent geometry : bond 0.00381 (19484) covalent geometry : angle 0.71264 (26440) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4712 Ramachandran restraints generated. 2356 Oldfield, 0 Emsley, 2356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 370 time to evaluate : 1.974 Fit side-chains REVERT: A 96 MET cc_start: 0.7466 (mmm) cc_final: 0.7178 (mmm) REVERT: A 158 ASN cc_start: 0.7751 (m-40) cc_final: 0.7493 (m-40) REVERT: A 345 MET cc_start: 0.8245 (mmm) cc_final: 0.8002 (mmp) REVERT: A 550 ASP cc_start: 0.7882 (t0) cc_final: 0.7401 (p0) REVERT: B 96 MET cc_start: 0.7804 (mmm) cc_final: 0.7481 (mmm) REVERT: B 345 MET cc_start: 0.8449 (mmm) cc_final: 0.8201 (mmm) REVERT: B 435 MET cc_start: 0.7682 (mmt) cc_final: 0.7415 (mmt) REVERT: B 540 ILE cc_start: 0.8955 (mm) cc_final: 0.8729 (mt) REVERT: B 550 ASP cc_start: 0.7750 (t0) cc_final: 0.7243 (p0) REVERT: B 580 ASP cc_start: 0.7824 (t0) cc_final: 0.7432 (m-30) REVERT: C 78 MET cc_start: 0.6762 (pmm) cc_final: 0.6547 (pmm) REVERT: C 80 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6724 (mt-10) REVERT: C 96 MET cc_start: 0.7596 (mmm) cc_final: 0.7270 (mmm) REVERT: C 345 MET cc_start: 0.7871 (mmm) cc_final: 0.7657 (mmt) REVERT: C 565 ILE cc_start: 0.9263 (tp) cc_final: 0.8836 (mm) REVERT: C 580 ASP cc_start: 0.8224 (t0) cc_final: 0.7163 (m-30) REVERT: D 54 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7822 (ttpt) REVERT: D 61 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8201 (mp) REVERT: D 118 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: D 158 ASN cc_start: 0.7726 (m-40) cc_final: 0.7495 (m-40) outliers start: 101 outliers final: 62 residues processed: 433 average time/residue: 0.2613 time to fit residues: 179.0945 Evaluate side-chains 404 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 338 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 265 HIS Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 CYS Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 378 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 455 SER Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 631 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 265 HIS Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 455 SER Chi-restraints excluded: chain B residue 470 ARG Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 631 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 80 GLU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 265 HIS Chi-restraints excluded: chain C residue 276 THR Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 378 MET Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 514 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 61 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 118 GLN Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 284 ASP Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 330 CYS Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 346 CYS Chi-restraints excluded: chain D residue 397 ILE Chi-restraints excluded: chain D residue 441 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 470 ARG Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 538 LEU Chi-restraints excluded: chain D residue 539 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.2776 > 50: distance: 23 - 24: 15.866 distance: 24 - 25: 15.266 distance: 24 - 27: 12.220 distance: 25 - 26: 17.175 distance: 25 - 29: 22.902 distance: 27 - 28: 15.927 distance: 29 - 30: 27.305 distance: 30 - 31: 27.745 distance: 30 - 33: 12.435 distance: 31 - 32: 38.690 distance: 31 - 43: 26.788 distance: 33 - 34: 15.636 distance: 34 - 35: 26.491 distance: 34 - 36: 24.930 distance: 35 - 37: 4.750 distance: 36 - 38: 47.445 distance: 36 - 39: 16.729 distance: 37 - 38: 48.605 distance: 38 - 40: 34.407 distance: 39 - 41: 16.757 distance: 40 - 42: 18.229 distance: 41 - 42: 10.077 distance: 43 - 44: 11.821 distance: 44 - 45: 28.794 distance: 44 - 47: 28.611 distance: 45 - 46: 39.311 distance: 45 - 48: 18.345 distance: 46 - 74: 21.063 distance: 48 - 49: 15.457 distance: 49 - 50: 9.487 distance: 49 - 52: 21.494 distance: 50 - 51: 18.269 distance: 50 - 57: 10.879 distance: 51 - 82: 20.709 distance: 52 - 53: 36.675 distance: 53 - 54: 12.860 distance: 54 - 55: 27.468 distance: 54 - 56: 21.335 distance: 57 - 58: 13.438 distance: 58 - 59: 23.141 distance: 58 - 61: 17.460 distance: 59 - 60: 11.726 distance: 59 - 63: 23.565 distance: 60 - 91: 12.530 distance: 61 - 62: 23.896 distance: 63 - 64: 13.023 distance: 64 - 65: 10.852 distance: 64 - 67: 18.908 distance: 65 - 66: 17.236 distance: 65 - 74: 19.194 distance: 66 - 100: 18.205 distance: 67 - 68: 17.498 distance: 68 - 69: 8.525 distance: 69 - 70: 18.258 distance: 70 - 71: 24.619 distance: 71 - 72: 24.815 distance: 71 - 73: 13.241 distance: 74 - 75: 9.118 distance: 75 - 76: 3.386 distance: 75 - 78: 22.210 distance: 76 - 77: 14.687 distance: 76 - 82: 13.094 distance: 77 - 106: 14.091 distance: 78 - 79: 37.436 distance: 79 - 80: 22.677 distance: 79 - 81: 22.224 distance: 82 - 83: 4.740 distance: 83 - 84: 5.703 distance: 83 - 86: 11.597 distance: 84 - 91: 10.401 distance: 85 - 114: 5.097 distance: 86 - 87: 23.591 distance: 87 - 88: 9.148 distance: 88 - 89: 18.482 distance: 88 - 90: 21.340 distance: 91 - 92: 7.266 distance: 92 - 93: 17.704 distance: 92 - 95: 7.538 distance: 93 - 94: 28.543 distance: 93 - 100: 13.680 distance: 95 - 96: 7.775 distance: 96 - 97: 16.451 distance: 97 - 98: 11.724 distance: 97 - 99: 16.525