Starting phenix.real_space_refine on Thu Aug 6 18:14:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9shm_54904/08_2026/9shm_54904_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9shm_54904/08_2026/9shm_54904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9shm_54904/08_2026/9shm_54904_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9shm_54904/08_2026/9shm_54904_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9shm_54904/08_2026/9shm_54904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9shm_54904/08_2026/9shm_54904.map" } resolution = 2.0 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= 0.001 sd= 0.038 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 2 5.49 5 S 44 5.16 5 C 5060 2.51 5 N 1386 2.21 5 O 1494 1.98 5 H 7972 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15960 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 7916 Classifications: {'peptide': 507} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 481} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'HEM': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Restraints were copied for chains: B Time building chain proxies: 7.07, per 1000 atoms: 0.44 Number of scatterers: 15960 At special positions: 0 Unit cell: (96.728, 100.344, 87.688, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 44 16.00 P 2 15.00 O 1494 8.00 N 1386 7.00 C 5060 6.00 H 7972 1.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 431.6 milliseconds 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 8 sheets defined 47.3% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.508A pdb=" N GLU A 62 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 118 through 133 removed outlier: 4.182A pdb=" N ILE A 122 " --> pdb=" O VAL A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.531A pdb=" N VAL A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 226 through 235 removed outlier: 3.793A pdb=" N HIS A 232 " --> pdb=" O ASN A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 244 Processing helix chain 'A' and resid 258 through 272 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 316 through 320 Processing helix chain 'A' and resid 327 through 343 Processing helix chain 'A' and resid 347 through 361 removed outlier: 3.888A pdb=" N LYS A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.824A pdb=" N ASN A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N MET A 382 " --> pdb=" O ARG A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 394 Processing helix chain 'A' and resid 398 through 405 removed outlier: 4.123A pdb=" N LYS A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 412 removed outlier: 6.149A pdb=" N TRP A 409 " --> pdb=" O LYS A 406 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS A 411 " --> pdb=" O TRP A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 417 removed outlier: 3.524A pdb=" N GLU A 416 " --> pdb=" O ARG A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 Processing helix chain 'A' and resid 461 through 470 Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.852A pdb=" N LYS A 481 " --> pdb=" O GLN A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 535 through 547 Processing helix chain 'B' and resid 59 through 63 removed outlier: 3.507A pdb=" N GLU B 62 " --> pdb=" O PRO B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 83 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 111 through 113 No H-bonds generated for 'chain 'B' and resid 111 through 113' Processing helix chain 'B' and resid 118 through 133 removed outlier: 4.182A pdb=" N ILE B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 162 Processing helix chain 'B' and resid 174 through 185 removed outlier: 3.531A pdb=" N VAL B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 226 through 235 removed outlier: 3.792A pdb=" N HIS B 232 " --> pdb=" O ASN B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 244 Processing helix chain 'B' and resid 258 through 272 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 316 through 320 Processing helix chain 'B' and resid 327 through 343 Processing helix chain 'B' and resid 347 through 361 removed outlier: 3.889A pdb=" N LYS B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 364 No H-bonds generated for 'chain 'B' and resid 362 through 364' Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.823A pdb=" N ASN B 380 " --> pdb=" O SER B 377 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET B 382 " --> pdb=" O ARG B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 394 Processing helix chain 'B' and resid 398 through 405 removed outlier: 4.124A pdb=" N LYS B 405 " --> pdb=" O ASP B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 removed outlier: 6.149A pdb=" N TRP B 409 " --> pdb=" O LYS B 406 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N HIS B 411 " --> pdb=" O TRP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 417 removed outlier: 3.525A pdb=" N GLU B 416 " --> pdb=" O ARG B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 442 Processing helix chain 'B' and resid 461 through 470 Processing helix chain 'B' and resid 478 through 482 removed outlier: 3.852A pdb=" N LYS B 481 " --> pdb=" O GLN B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 535 through 547 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 77 removed outlier: 7.478A pdb=" N LEU A 77 " --> pdb=" O ARG B 91 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU B 105 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER B 254 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU B 251 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL B 280 " --> pdb=" O LEU B 251 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA B 253 " --> pdb=" O VAL B 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 326 removed outlier: 6.327A pdb=" N LEU A 251 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL A 280 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA A 253 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER A 254 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU A 105 " --> pdb=" O ILE A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 191 removed outlier: 6.556A pdb=" N CYS A 165 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL A 189 " --> pdb=" O CYS A 165 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE A 167 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR A 191 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N MET A 169 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE A 142 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 168 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU A 144 " --> pdb=" O VAL A 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 445 through 449 Processing sheet with id=AA5, first strand: chain 'A' and resid 488 through 490 removed outlier: 6.327A pdb=" N LYS A 488 " --> pdb=" O LEU A 510 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL A 512 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ILE A 490 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N GLU A 514 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 532 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N HIS A 513 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL A 530 " --> pdb=" O HIS A 513 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLN A 515 " --> pdb=" O GLN A 528 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLN A 528 " --> pdb=" O GLN A 515 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN A 517 " --> pdb=" O GLN A 526 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLN A 526 " --> pdb=" O GLN A 517 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 6.556A pdb=" N CYS B 165 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N VAL B 189 " --> pdb=" O CYS B 165 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE B 167 " --> pdb=" O VAL B 189 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR B 191 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N MET B 169 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ILE B 142 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL B 168 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU B 144 " --> pdb=" O VAL B 168 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 445 through 449 Processing sheet with id=AA8, first strand: chain 'B' and resid 488 through 490 removed outlier: 6.326A pdb=" N LYS B 488 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL B 512 " --> pdb=" O LYS B 488 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N ILE B 490 " --> pdb=" O VAL B 512 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLU B 514 " --> pdb=" O ILE B 490 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 532 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N HIS B 513 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N VAL B 530 " --> pdb=" O HIS B 513 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N GLN B 515 " --> pdb=" O GLN B 528 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLN B 528 " --> pdb=" O GLN B 515 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLN B 517 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLN B 526 " --> pdb=" O GLN B 517 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 876 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: 3.36 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.08: 7952 1.08 - 1.32: 1381 1.32 - 1.56: 6713 1.56 - 1.80: 53 1.80 - 2.05: 25 Bond restraints: 16124 Sorted by residual: bond pdb=" CA P1T B 602 " pdb=" C P1T B 602 " ideal model delta sigma weight residual 1.537 1.397 0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" CA P1T A 602 " pdb=" C P1T A 602 " ideal model delta sigma weight residual 1.537 1.397 0.140 2.00e-02 2.50e+03 4.93e+01 bond pdb=" OP4 P1T A 602 " pdb=" P P1T A 602 " ideal model delta sigma weight residual 1.722 1.603 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" OP4 P1T B 602 " pdb=" P P1T B 602 " ideal model delta sigma weight residual 1.722 1.603 0.119 2.00e-02 2.50e+03 3.54e+01 bond pdb=" C P1T A 602 " pdb=" O P1T A 602 " ideal model delta sigma weight residual 1.241 1.153 0.088 2.00e-02 2.50e+03 1.93e+01 ... (remaining 16119 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 29072 1.94 - 3.88: 161 3.88 - 5.82: 19 5.82 - 7.76: 4 7.76 - 9.70: 4 Bond angle restraints: 29260 Sorted by residual: angle pdb=" O P1T B 602 " pdb=" C P1T B 602 " pdb=" OXT P1T B 602 " ideal model delta sigma weight residual 127.38 117.68 9.70 3.00e+00 1.11e-01 1.04e+01 angle pdb=" O P1T A 602 " pdb=" C P1T A 602 " pdb=" OXT P1T A 602 " ideal model delta sigma weight residual 127.38 117.74 9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" CA P1T B 602 " pdb=" N P1T B 602 " pdb=" C4A P1T B 602 " ideal model delta sigma weight residual 120.29 127.81 -7.52 3.00e+00 1.11e-01 6.29e+00 angle pdb=" CA P1T A 602 " pdb=" N P1T A 602 " pdb=" C4A P1T A 602 " ideal model delta sigma weight residual 120.29 127.73 -7.44 3.00e+00 1.11e-01 6.15e+00 angle pdb=" CA P1T B 602 " pdb=" C P1T B 602 " pdb=" O P1T B 602 " ideal model delta sigma weight residual 117.37 123.37 -6.00 3.00e+00 1.11e-01 4.00e+00 ... (remaining 29255 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 6804 17.46 - 34.92: 518 34.92 - 52.38: 104 52.38 - 69.84: 58 69.84 - 87.29: 8 Dihedral angle restraints: 7492 sinusoidal: 4214 harmonic: 3278 Sorted by residual: dihedral pdb=" C P1T B 602 " pdb=" N P1T B 602 " pdb=" CA P1T B 602 " pdb=" CB P1T B 602 " ideal model delta harmonic sigma weight residual -122.60 -178.17 55.57 0 2.50e+00 1.60e-01 4.94e+02 dihedral pdb=" C P1T A 602 " pdb=" N P1T A 602 " pdb=" CA P1T A 602 " pdb=" CB P1T A 602 " ideal model delta harmonic sigma weight residual -122.60 -178.08 55.48 0 2.50e+00 1.60e-01 4.92e+02 dihedral pdb=" N P1T B 602 " pdb=" C P1T B 602 " pdb=" CA P1T B 602 " pdb=" CB P1T B 602 " ideal model delta harmonic sigma weight residual 122.80 178.12 -55.32 0 2.50e+00 1.60e-01 4.90e+02 ... (remaining 7489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 742 0.030 - 0.059: 349 0.059 - 0.089: 58 0.089 - 0.118: 64 0.118 - 0.148: 27 Chirality restraints: 1240 Sorted by residual: chirality pdb=" CA VAL B 449 " pdb=" N VAL B 449 " pdb=" C VAL B 449 " pdb=" CB VAL B 449 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA VAL A 449 " pdb=" N VAL A 449 " pdb=" C VAL A 449 " pdb=" CB VAL A 449 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA VAL A 533 " pdb=" N VAL A 533 " pdb=" C VAL A 533 " pdb=" CB VAL A 533 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.58e-01 ... (remaining 1237 not shown) Planarity restraints: 2378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 123 " 0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C SER A 123 " -0.028 2.00e-02 2.50e+03 pdb=" O SER A 123 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 124 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 123 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C SER B 123 " 0.028 2.00e-02 2.50e+03 pdb=" O SER B 123 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU B 124 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 124 " -0.007 2.00e-02 2.50e+03 1.41e-02 1.99e+00 pdb=" C LEU B 124 " 0.024 2.00e-02 2.50e+03 pdb=" O LEU B 124 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG B 125 " -0.008 2.00e-02 2.50e+03 ... (remaining 2375 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.36: 6011 2.36 - 2.92: 37550 2.92 - 3.48: 43778 3.48 - 4.04: 61529 4.04 - 4.60: 89131 Nonbonded interactions: 237999 Sorted by model distance: nonbonded pdb=" HD2 HIS A 232 " pdb=" HG1 THR A 236 " model vdw 1.805 2.100 nonbonded pdb=" HD2 HIS B 232 " pdb=" HG1 THR B 236 " model vdw 1.806 2.100 nonbonded pdb="HD21 ASN B 228 " pdb=" HG1 THR B 257 " model vdw 1.843 2.100 nonbonded pdb="HD21 ASN A 228 " pdb=" HG1 THR A 257 " model vdw 1.844 2.100 nonbonded pdb=" HZ3 LYS A 98 " pdb="HE22 GLN A 341 " model vdw 1.907 2.100 ... (remaining 237994 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.830 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: 0.090 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.720 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 8154 Z= 0.228 Angle : 0.599 9.698 11070 Z= 0.281 Chirality : 0.042 0.148 1240 Planarity : 0.004 0.032 1416 Dihedral : 13.310 87.294 3054 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % 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: 1.40 (0.27), residues: 1010 helix: 0.88 (0.28), residues: 380 sheet: 1.30 (0.37), residues: 154 loop : 1.07 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 389 TYR 0.006 0.001 TYR B 233 PHE 0.007 0.001 PHE B 385 TRP 0.004 0.001 TRP A 323 HIS 0.008 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.23 ( 8152) covalent geometry : angle 0.59934 / 0.28 (11070) hydrogen bonds : bond 0.14517 / 10.23 ( 322) hydrogen bonds : angle 6.66358 / 4.77 ( 876) Misc. bond : bond 0.05059 / 2.54 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.328 Fit side-chains REVERT: A 247 LYS cc_start: 0.7879 (ptpp) cc_final: 0.7295 (pptt) REVERT: A 491 ARG cc_start: 0.7286 (mtm110) cc_final: 0.6926 (mmp80) REVERT: B 247 LYS cc_start: 0.7882 (ptpp) cc_final: 0.7298 (pptt) REVERT: B 491 ARG cc_start: 0.7287 (mtm110) cc_final: 0.6929 (mmp80) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 1.2753 time to fit residues: 168.2222 Evaluate side-chains 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.121614 restraints weight = 17807.236| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.15 r_work: 0.3240 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8154 Z= 0.130 Angle : 0.565 7.891 11070 Z= 0.279 Chirality : 0.043 0.149 1240 Planarity : 0.006 0.131 1416 Dihedral : 7.617 73.402 1128 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.05 % Allowed : 5.01 % Favored : 93.94 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % 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: 1.75 (0.27), residues: 1010 helix: 0.98 (0.28), residues: 386 sheet: 1.34 (0.37), residues: 154 loop : 1.53 (0.31), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 132 TYR 0.007 0.002 TYR B 223 PHE 0.009 0.001 PHE A 111 TRP 0.005 0.001 TRP A 390 HIS 0.007 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 8152) covalent geometry : angle 0.56458 / 0.28 (11070) hydrogen bonds : bond 0.04556 / 3.21 ( 322) hydrogen bonds : angle 5.28917 / 3.82 ( 876) Misc. bond : bond 0.02196 / 1.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.330 Fit side-chains REVERT: A 247 LYS cc_start: 0.7977 (ptpp) cc_final: 0.7447 (pptt) REVERT: A 436 GLU cc_start: 0.7268 (mt-10) cc_final: 0.7065 (mt-10) REVERT: A 491 ARG cc_start: 0.7470 (mtm110) cc_final: 0.7206 (mmp80) REVERT: B 247 LYS cc_start: 0.7979 (ptpp) cc_final: 0.7451 (pptt) REVERT: B 436 GLU cc_start: 0.7247 (mt-10) cc_final: 0.7041 (mt-10) REVERT: B 491 ARG cc_start: 0.7467 (mtm110) cc_final: 0.7204 (mmp80) outliers start: 9 outliers final: 2 residues processed: 129 average time/residue: 1.1330 time to fit residues: 155.1411 Evaluate side-chains 112 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 110 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain B residue 98 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 ASN B 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.152178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118412 restraints weight = 17869.651| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.16 r_work: 0.3195 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 2.18 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8154 Z= 0.153 Angle : 0.577 7.642 11070 Z= 0.289 Chirality : 0.043 0.151 1240 Planarity : 0.006 0.131 1416 Dihedral : 7.777 75.717 1128 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.93 % Allowed : 6.06 % Favored : 93.01 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % 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: 1.70 (0.27), residues: 1010 helix: 0.93 (0.27), residues: 380 sheet: 1.16 (0.36), residues: 154 loop : 1.56 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 121 TYR 0.011 0.002 TYR A 223 PHE 0.011 0.002 PHE B 99 TRP 0.006 0.001 TRP B 390 HIS 0.009 0.002 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 8152) covalent geometry : angle 0.57715 / 0.29 (11070) hydrogen bonds : bond 0.05074 / 3.61 ( 322) hydrogen bonds : angle 5.35892 / 3.87 ( 876) Misc. bond : bond 0.01904 / 0.97 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.428 Fit side-chains REVERT: A 247 LYS cc_start: 0.8091 (ptpp) cc_final: 0.7564 (pptt) REVERT: A 491 ARG cc_start: 0.7618 (mtm110) cc_final: 0.7294 (mmp80) REVERT: B 247 LYS cc_start: 0.8080 (ptpp) cc_final: 0.7551 (pptt) REVERT: B 491 ARG cc_start: 0.7621 (mtm110) cc_final: 0.7301 (mmp80) outliers start: 8 outliers final: 2 residues processed: 117 average time/residue: 1.2076 time to fit residues: 149.7096 Evaluate side-chains 113 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain B residue 98 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.0010 chunk 32 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 ASN B 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.151332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118428 restraints weight = 17839.564| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.13 r_work: 0.3194 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8154 Z= 0.153 Angle : 0.575 7.571 11070 Z= 0.290 Chirality : 0.043 0.150 1240 Planarity : 0.006 0.131 1416 Dihedral : 7.899 76.009 1128 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.93 % Allowed : 5.83 % Favored : 93.24 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % 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: 1.66 (0.27), residues: 1010 helix: 0.92 (0.27), residues: 380 sheet: 1.07 (0.36), residues: 154 loop : 1.55 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 121 TYR 0.012 0.002 TYR A 223 PHE 0.011 0.002 PHE B 99 TRP 0.006 0.001 TRP B 390 HIS 0.008 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8152) covalent geometry : angle 0.57533 / 0.29 (11070) hydrogen bonds : bond 0.04878 / 3.48 ( 322) hydrogen bonds : angle 5.29341 / 3.82 ( 876) Misc. bond : bond 0.02746 / 1.37 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 128 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8160 (ptpp) cc_final: 0.7645 (pptt) REVERT: A 460 THR cc_start: 0.8397 (m) cc_final: 0.7985 (p) REVERT: A 491 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7341 (mmp80) REVERT: B 247 LYS cc_start: 0.8159 (ptpp) cc_final: 0.7645 (pptt) REVERT: B 460 THR cc_start: 0.8405 (m) cc_final: 0.7993 (p) REVERT: B 491 ARG cc_start: 0.7687 (mtm110) cc_final: 0.7347 (mmp80) outliers start: 8 outliers final: 4 residues processed: 132 average time/residue: 0.9846 time to fit residues: 138.7125 Evaluate side-chains 124 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 436 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 42 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 ASN B 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.151236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.118517 restraints weight = 17990.603| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.13 r_work: 0.3196 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8154 Z= 0.149 Angle : 0.568 7.621 11070 Z= 0.287 Chirality : 0.043 0.149 1240 Planarity : 0.006 0.131 1416 Dihedral : 7.870 75.344 1128 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.78 % Favored : 98.02 % Rotamer: Outliers : 0.93 % Allowed : 6.53 % Favored : 92.54 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % 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: 1.67 (0.26), residues: 1010 helix: 0.98 (0.27), residues: 380 sheet: 0.95 (0.36), residues: 154 loop : 1.54 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 121 TYR 0.012 0.002 TYR A 223 PHE 0.010 0.002 PHE B 99 TRP 0.006 0.001 TRP B 390 HIS 0.008 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 8152) covalent geometry : angle 0.56815 / 0.29 (11070) hydrogen bonds : bond 0.04830 / 3.45 ( 322) hydrogen bonds : angle 5.25391 / 3.79 ( 876) Misc. bond : bond 0.02645 / 1.33 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 120 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8161 (ptpp) cc_final: 0.7655 (pptt) REVERT: A 460 THR cc_start: 0.8394 (m) cc_final: 0.7986 (p) REVERT: A 491 ARG cc_start: 0.7711 (mtm110) cc_final: 0.7355 (mmp80) REVERT: B 247 LYS cc_start: 0.8155 (ptpp) cc_final: 0.7654 (pptt) REVERT: B 460 THR cc_start: 0.8391 (m) cc_final: 0.7981 (p) REVERT: B 491 ARG cc_start: 0.7711 (mtm110) cc_final: 0.7344 (mmp80) outliers start: 8 outliers final: 6 residues processed: 122 average time/residue: 1.0354 time to fit residues: 133.9574 Evaluate side-chains 124 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 436 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 ASN B 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.116336 restraints weight = 17786.932| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.16 r_work: 0.3170 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8154 Z= 0.189 Angle : 0.615 7.722 11070 Z= 0.315 Chirality : 0.045 0.152 1240 Planarity : 0.007 0.131 1416 Dihedral : 8.042 76.506 1128 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.93 % Allowed : 6.88 % Favored : 92.19 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % 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: 1.54 (0.26), residues: 1010 helix: 0.80 (0.27), residues: 380 sheet: 0.90 (0.36), residues: 154 loop : 1.54 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 121 TYR 0.014 0.003 TYR B 223 PHE 0.015 0.002 PHE A 385 TRP 0.007 0.001 TRP B 390 HIS 0.008 0.002 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 ( 8152) covalent geometry : angle 0.61492 / 0.31 (11070) hydrogen bonds : bond 0.05414 / 3.88 ( 322) hydrogen bonds : angle 5.43428 / 3.90 ( 876) Misc. bond : bond 0.02143 / 1.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8205 (ptpp) cc_final: 0.7650 (pptt) REVERT: A 460 THR cc_start: 0.8394 (m) cc_final: 0.7986 (p) REVERT: A 491 ARG cc_start: 0.7707 (mtm110) cc_final: 0.7323 (mtp85) REVERT: B 247 LYS cc_start: 0.8201 (ptpp) cc_final: 0.7649 (pptt) REVERT: B 460 THR cc_start: 0.8403 (m) cc_final: 0.7997 (p) REVERT: B 491 ARG cc_start: 0.7706 (mtm110) cc_final: 0.7337 (mtp85) outliers start: 8 outliers final: 6 residues processed: 124 average time/residue: 1.0513 time to fit residues: 138.9559 Evaluate side-chains 126 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 436 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 85 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 91 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 0.2980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 ASN B 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.151017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.117804 restraints weight = 17805.600| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.15 r_work: 0.3189 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8154 Z= 0.154 Angle : 0.575 7.647 11070 Z= 0.291 Chirality : 0.043 0.150 1240 Planarity : 0.006 0.131 1416 Dihedral : 7.888 73.208 1128 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.98 % Favored : 97.82 % Rotamer: Outliers : 0.70 % Allowed : 7.81 % Favored : 91.49 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % 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: 1.62 (0.26), residues: 1010 helix: 0.95 (0.27), residues: 380 sheet: 0.93 (0.36), residues: 154 loop : 1.51 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 121 TYR 0.014 0.002 TYR A 223 PHE 0.010 0.002 PHE A 99 TRP 0.006 0.001 TRP B 390 HIS 0.007 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 ( 8152) covalent geometry : angle 0.57478 / 0.29 (11070) hydrogen bonds : bond 0.04902 / 3.51 ( 322) hydrogen bonds : angle 5.26763 / 3.79 ( 876) Misc. bond : bond 0.02460 / 1.24 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8189 (ptpp) cc_final: 0.7647 (pptt) REVERT: A 460 THR cc_start: 0.8389 (m) cc_final: 0.7975 (p) REVERT: A 491 ARG cc_start: 0.7710 (mtm110) cc_final: 0.7324 (mtp85) REVERT: B 247 LYS cc_start: 0.8186 (ptpp) cc_final: 0.7646 (pptt) REVERT: B 460 THR cc_start: 0.8398 (m) cc_final: 0.7983 (p) REVERT: B 491 ARG cc_start: 0.7714 (mtm110) cc_final: 0.7329 (mtp85) outliers start: 6 outliers final: 6 residues processed: 121 average time/residue: 1.2575 time to fit residues: 162.1331 Evaluate side-chains 122 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 436 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 ASN B 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.119097 restraints weight = 18051.754| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.13 r_work: 0.3209 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8154 Z= 0.131 Angle : 0.552 7.509 11070 Z= 0.277 Chirality : 0.043 0.147 1240 Planarity : 0.006 0.131 1416 Dihedral : 7.763 71.856 1128 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.18 % Favored : 97.62 % Rotamer: Outliers : 0.70 % Allowed : 8.28 % Favored : 91.03 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % 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: 1.73 (0.26), residues: 1010 helix: 1.13 (0.27), residues: 380 sheet: 0.96 (0.36), residues: 154 loop : 1.50 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 413 TYR 0.012 0.002 TYR A 223 PHE 0.009 0.001 PHE A 111 TRP 0.005 0.001 TRP B 390 HIS 0.006 0.001 HIS A 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 8152) covalent geometry : angle 0.55213 / 0.28 (11070) hydrogen bonds : bond 0.04562 / 3.25 ( 322) hydrogen bonds : angle 5.12347 / 3.69 ( 876) Misc. bond : bond 0.03226 / 1.62 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8182 (ptpp) cc_final: 0.7686 (pptt) REVERT: A 460 THR cc_start: 0.8419 (m) cc_final: 0.8006 (p) REVERT: A 491 ARG cc_start: 0.7730 (mtm110) cc_final: 0.7366 (mtp85) REVERT: B 247 LYS cc_start: 0.8181 (ptpp) cc_final: 0.7685 (pptt) REVERT: B 460 THR cc_start: 0.8430 (m) cc_final: 0.8016 (p) REVERT: B 491 ARG cc_start: 0.7730 (mtm110) cc_final: 0.7369 (mtp85) outliers start: 6 outliers final: 6 residues processed: 124 average time/residue: 1.2230 time to fit residues: 161.2752 Evaluate side-chains 124 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 436 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 ASN B 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.151489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.118280 restraints weight = 17839.567| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.15 r_work: 0.3195 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8154 Z= 0.146 Angle : 0.570 7.560 11070 Z= 0.288 Chirality : 0.043 0.148 1240 Planarity : 0.007 0.131 1416 Dihedral : 7.819 73.853 1128 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.98 % Favored : 97.82 % Rotamer: Outliers : 0.70 % Allowed : 8.51 % Favored : 90.79 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % 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: 1.73 (0.27), residues: 1010 helix: 1.11 (0.27), residues: 380 sheet: 0.96 (0.36), residues: 154 loop : 1.52 (0.30), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 413 TYR 0.013 0.002 TYR A 223 PHE 0.010 0.002 PHE A 99 TRP 0.006 0.001 TRP B 390 HIS 0.007 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 8152) covalent geometry : angle 0.56961 / 0.29 (11070) hydrogen bonds : bond 0.04806 / 3.43 ( 322) hydrogen bonds : angle 5.18394 / 3.73 ( 876) Misc. bond : bond 0.02556 / 1.29 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8197 (ptpp) cc_final: 0.7671 (pptt) REVERT: A 460 THR cc_start: 0.8444 (m) cc_final: 0.8054 (p) REVERT: A 491 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7397 (mtp85) REVERT: B 247 LYS cc_start: 0.8193 (ptpp) cc_final: 0.7669 (pptt) REVERT: B 460 THR cc_start: 0.8450 (m) cc_final: 0.8054 (p) REVERT: B 491 ARG cc_start: 0.7763 (mtm110) cc_final: 0.7405 (mtp85) outliers start: 6 outliers final: 6 residues processed: 122 average time/residue: 1.1211 time to fit residues: 145.6886 Evaluate side-chains 124 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain A residue 436 GLU Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 366 GLU Chi-restraints excluded: chain B residue 436 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.0060 chunk 32 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 0.0060 chunk 88 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 9 optimal weight: 0.0770 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 51 optimal weight: 0.2980 overall best weight: 0.2170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 ASN B 541 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.155777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124336 restraints weight = 18240.264| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.12 r_work: 0.3278 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8154 Z= 0.097 Angle : 0.513 8.087 11070 Z= 0.253 Chirality : 0.042 0.141 1240 Planarity : 0.006 0.132 1416 Dihedral : 7.448 71.787 1128 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.98 % Favored : 97.82 % Rotamer: Outliers : 0.47 % Allowed : 8.86 % Favored : 90.68 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % 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: 2.05 (0.27), residues: 1010 helix: 1.50 (0.28), residues: 382 sheet: 0.97 (0.37), residues: 150 loop : 1.63 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 413 TYR 0.007 0.001 TYR B 233 PHE 0.009 0.001 PHE A 111 TRP 0.004 0.001 TRP B 323 HIS 0.004 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 ( 8152) covalent geometry : angle 0.51346 / 0.25 (11070) hydrogen bonds : bond 0.03594 / 2.52 ( 322) hydrogen bonds : angle 4.76925 / 3.45 ( 876) Misc. bond : bond 0.06267 / 3.14 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LYS cc_start: 0.8115 (ptpp) cc_final: 0.7614 (pptt) REVERT: A 460 THR cc_start: 0.8459 (m) cc_final: 0.8123 (p) REVERT: A 491 ARG cc_start: 0.7733 (mtm110) cc_final: 0.7368 (mmp80) REVERT: B 247 LYS cc_start: 0.8115 (ptpp) cc_final: 0.7611 (pptt) REVERT: B 460 THR cc_start: 0.8467 (m) cc_final: 0.8127 (p) REVERT: B 491 ARG cc_start: 0.7736 (mtm110) cc_final: 0.7383 (mmp80) outliers start: 4 outliers final: 2 residues processed: 124 average time/residue: 1.2466 time to fit residues: 164.2198 Evaluate side-chains 118 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 GLU Chi-restraints excluded: chain B residue 366 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.151505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.118244 restraints weight = 17765.705| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.14 r_work: 0.3196 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8154 Z= 0.153 Angle : 0.575 7.756 11070 Z= 0.291 Chirality : 0.043 0.149 1240 Planarity : 0.007 0.131 1416 Dihedral : 7.769 75.982 1128 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % 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: 1.86 (0.27), residues: 1010 helix: 1.29 (0.28), residues: 380 sheet: 0.86 (0.36), residues: 150 loop : 1.59 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 413 TYR 0.012 0.002 TYR B 223 PHE 0.011 0.002 PHE B 99 TRP 0.007 0.001 TRP A 390 HIS 0.007 0.001 HIS B 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 ( 8152) covalent geometry : angle 0.57520 / 0.29 (11070) hydrogen bonds : bond 0.04836 / 3.45 ( 322) hydrogen bonds : angle 5.14339 / 3.70 ( 876) Misc. bond : bond 0.02482 / 1.24 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6380.40 seconds wall clock time: 108 minutes 24.33 seconds (6504.33 seconds total)