Starting phenix.real_space_refine on Fri Jul 3 02:49:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ps8_71826/07_2026/9ps8_71826.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ps8_71826/07_2026/9ps8_71826.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ps8_71826/07_2026/9ps8_71826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ps8_71826/07_2026/9ps8_71826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ps8_71826/07_2026/9ps8_71826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ps8_71826/07_2026/9ps8_71826.map" } resolution = 2.97 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= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 54 5.16 5 C 7545 2.51 5 N 1809 2.21 5 O 1914 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11325 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3774 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 21, 'TRANS': 466} Chain breaks: 1 Chain: "B" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3774 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 21, 'TRANS': 466} Chain breaks: 1 Chain: "C" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3774 Classifications: {'peptide': 488} Link IDs: {'PTRANS': 21, 'TRANS': 466} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' CA': 1} Chain breaks: 1 Time building chain proxies: 2.79, per 1000 atoms: 0.25 Number of scatterers: 11325 At special positions: 0 Unit cell: (130.38, 122.18, 82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 54 16.00 O 1914 8.00 N 1809 7.00 C 7545 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 74 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.03 Conformation dependent library (CDL) restraints added in 538.2 milliseconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 9 sheets defined 85.0% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 54 through 59 removed outlier: 4.181A pdb=" N SER A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 71 removed outlier: 4.700A pdb=" N CYS A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 75 Processing helix chain 'A' and resid 83 through 89 Processing helix chain 'A' and resid 95 through 121 removed outlier: 3.612A pdb=" N LEU A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'A' and resid 136 through 162 removed outlier: 4.251A pdb=" N LEU A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ALA A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Proline residue: A 152 - end of helix Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 193 removed outlier: 3.746A pdb=" N ILE A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 185 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ALA A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 223 Processing helix chain 'A' and resid 227 through 254 Processing helix chain 'A' and resid 301 through 310 Processing helix chain 'A' and resid 313 through 320 removed outlier: 3.502A pdb=" N THR A 319 " --> pdb=" O ARG A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 342 Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 355 through 374 removed outlier: 3.736A pdb=" N VAL A 364 " --> pdb=" O CYS A 360 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 390 through 409 Processing helix chain 'A' and resid 417 through 452 removed outlier: 4.036A pdb=" N PHE A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA A 422 " --> pdb=" O HIS A 418 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 423 " --> pdb=" O TRP A 419 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 424 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA A 436 " --> pdb=" O TRP A 432 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 482 removed outlier: 4.609A pdb=" N LEU A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N LEU A 463 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLY A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP A 471 " --> pdb=" O ASN A 467 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 515 removed outlier: 3.515A pdb=" N ALA A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 492 " --> pdb=" O PHE A 488 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ILE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 549 Proline residue: A 547 - end of helix Processing helix chain 'A' and resid 554 through 577 removed outlier: 3.927A pdb=" N GLY A 558 " --> pdb=" O SER A 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 72 through 75 Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 95 through 121 removed outlier: 3.561A pdb=" N ALA B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 133 removed outlier: 3.576A pdb=" N ASN B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 163 removed outlier: 4.262A pdb=" N LEU B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Proline residue: B 152 - end of helix removed outlier: 4.104A pdb=" N ASP B 163 " --> pdb=" O VAL B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 193 removed outlier: 3.613A pdb=" N VAL B 185 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 223 Processing helix chain 'B' and resid 227 through 254 Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 313 through 319 removed outlier: 3.663A pdb=" N THR B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 342 Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 355 through 374 removed outlier: 3.583A pdb=" N VAL B 364 " --> pdb=" O CYS B 360 " (cutoff:3.500A) Proline residue: B 367 - end of helix Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 390 through 409 Processing helix chain 'B' and resid 417 through 452 removed outlier: 4.030A pdb=" N PHE B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 422 " --> pdb=" O HIS B 418 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 423 " --> pdb=" O TRP B 419 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER B 429 " --> pdb=" O GLY B 425 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA B 436 " --> pdb=" O TRP B 432 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER B 446 " --> pdb=" O ASN B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 482 removed outlier: 4.065A pdb=" N LEU B 458 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LEU B 460 " --> pdb=" O THR B 456 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N LEU B 463 " --> pdb=" O GLY B 459 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLY B 470 " --> pdb=" O GLY B 466 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ASP B 471 " --> pdb=" O ASN B 467 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 515 removed outlier: 3.643A pdb=" N ALA B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHE B 492 " --> pdb=" O PHE B 488 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ILE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 549 removed outlier: 4.666A pdb=" N TRP B 529 " --> pdb=" O GLY B 525 " (cutoff:3.500A) Proline residue: B 547 - end of helix Processing helix chain 'B' and resid 554 through 577 removed outlier: 3.872A pdb=" N GLY B 558 " --> pdb=" O SER B 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 59 removed outlier: 3.971A pdb=" N CYS C 57 " --> pdb=" O ARG C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 62 No H-bonds generated for 'chain 'C' and resid 60 through 62' Processing helix chain 'C' and resid 63 through 71 Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 95 through 121 removed outlier: 3.565A pdb=" N ALA C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 133 Processing helix chain 'C' and resid 136 through 162 removed outlier: 4.716A pdb=" N LEU C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ALA C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) Proline residue: C 152 - end of helix Processing helix chain 'C' and resid 163 through 165 No H-bonds generated for 'chain 'C' and resid 163 through 165' Processing helix chain 'C' and resid 166 through 193 removed outlier: 3.502A pdb=" N ALA C 170 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 182 " --> pdb=" O GLY C 178 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL C 185 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 223 removed outlier: 3.585A pdb=" N PHE C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 254 Processing helix chain 'C' and resid 301 through 309 Processing helix chain 'C' and resid 313 through 320 Processing helix chain 'C' and resid 321 through 342 Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 355 through 374 removed outlier: 3.936A pdb=" N VAL C 364 " --> pdb=" O CYS C 360 " (cutoff:3.500A) Proline residue: C 367 - end of helix Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.512A pdb=" N ILE C 381 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 382 " --> pdb=" O VAL C 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 377 through 382' Processing helix chain 'C' and resid 385 through 387 No H-bonds generated for 'chain 'C' and resid 385 through 387' Processing helix chain 'C' and resid 390 through 409 Processing helix chain 'C' and resid 417 through 452 removed outlier: 4.016A pdb=" N PHE C 421 " --> pdb=" O LEU C 417 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA C 422 " --> pdb=" O HIS C 418 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N SER C 429 " --> pdb=" O GLY C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 481 removed outlier: 4.130A pdb=" N LEU C 463 " --> pdb=" O GLY C 459 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ALA C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP C 465 " --> pdb=" O THR C 461 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY C 470 " --> pdb=" O GLY C 466 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP C 471 " --> pdb=" O ASN C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 515 removed outlier: 3.516A pdb=" N ALA C 487 " --> pdb=" O TYR C 483 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE C 492 " --> pdb=" O PHE C 488 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE C 495 " --> pdb=" O CYS C 491 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 496 " --> pdb=" O PHE C 492 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE C 497 " --> pdb=" O GLY C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 549 Proline residue: C 547 - end of helix Processing helix chain 'C' and resid 554 through 577 removed outlier: 3.881A pdb=" N GLY C 558 " --> pdb=" O SER C 554 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 196 removed outlier: 3.653A pdb=" N PHE A 195 " --> pdb=" O LEU A 553 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA3, first strand: chain 'A' and resid 383 through 384 removed outlier: 3.533A pdb=" N LEU A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 195 through 196 removed outlier: 3.547A pdb=" N PHE B 195 " --> pdb=" O LEU B 553 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 224 through 226 Processing sheet with id=AA6, first strand: chain 'B' and resid 383 through 384 removed outlier: 3.581A pdb=" N LEU B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 195 through 196 removed outlier: 3.546A pdb=" N PHE C 195 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AA9, first strand: chain 'C' and resid 383 through 384 872 hydrogen bonds defined for protein. 2583 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: 1.84 Time building geometry restraints manager: 1.27 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: 2069 1.33 - 1.45: 2934 1.45 - 1.58: 6541 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 11610 Sorted by residual: bond pdb=" C PRO A 414 " pdb=" O PRO A 414 " ideal model delta sigma weight residual 1.246 1.208 0.038 8.50e-03 1.38e+04 1.97e+01 bond pdb=" CA ASP B 471 " pdb=" C ASP B 471 " ideal model delta sigma weight residual 1.524 1.475 0.048 1.27e-02 6.20e+03 1.45e+01 bond pdb=" N VAL B 457 " pdb=" CA VAL B 457 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.23e-02 6.61e+03 1.32e+01 bond pdb=" N LEU A 453 " pdb=" CA LEU A 453 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.22e-02 6.72e+03 1.04e+01 bond pdb=" N SER A 454 " pdb=" CA SER A 454 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.22e-02 6.72e+03 9.76e+00 ... (remaining 11605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 15449 2.03 - 4.06: 347 4.06 - 6.09: 65 6.09 - 8.12: 4 8.12 - 10.15: 5 Bond angle restraints: 15870 Sorted by residual: angle pdb=" C GLY B 459 " pdb=" N LEU B 460 " pdb=" CA LEU B 460 " ideal model delta sigma weight residual 122.60 113.36 9.24 1.88e+00 2.83e-01 2.42e+01 angle pdb=" N SER A 162 " pdb=" CA SER A 162 " pdb=" C SER A 162 " ideal model delta sigma weight residual 112.38 117.72 -5.34 1.22e+00 6.72e-01 1.91e+01 angle pdb=" O PRO A 414 " pdb=" C PRO A 414 " pdb=" N PRO A 415 " ideal model delta sigma weight residual 121.31 119.35 1.96 4.60e-01 4.73e+00 1.82e+01 angle pdb=" N ASN A 94 " pdb=" CA ASN A 94 " pdb=" C ASN A 94 " ideal model delta sigma weight residual 111.82 106.90 4.92 1.16e+00 7.43e-01 1.80e+01 angle pdb=" N VAL A 450 " pdb=" CA VAL A 450 " pdb=" C VAL A 450 " ideal model delta sigma weight residual 110.62 106.37 4.25 1.02e+00 9.61e-01 1.74e+01 ... (remaining 15865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5990 17.95 - 35.91: 555 35.91 - 53.86: 119 53.86 - 71.81: 20 71.81 - 89.77: 9 Dihedral angle restraints: 6693 sinusoidal: 2478 harmonic: 4215 Sorted by residual: dihedral pdb=" CB CYS C 65 " pdb=" SG CYS C 65 " pdb=" SG CYS C 89 " pdb=" CB CYS C 89 " ideal model delta sinusoidal sigma weight residual -86.00 -172.89 86.89 1 1.00e+01 1.00e-02 9.08e+01 dihedral pdb=" CB CYS C 53 " pdb=" SG CYS C 53 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual 93.00 135.01 -42.01 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CB CYS B 53 " pdb=" SG CYS B 53 " pdb=" SG CYS B 74 " pdb=" CB CYS B 74 " ideal model delta sinusoidal sigma weight residual 93.00 129.04 -36.04 1 1.00e+01 1.00e-02 1.84e+01 ... (remaining 6690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1483 0.046 - 0.092: 367 0.092 - 0.139: 69 0.139 - 0.185: 7 0.185 - 0.231: 6 Chirality restraints: 1932 Sorted by residual: chirality pdb=" CB VAL B 457 " pdb=" CA VAL B 457 " pdb=" CG1 VAL B 457 " pdb=" CG2 VAL B 457 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA LEU C 339 " pdb=" N LEU C 339 " pdb=" C LEU C 339 " pdb=" CB LEU C 339 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA VAL A 450 " pdb=" N VAL A 450 " pdb=" C VAL A 450 " pdb=" CB VAL A 450 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.19 2.00e-01 2.50e+01 9.44e-01 ... (remaining 1929 not shown) Planarity restraints: 1929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 161 " -0.026 2.00e-02 2.50e+03 5.16e-02 2.66e+01 pdb=" C PHE A 161 " 0.089 2.00e-02 2.50e+03 pdb=" O PHE A 161 " -0.033 2.00e-02 2.50e+03 pdb=" N SER A 162 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 411 " 0.022 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C ASN A 411 " -0.074 2.00e-02 2.50e+03 pdb=" O ASN A 411 " 0.027 2.00e-02 2.50e+03 pdb=" N SER A 412 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 452 " 0.020 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C ARG B 452 " -0.074 2.00e-02 2.50e+03 pdb=" O ARG B 452 " 0.029 2.00e-02 2.50e+03 pdb=" N LEU B 453 " 0.025 2.00e-02 2.50e+03 ... (remaining 1926 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 52 2.59 - 3.17: 10099 3.17 - 3.75: 17833 3.75 - 4.32: 22027 4.32 - 4.90: 37654 Nonbonded interactions: 87665 Sorted by model distance: nonbonded pdb=" OD2 ASP A 153 " pdb="CA CA A 601 " model vdw 2.014 3.250 nonbonded pdb=" OG SER B 517 " pdb=" OE1 GLU B 518 " model vdw 2.229 3.040 nonbonded pdb=" O PHE B 426 " pdb=" OG SER B 429 " model vdw 2.231 3.040 nonbonded pdb=" O TRP C 317 " pdb=" NZ LYS C 325 " model vdw 2.235 3.120 nonbonded pdb=" O ALA B 160 " pdb=" OG1 THR B 166 " model vdw 2.240 3.040 ... (remaining 87660 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' selection = chain 'C' } 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: 2.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.480 Find NCS groups from input model: 0.220 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11616 Z= 0.261 Angle : 0.713 10.148 15882 Z= 0.438 Chirality : 0.042 0.231 1932 Planarity : 0.005 0.052 1929 Dihedral : 14.791 89.766 3969 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.87 % Allowed : 16.91 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.74 (0.22), residues: 1452 helix: 1.55 (0.16), residues: 1105 sheet: None (None), residues: 0 loop : 0.05 (0.36), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 70 TYR 0.019 0.001 TYR B 382 PHE 0.014 0.001 PHE A 147 TRP 0.028 0.001 TRP C 354 HIS 0.004 0.001 HIS B 581 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.26 (11610) covalent geometry : angle 0.71325 / 0.44 (15870) SS BOND : bond 0.00263 / 0.18 ( 6) SS BOND : angle 0.43503 / 0.23 ( 12) hydrogen bonds : bond 0.14749 / 10.04 ( 872) hydrogen bonds : angle 6.46627 / 4.74 ( 2583) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 322 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7237 (tt) REVERT: A 120 LYS cc_start: 0.7938 (mptt) cc_final: 0.7589 (mptt) REVERT: A 225 ILE cc_start: 0.6891 (mt) cc_final: 0.6284 (tt) REVERT: A 243 THR cc_start: 0.7954 (m) cc_final: 0.7651 (t) REVERT: A 305 LEU cc_start: 0.8189 (tp) cc_final: 0.7977 (tm) REVERT: A 356 ARG cc_start: 0.6365 (ttt-90) cc_final: 0.5285 (ttt-90) REVERT: A 480 ARG cc_start: 0.8270 (mmm-85) cc_final: 0.7015 (mtm180) REVERT: A 498 ASN cc_start: 0.8089 (m-40) cc_final: 0.7865 (m-40) REVERT: A 521 LEU cc_start: 0.7896 (mt) cc_final: 0.7601 (mt) REVERT: B 54 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.7487 (mtp85) REVERT: B 67 PHE cc_start: 0.8707 (t80) cc_final: 0.8396 (t80) REVERT: B 90 TYR cc_start: 0.7338 (t80) cc_final: 0.6817 (t80) REVERT: B 147 PHE cc_start: 0.7589 (m-80) cc_final: 0.7336 (m-80) REVERT: B 149 ASN cc_start: 0.8339 (m-40) cc_final: 0.7986 (m110) REVERT: B 227 LEU cc_start: 0.8394 (tt) cc_final: 0.8038 (tm) REVERT: B 310 ASN cc_start: 0.8094 (t0) cc_final: 0.7742 (t0) REVERT: B 346 ASP cc_start: 0.7767 (t0) cc_final: 0.7173 (t0) REVERT: B 352 ARG cc_start: 0.8194 (mmt180) cc_final: 0.7597 (mmm-85) REVERT: B 359 ASN cc_start: 0.8102 (m-40) cc_final: 0.7821 (m-40) REVERT: B 366 SER cc_start: 0.7995 (m) cc_final: 0.7750 (p) REVERT: B 371 VAL cc_start: 0.8285 (t) cc_final: 0.7966 (m) REVERT: B 480 ARG cc_start: 0.8077 (mmm-85) cc_final: 0.7724 (mtp180) REVERT: B 508 LEU cc_start: 0.8319 (tp) cc_final: 0.7872 (tp) REVERT: B 512 VAL cc_start: 0.8351 (t) cc_final: 0.8050 (p) REVERT: C 54 ARG cc_start: 0.8001 (ttm110) cc_final: 0.7495 (ttm110) REVERT: C 64 ARG cc_start: 0.8106 (mmt90) cc_final: 0.7820 (mpt-90) REVERT: C 82 ASP cc_start: 0.7052 (t0) cc_final: 0.6546 (t0) REVERT: C 224 ARG cc_start: 0.7877 (ptt-90) cc_final: 0.7591 (ptt-90) REVERT: C 233 TYR cc_start: 0.8605 (m-80) cc_final: 0.8316 (m-80) REVERT: C 239 PHE cc_start: 0.8252 (t80) cc_final: 0.7967 (t80) REVERT: C 243 THR cc_start: 0.8106 (m) cc_final: 0.7857 (t) REVERT: C 315 ARG cc_start: 0.7990 (mpt180) cc_final: 0.7659 (mpt180) REVERT: C 335 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: C 355 LYS cc_start: 0.6153 (mmtm) cc_final: 0.5907 (mmtp) REVERT: C 371 VAL cc_start: 0.8302 (t) cc_final: 0.8062 (m) REVERT: C 449 VAL cc_start: 0.8651 (t) cc_final: 0.8449 (p) REVERT: C 452 ARG cc_start: 0.8117 (mtm110) cc_final: 0.7647 (mtm110) REVERT: C 489 SER cc_start: 0.8386 (t) cc_final: 0.8074 (p) REVERT: C 513 ARG cc_start: 0.8278 (ttm170) cc_final: 0.8057 (ttp80) outliers start: 23 outliers final: 6 residues processed: 343 average time/residue: 0.3658 time to fit residues: 141.1154 Evaluate side-chains 295 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 287 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 349 LYS Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain C residue 335 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 ASN A 359 ASN B 125 ASN B 149 ASN B 481 GLN C 60 ASN C 411 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.149904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121173 restraints weight = 18061.931| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.53 r_work: 0.3501 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11616 Z= 0.153 Angle : 0.618 8.512 15882 Z= 0.303 Chirality : 0.041 0.207 1932 Planarity : 0.004 0.044 1929 Dihedral : 5.482 61.272 1585 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.31 % Allowed : 20.81 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.64 (0.22), residues: 1452 helix: 2.25 (0.15), residues: 1124 sheet: None (None), residues: 0 loop : 0.05 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 485 TYR 0.014 0.001 TYR A 83 PHE 0.027 0.001 PHE B 147 TRP 0.011 0.001 TRP C 354 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (11610) covalent geometry : angle 0.61856 / 0.30 (15870) SS BOND : bond 0.00044 / 0.02 ( 6) SS BOND : angle 0.27072 / 0.15 ( 12) hydrogen bonds : bond 0.05607 / 3.77 ( 872) hydrogen bonds : angle 4.27080 / 3.17 ( 2583) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 304 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7206 (tt) REVERT: A 134 LYS cc_start: 0.8595 (mmtp) cc_final: 0.8311 (mmtp) REVERT: A 139 VAL cc_start: 0.8294 (p) cc_final: 0.8074 (t) REVERT: A 205 ASP cc_start: 0.8282 (m-30) cc_final: 0.8054 (m-30) REVERT: A 305 LEU cc_start: 0.8595 (tp) cc_final: 0.8317 (tm) REVERT: A 327 LEU cc_start: 0.7755 (tt) cc_final: 0.7518 (tm) REVERT: A 346 ASP cc_start: 0.7885 (t0) cc_final: 0.7616 (t0) REVERT: A 356 ARG cc_start: 0.7300 (ttt-90) cc_final: 0.5901 (ttt-90) REVERT: A 480 ARG cc_start: 0.8474 (mmm-85) cc_final: 0.7462 (mtm180) REVERT: A 498 ASN cc_start: 0.8302 (m-40) cc_final: 0.8066 (m-40) REVERT: A 501 VAL cc_start: 0.8678 (OUTLIER) cc_final: 0.8412 (t) REVERT: B 57 CYS cc_start: 0.7387 (p) cc_final: 0.6940 (p) REVERT: B 67 PHE cc_start: 0.8744 (t80) cc_final: 0.8518 (t80) REVERT: B 90 TYR cc_start: 0.7395 (t80) cc_final: 0.6979 (t80) REVERT: B 147 PHE cc_start: 0.7817 (m-80) cc_final: 0.7481 (m-80) REVERT: B 227 LEU cc_start: 0.8538 (tt) cc_final: 0.8332 (tm) REVERT: B 310 ASN cc_start: 0.8229 (t0) cc_final: 0.7915 (t0) REVERT: B 346 ASP cc_start: 0.7942 (t0) cc_final: 0.7459 (t0) REVERT: B 352 ARG cc_start: 0.8371 (mmt180) cc_final: 0.7904 (mmm-85) REVERT: B 359 ASN cc_start: 0.8230 (m-40) cc_final: 0.8023 (m-40) REVERT: B 366 SER cc_start: 0.8161 (m) cc_final: 0.7946 (p) REVERT: B 371 VAL cc_start: 0.8586 (t) cc_final: 0.8251 (m) REVERT: B 387 LEU cc_start: 0.3030 (OUTLIER) cc_final: 0.2779 (pp) REVERT: B 442 ASN cc_start: 0.8637 (m-40) cc_final: 0.8330 (m110) REVERT: B 480 ARG cc_start: 0.8295 (mmm-85) cc_final: 0.8002 (mtm180) REVERT: C 54 ARG cc_start: 0.8081 (ttm110) cc_final: 0.7681 (ttm110) REVERT: C 64 ARG cc_start: 0.8302 (mmt90) cc_final: 0.7996 (mpt-90) REVERT: C 85 LYS cc_start: 0.8645 (mtpm) cc_final: 0.8428 (mtpp) REVERT: C 125 ASN cc_start: 0.8458 (OUTLIER) cc_final: 0.8219 (t0) REVERT: C 239 PHE cc_start: 0.8608 (t80) cc_final: 0.8290 (t80) REVERT: C 315 ARG cc_start: 0.7978 (mpt180) cc_final: 0.7727 (mpt180) REVERT: C 332 LEU cc_start: 0.8529 (mt) cc_final: 0.8285 (mt) REVERT: C 335 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: C 359 ASN cc_start: 0.8233 (m-40) cc_final: 0.8030 (m-40) REVERT: C 371 VAL cc_start: 0.8672 (t) cc_final: 0.8469 (m) REVERT: C 452 ARG cc_start: 0.8478 (mtm110) cc_final: 0.8170 (mtm110) REVERT: C 469 ILE cc_start: 0.8194 (tt) cc_final: 0.7772 (pp) REVERT: C 471 ASP cc_start: 0.8070 (m-30) cc_final: 0.7855 (m-30) REVERT: C 486 MET cc_start: 0.8471 (mmp) cc_final: 0.8244 (mmp) REVERT: C 489 SER cc_start: 0.8506 (t) cc_final: 0.8268 (p) REVERT: C 505 LEU cc_start: 0.8339 (tp) cc_final: 0.8068 (tp) REVERT: C 563 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8452 (tt) outliers start: 53 outliers final: 23 residues processed: 335 average time/residue: 0.3810 time to fit residues: 142.8868 Evaluate side-chains 311 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 282 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 35 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 121 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 0.3980 chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN B 149 ASN C 60 ASN C 411 ASN C 581 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.149123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.120461 restraints weight = 18061.404| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 2.53 r_work: 0.3490 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11616 Z= 0.140 Angle : 0.580 7.778 15882 Z= 0.285 Chirality : 0.040 0.242 1932 Planarity : 0.004 0.045 1929 Dihedral : 5.044 59.356 1579 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.63 % Allowed : 21.38 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.93 (0.22), residues: 1452 helix: 2.50 (0.15), residues: 1118 sheet: None (None), residues: 0 loop : -0.01 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 445 TYR 0.021 0.001 TYR A 382 PHE 0.019 0.001 PHE B 147 TRP 0.010 0.001 TRP C 354 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (11610) covalent geometry : angle 0.58027 / 0.29 (15870) SS BOND : bond 0.00070 / 0.03 ( 6) SS BOND : angle 0.24020 / 0.13 ( 12) hydrogen bonds : bond 0.05065 / 3.41 ( 872) hydrogen bonds : angle 3.95463 / 2.93 ( 2583) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 287 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7132 (tt) REVERT: A 134 LYS cc_start: 0.8630 (mmtp) cc_final: 0.8340 (mmtp) REVERT: A 149 ASN cc_start: 0.7986 (m-40) cc_final: 0.7588 (m110) REVERT: A 166 THR cc_start: 0.6932 (OUTLIER) cc_final: 0.6427 (p) REVERT: A 205 ASP cc_start: 0.8333 (m-30) cc_final: 0.8106 (m-30) REVERT: A 222 LEU cc_start: 0.8774 (mt) cc_final: 0.8560 (mm) REVERT: A 305 LEU cc_start: 0.8617 (tp) cc_final: 0.8364 (tm) REVERT: A 327 LEU cc_start: 0.7840 (tt) cc_final: 0.7601 (tm) REVERT: A 346 ASP cc_start: 0.7908 (t0) cc_final: 0.7542 (t0) REVERT: A 356 ARG cc_start: 0.7463 (ttt-90) cc_final: 0.6182 (ttt-90) REVERT: A 442 ASN cc_start: 0.6659 (m-40) cc_final: 0.6425 (m110) REVERT: A 453 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5653 (tm) REVERT: A 471 ASP cc_start: 0.7194 (m-30) cc_final: 0.6947 (m-30) REVERT: A 480 ARG cc_start: 0.8515 (mmm-85) cc_final: 0.7553 (mtm180) REVERT: A 501 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8444 (t) REVERT: B 67 PHE cc_start: 0.8794 (t80) cc_final: 0.8560 (t80) REVERT: B 90 TYR cc_start: 0.7428 (t80) cc_final: 0.6978 (t80) REVERT: B 147 PHE cc_start: 0.7787 (m-80) cc_final: 0.7442 (m-80) REVERT: B 227 LEU cc_start: 0.8509 (tt) cc_final: 0.8276 (tm) REVERT: B 310 ASN cc_start: 0.8238 (t0) cc_final: 0.7939 (t0) REVERT: B 346 ASP cc_start: 0.7954 (t0) cc_final: 0.7481 (t0) REVERT: B 351 ASP cc_start: 0.8346 (p0) cc_final: 0.8111 (p0) REVERT: B 352 ARG cc_start: 0.8372 (mmt180) cc_final: 0.7867 (mmm-85) REVERT: B 366 SER cc_start: 0.8189 (m) cc_final: 0.7955 (p) REVERT: B 371 VAL cc_start: 0.8601 (t) cc_final: 0.8286 (m) REVERT: B 387 LEU cc_start: 0.2997 (OUTLIER) cc_final: 0.2747 (pp) REVERT: B 442 ASN cc_start: 0.8704 (m-40) cc_final: 0.8429 (m110) REVERT: B 480 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.8037 (mtm180) REVERT: C 54 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7677 (ttm110) REVERT: C 64 ARG cc_start: 0.8301 (mmt90) cc_final: 0.7936 (mpt-90) REVERT: C 82 ASP cc_start: 0.7155 (t0) cc_final: 0.6754 (t0) REVERT: C 85 LYS cc_start: 0.8664 (mtpm) cc_final: 0.8083 (mtpp) REVERT: C 101 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7724 (m) REVERT: C 125 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8174 (t0) REVERT: C 239 PHE cc_start: 0.8712 (t80) cc_final: 0.8456 (t80) REVERT: C 315 ARG cc_start: 0.8026 (mpt180) cc_final: 0.7771 (mpt180) REVERT: C 332 LEU cc_start: 0.8683 (mt) cc_final: 0.8309 (mt) REVERT: C 335 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: C 359 ASN cc_start: 0.8277 (m-40) cc_final: 0.8055 (m-40) REVERT: C 371 VAL cc_start: 0.8689 (t) cc_final: 0.8478 (m) REVERT: C 452 ARG cc_start: 0.8395 (mtm110) cc_final: 0.8073 (mtm110) REVERT: C 469 ILE cc_start: 0.8203 (tt) cc_final: 0.7757 (pp) REVERT: C 471 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: C 486 MET cc_start: 0.8420 (mmp) cc_final: 0.8181 (mmp) REVERT: C 489 SER cc_start: 0.8586 (t) cc_final: 0.8346 (p) REVERT: C 563 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8473 (tt) outliers start: 57 outliers final: 29 residues processed: 321 average time/residue: 0.3700 time to fit residues: 132.9051 Evaluate side-chains 318 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 279 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 196 MET Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 443 ILE Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 335 GLU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 45 optimal weight: 0.0670 chunk 42 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN A 467 ASN A 552 GLN B 149 ASN B 467 ASN C 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.146774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.118125 restraints weight = 17862.880| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.53 r_work: 0.3453 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11616 Z= 0.163 Angle : 0.590 8.873 15882 Z= 0.293 Chirality : 0.041 0.244 1932 Planarity : 0.004 0.047 1929 Dihedral : 4.878 58.095 1577 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 5.04 % Allowed : 21.63 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.94 (0.22), residues: 1452 helix: 2.53 (0.15), residues: 1117 sheet: None (None), residues: 0 loop : -0.11 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 485 TYR 0.018 0.001 TYR C 221 PHE 0.014 0.001 PHE B 147 TRP 0.010 0.001 TRP C 354 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (11610) covalent geometry : angle 0.58972 / 0.29 (15870) SS BOND : bond 0.00534 / 0.18 ( 6) SS BOND : angle 0.44303 / 0.25 ( 12) hydrogen bonds : bond 0.05388 / 3.63 ( 872) hydrogen bonds : angle 3.92528 / 2.92 ( 2583) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 295 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7131 (tt) REVERT: A 134 LYS cc_start: 0.8600 (mmtp) cc_final: 0.8325 (mmtp) REVERT: A 149 ASN cc_start: 0.7964 (m-40) cc_final: 0.7499 (m110) REVERT: A 205 ASP cc_start: 0.8382 (m-30) cc_final: 0.8173 (m-30) REVERT: A 222 LEU cc_start: 0.8803 (mt) cc_final: 0.8589 (mm) REVERT: A 305 LEU cc_start: 0.8648 (tp) cc_final: 0.8400 (tm) REVERT: A 327 LEU cc_start: 0.7887 (tt) cc_final: 0.7635 (tm) REVERT: A 346 ASP cc_start: 0.8020 (t0) cc_final: 0.7676 (t0) REVERT: A 356 ARG cc_start: 0.7586 (ttt-90) cc_final: 0.6219 (ttt-90) REVERT: A 442 ASN cc_start: 0.6992 (m-40) cc_final: 0.6755 (m110) REVERT: A 453 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.5675 (tm) REVERT: A 463 LEU cc_start: 0.7390 (pt) cc_final: 0.7176 (pt) REVERT: A 471 ASP cc_start: 0.7250 (m-30) cc_final: 0.6971 (m-30) REVERT: A 480 ARG cc_start: 0.8613 (mmm-85) cc_final: 0.7641 (mtm180) REVERT: B 67 PHE cc_start: 0.8747 (t80) cc_final: 0.8518 (t80) REVERT: B 84 LEU cc_start: 0.8728 (mm) cc_final: 0.8456 (mp) REVERT: B 90 TYR cc_start: 0.7470 (t80) cc_final: 0.7050 (t80) REVERT: B 227 LEU cc_start: 0.8572 (tt) cc_final: 0.8314 (tm) REVERT: B 310 ASN cc_start: 0.8299 (t0) cc_final: 0.8088 (t0) REVERT: B 339 LEU cc_start: 0.8781 (mt) cc_final: 0.8529 (mm) REVERT: B 346 ASP cc_start: 0.7972 (t0) cc_final: 0.7557 (t0) REVERT: B 366 SER cc_start: 0.8224 (m) cc_final: 0.7948 (p) REVERT: B 371 VAL cc_start: 0.8624 (t) cc_final: 0.8301 (m) REVERT: B 387 LEU cc_start: 0.2940 (OUTLIER) cc_final: 0.2696 (pp) REVERT: B 480 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.8043 (ttm170) REVERT: C 54 ARG cc_start: 0.8290 (ttm110) cc_final: 0.7840 (ttm110) REVERT: C 64 ARG cc_start: 0.8303 (mmt90) cc_final: 0.8095 (mmt90) REVERT: C 85 LYS cc_start: 0.8669 (mtpm) cc_final: 0.8272 (mtpp) REVERT: C 101 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7796 (m) REVERT: C 125 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8193 (t0) REVERT: C 154 ILE cc_start: 0.8330 (mt) cc_final: 0.8117 (mp) REVERT: C 162 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8490 (p) REVERT: C 163 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7432 (t0) REVERT: C 239 PHE cc_start: 0.8756 (t80) cc_final: 0.8462 (t80) REVERT: C 244 VAL cc_start: 0.8359 (t) cc_final: 0.8016 (t) REVERT: C 315 ARG cc_start: 0.8035 (mpt180) cc_final: 0.7756 (mpt180) REVERT: C 335 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7569 (mt-10) REVERT: C 353 ASN cc_start: 0.8114 (m-40) cc_final: 0.7898 (m-40) REVERT: C 355 LYS cc_start: 0.7054 (mmtp) cc_final: 0.6808 (mmtm) REVERT: C 371 VAL cc_start: 0.8768 (t) cc_final: 0.8538 (m) REVERT: C 429 SER cc_start: 0.8542 (t) cc_final: 0.8235 (p) REVERT: C 452 ARG cc_start: 0.8421 (mtm110) cc_final: 0.8073 (mtm110) REVERT: C 471 ASP cc_start: 0.8058 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: C 486 MET cc_start: 0.8416 (mmp) cc_final: 0.8143 (mmp) REVERT: C 489 SER cc_start: 0.8598 (t) cc_final: 0.8346 (p) outliers start: 62 outliers final: 26 residues processed: 324 average time/residue: 0.3699 time to fit residues: 133.5275 Evaluate side-chains 324 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 290 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 416 ARG Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 210 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 142 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN A 467 ASN A 552 GLN B 149 ASN B 434 ASN B 442 ASN C 60 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.146997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118507 restraints weight = 17720.857| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.49 r_work: 0.3460 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11616 Z= 0.155 Angle : 0.586 9.617 15882 Z= 0.292 Chirality : 0.041 0.306 1932 Planarity : 0.004 0.044 1929 Dihedral : 4.717 56.204 1574 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.31 % Allowed : 23.01 % Favored : 72.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.91 (0.22), residues: 1452 helix: 2.54 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -0.19 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 445 TYR 0.017 0.001 TYR A 83 PHE 0.013 0.001 PHE A 122 TRP 0.009 0.001 TRP C 354 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (11610) covalent geometry : angle 0.58630 / 0.29 (15870) SS BOND : bond 0.00107 / 0.04 ( 6) SS BOND : angle 0.48330 / 0.28 ( 12) hydrogen bonds : bond 0.05216 / 3.50 ( 872) hydrogen bonds : angle 3.89442 / 2.90 ( 2583) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 308 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8586 (mmtp) cc_final: 0.8314 (mmtp) REVERT: A 138 ASN cc_start: 0.7160 (OUTLIER) cc_final: 0.6913 (t0) REVERT: A 149 ASN cc_start: 0.7946 (m-40) cc_final: 0.7485 (m110) REVERT: A 205 ASP cc_start: 0.8392 (m-30) cc_final: 0.8146 (m-30) REVERT: A 222 LEU cc_start: 0.8806 (mt) cc_final: 0.8588 (mm) REVERT: A 305 LEU cc_start: 0.8626 (tp) cc_final: 0.8399 (tm) REVERT: A 327 LEU cc_start: 0.7905 (tt) cc_final: 0.7658 (tm) REVERT: A 346 ASP cc_start: 0.8007 (t0) cc_final: 0.7633 (t0) REVERT: A 356 ARG cc_start: 0.7641 (ttt-90) cc_final: 0.6202 (ttt-90) REVERT: A 442 ASN cc_start: 0.7031 (m-40) cc_final: 0.6795 (m110) REVERT: A 453 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5632 (tm) REVERT: A 471 ASP cc_start: 0.7189 (m-30) cc_final: 0.6919 (m-30) REVERT: A 480 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.7712 (mtm180) REVERT: B 67 PHE cc_start: 0.8753 (t80) cc_final: 0.8536 (t80) REVERT: B 85 LYS cc_start: 0.8130 (tmtt) cc_final: 0.7833 (tmtt) REVERT: B 90 TYR cc_start: 0.7460 (t80) cc_final: 0.7036 (t80) REVERT: B 227 LEU cc_start: 0.8539 (tt) cc_final: 0.8280 (tm) REVERT: B 310 ASN cc_start: 0.8329 (t0) cc_final: 0.8054 (t0) REVERT: B 316 LYS cc_start: 0.8534 (mptt) cc_final: 0.8111 (mptt) REVERT: B 331 LYS cc_start: 0.8361 (mtpt) cc_final: 0.8095 (mtmm) REVERT: B 339 LEU cc_start: 0.8792 (mt) cc_final: 0.8551 (mm) REVERT: B 346 ASP cc_start: 0.7966 (t0) cc_final: 0.7553 (t0) REVERT: B 351 ASP cc_start: 0.8395 (p0) cc_final: 0.8169 (p0) REVERT: B 366 SER cc_start: 0.8283 (m) cc_final: 0.7970 (p) REVERT: B 371 VAL cc_start: 0.8612 (t) cc_final: 0.8274 (m) REVERT: B 387 LEU cc_start: 0.2954 (OUTLIER) cc_final: 0.2706 (pp) REVERT: B 480 ARG cc_start: 0.8381 (mmm-85) cc_final: 0.8062 (ttm170) REVERT: C 54 ARG cc_start: 0.8317 (ttm110) cc_final: 0.7856 (ttm110) REVERT: C 64 ARG cc_start: 0.8313 (mmt90) cc_final: 0.8102 (mmt90) REVERT: C 85 LYS cc_start: 0.8682 (mtpm) cc_final: 0.8301 (mtpp) REVERT: C 101 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7765 (m) REVERT: C 125 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8196 (t0) REVERT: C 154 ILE cc_start: 0.8357 (mt) cc_final: 0.8123 (mp) REVERT: C 163 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7536 (t0) REVERT: C 239 PHE cc_start: 0.8769 (t80) cc_final: 0.8507 (t80) REVERT: C 244 VAL cc_start: 0.8388 (t) cc_final: 0.8070 (t) REVERT: C 315 ARG cc_start: 0.8000 (mpt180) cc_final: 0.7724 (mpt180) REVERT: C 335 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7730 (mt-10) REVERT: C 353 ASN cc_start: 0.8155 (m-40) cc_final: 0.7892 (m-40) REVERT: C 371 VAL cc_start: 0.8820 (t) cc_final: 0.8580 (m) REVERT: C 429 SER cc_start: 0.8538 (t) cc_final: 0.8200 (p) REVERT: C 452 ARG cc_start: 0.8389 (mtm110) cc_final: 0.8056 (mtm110) REVERT: C 471 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: C 486 MET cc_start: 0.8396 (mmp) cc_final: 0.8142 (mmp) REVERT: C 489 SER cc_start: 0.8596 (t) cc_final: 0.8316 (p) outliers start: 53 outliers final: 28 residues processed: 335 average time/residue: 0.3558 time to fit residues: 132.7669 Evaluate side-chains 328 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 293 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 579 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 116 optimal weight: 7.9990 chunk 75 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 21 optimal weight: 0.4980 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN A 467 ASN B 149 ASN B 442 ASN B 467 ASN B 481 GLN B 549 GLN C 60 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.146648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.118148 restraints weight = 17771.427| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.49 r_work: 0.3453 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11616 Z= 0.155 Angle : 0.593 10.919 15882 Z= 0.293 Chirality : 0.041 0.303 1932 Planarity : 0.004 0.050 1929 Dihedral : 4.385 49.806 1572 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.15 % Allowed : 23.90 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.89 (0.22), residues: 1452 helix: 2.51 (0.15), residues: 1116 sheet: None (None), residues: 0 loop : -0.15 (0.37), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 485 TYR 0.016 0.001 TYR C 221 PHE 0.013 0.001 PHE A 122 TRP 0.011 0.001 TRP C 354 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (11610) covalent geometry : angle 0.59311 / 0.29 (15870) SS BOND : bond 0.00383 / 0.19 ( 6) SS BOND : angle 0.73954 / 0.45 ( 12) hydrogen bonds : bond 0.05224 / 3.51 ( 872) hydrogen bonds : angle 3.87542 / 2.88 ( 2583) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 304 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8579 (mmtp) cc_final: 0.8312 (mmtp) REVERT: A 138 ASN cc_start: 0.7161 (OUTLIER) cc_final: 0.6924 (t0) REVERT: A 149 ASN cc_start: 0.7953 (m-40) cc_final: 0.7497 (m110) REVERT: A 205 ASP cc_start: 0.8391 (m-30) cc_final: 0.8155 (m-30) REVERT: A 222 LEU cc_start: 0.8818 (mt) cc_final: 0.8601 (mm) REVERT: A 305 LEU cc_start: 0.8592 (tp) cc_final: 0.8380 (tm) REVERT: A 327 LEU cc_start: 0.7997 (tt) cc_final: 0.7760 (tm) REVERT: A 346 ASP cc_start: 0.8036 (t0) cc_final: 0.7661 (t0) REVERT: A 356 ARG cc_start: 0.7697 (ttt-90) cc_final: 0.6261 (ttt-90) REVERT: A 453 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5645 (tm) REVERT: A 471 ASP cc_start: 0.7183 (m-30) cc_final: 0.6938 (m-30) REVERT: A 480 ARG cc_start: 0.8572 (mmm-85) cc_final: 0.7737 (mtm180) REVERT: B 85 LYS cc_start: 0.8081 (tmtt) cc_final: 0.7772 (tmtt) REVERT: B 90 TYR cc_start: 0.7413 (t80) cc_final: 0.7069 (t80) REVERT: B 147 PHE cc_start: 0.7691 (m-10) cc_final: 0.7453 (m-80) REVERT: B 227 LEU cc_start: 0.8523 (tt) cc_final: 0.8260 (tm) REVERT: B 310 ASN cc_start: 0.8337 (t0) cc_final: 0.8130 (t0) REVERT: B 316 LYS cc_start: 0.8564 (mptt) cc_final: 0.8165 (mptt) REVERT: B 331 LYS cc_start: 0.8378 (mtpt) cc_final: 0.8108 (mtmm) REVERT: B 339 LEU cc_start: 0.8804 (mt) cc_final: 0.8573 (mm) REVERT: B 346 ASP cc_start: 0.8068 (t0) cc_final: 0.7674 (t0) REVERT: B 351 ASP cc_start: 0.8450 (p0) cc_final: 0.8234 (p0) REVERT: B 366 SER cc_start: 0.8293 (m) cc_final: 0.7987 (p) REVERT: B 371 VAL cc_start: 0.8630 (t) cc_final: 0.8288 (m) REVERT: B 387 LEU cc_start: 0.2972 (OUTLIER) cc_final: 0.2714 (pp) REVERT: B 480 ARG cc_start: 0.8407 (mmm-85) cc_final: 0.8078 (ttm170) REVERT: C 54 ARG cc_start: 0.8345 (ttm110) cc_final: 0.7903 (ttm110) REVERT: C 67 PHE cc_start: 0.8517 (t80) cc_final: 0.8279 (t80) REVERT: C 82 ASP cc_start: 0.7219 (t0) cc_final: 0.6726 (t0) REVERT: C 85 LYS cc_start: 0.8709 (mtpm) cc_final: 0.8130 (mtpp) REVERT: C 101 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7762 (m) REVERT: C 125 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.8175 (t0) REVERT: C 154 ILE cc_start: 0.8361 (mt) cc_final: 0.8127 (mp) REVERT: C 239 PHE cc_start: 0.8777 (t80) cc_final: 0.8520 (t80) REVERT: C 244 VAL cc_start: 0.8427 (t) cc_final: 0.8123 (t) REVERT: C 315 ARG cc_start: 0.7994 (mpt180) cc_final: 0.7713 (mpt180) REVERT: C 332 LEU cc_start: 0.8736 (mt) cc_final: 0.8483 (mt) REVERT: C 335 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7696 (mt-10) REVERT: C 371 VAL cc_start: 0.8837 (t) cc_final: 0.8594 (m) REVERT: C 429 SER cc_start: 0.8531 (t) cc_final: 0.8194 (p) REVERT: C 452 ARG cc_start: 0.8410 (mtm110) cc_final: 0.8073 (mtm110) REVERT: C 471 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: C 489 SER cc_start: 0.8576 (t) cc_final: 0.8313 (p) outliers start: 51 outliers final: 25 residues processed: 330 average time/residue: 0.3592 time to fit residues: 132.0602 Evaluate side-chains 329 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 298 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 109 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 ASN A 359 ASN A 442 ASN A 467 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 ASN B 442 ASN B 481 GLN B 549 GLN C 60 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.146550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.118097 restraints weight = 17939.223| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.51 r_work: 0.3455 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11616 Z= 0.150 Angle : 0.595 8.846 15882 Z= 0.293 Chirality : 0.041 0.308 1932 Planarity : 0.004 0.037 1929 Dihedral : 4.326 48.664 1572 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.47 % Allowed : 24.55 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.90 (0.22), residues: 1452 helix: 2.51 (0.15), residues: 1116 sheet: None (None), residues: 0 loop : -0.15 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 485 TYR 0.015 0.001 TYR C 221 PHE 0.014 0.001 PHE C 336 TRP 0.027 0.001 TRP A 432 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (11610) covalent geometry : angle 0.59465 / 0.29 (15870) SS BOND : bond 0.00216 / 0.10 ( 6) SS BOND : angle 0.76123 / 0.45 ( 12) hydrogen bonds : bond 0.05129 / 3.45 ( 872) hydrogen bonds : angle 3.86268 / 2.87 ( 2583) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 302 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7120 (tt) REVERT: A 134 LYS cc_start: 0.8562 (mmtp) cc_final: 0.8306 (mmtp) REVERT: A 138 ASN cc_start: 0.7193 (OUTLIER) cc_final: 0.6946 (t0) REVERT: A 149 ASN cc_start: 0.7933 (m-40) cc_final: 0.7446 (m110) REVERT: A 205 ASP cc_start: 0.8391 (m-30) cc_final: 0.8166 (m-30) REVERT: A 222 LEU cc_start: 0.8814 (mt) cc_final: 0.8605 (mm) REVERT: A 305 LEU cc_start: 0.8595 (tp) cc_final: 0.8365 (tm) REVERT: A 327 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7763 (tm) REVERT: A 346 ASP cc_start: 0.8039 (t0) cc_final: 0.7622 (t0) REVERT: A 356 ARG cc_start: 0.7704 (ttt-90) cc_final: 0.6287 (ttt-90) REVERT: A 453 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5563 (tm) REVERT: A 468 SER cc_start: 0.8191 (p) cc_final: 0.7923 (m) REVERT: A 471 ASP cc_start: 0.7178 (m-30) cc_final: 0.6920 (m-30) REVERT: A 480 ARG cc_start: 0.8578 (mmm-85) cc_final: 0.7771 (mtm180) REVERT: B 85 LYS cc_start: 0.8094 (tmtt) cc_final: 0.7786 (tmtt) REVERT: B 90 TYR cc_start: 0.7394 (t80) cc_final: 0.7033 (t80) REVERT: B 147 PHE cc_start: 0.7681 (m-10) cc_final: 0.7434 (m-80) REVERT: B 210 MET cc_start: 0.8885 (ttm) cc_final: 0.8592 (mtp) REVERT: B 227 LEU cc_start: 0.8519 (tt) cc_final: 0.8239 (tm) REVERT: B 310 ASN cc_start: 0.8340 (t0) cc_final: 0.8074 (t0) REVERT: B 316 LYS cc_start: 0.8595 (mptt) cc_final: 0.8239 (mptt) REVERT: B 331 LYS cc_start: 0.8376 (mtpt) cc_final: 0.8107 (mtmm) REVERT: B 339 LEU cc_start: 0.8818 (mt) cc_final: 0.8591 (mm) REVERT: B 346 ASP cc_start: 0.8061 (t0) cc_final: 0.7684 (t0) REVERT: B 351 ASP cc_start: 0.8463 (p0) cc_final: 0.8232 (p0) REVERT: B 366 SER cc_start: 0.8321 (m) cc_final: 0.7998 (p) REVERT: B 371 VAL cc_start: 0.8646 (t) cc_final: 0.8296 (m) REVERT: B 387 LEU cc_start: 0.3009 (OUTLIER) cc_final: 0.2744 (pp) REVERT: B 480 ARG cc_start: 0.8409 (mmm-85) cc_final: 0.8078 (ttm170) REVERT: C 85 LYS cc_start: 0.8700 (mtpm) cc_final: 0.8383 (mtpp) REVERT: C 125 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8169 (t0) REVERT: C 154 ILE cc_start: 0.8353 (mt) cc_final: 0.8123 (mp) REVERT: C 239 PHE cc_start: 0.8777 (t80) cc_final: 0.8520 (t80) REVERT: C 244 VAL cc_start: 0.8444 (t) cc_final: 0.8150 (t) REVERT: C 315 ARG cc_start: 0.7955 (mpt180) cc_final: 0.7675 (mpt180) REVERT: C 327 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8469 (tm) REVERT: C 371 VAL cc_start: 0.8851 (t) cc_final: 0.8605 (m) REVERT: C 429 SER cc_start: 0.8522 (t) cc_final: 0.8229 (p) REVERT: C 452 ARG cc_start: 0.8410 (mtm110) cc_final: 0.8187 (mtm180) REVERT: C 471 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: C 489 SER cc_start: 0.8582 (t) cc_final: 0.8316 (p) outliers start: 55 outliers final: 28 residues processed: 333 average time/residue: 0.3441 time to fit residues: 127.5429 Evaluate side-chains 333 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 297 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 405 THR Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 95 optimal weight: 0.0980 chunk 72 optimal weight: 0.0010 chunk 86 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 139 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 88 optimal weight: 0.5980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 ASN A 359 ASN A 442 ASN A 552 GLN B 411 ASN B 442 ASN B 467 ASN B 549 GLN C 411 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.148303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.119938 restraints weight = 17722.023| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.51 r_work: 0.3485 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11616 Z= 0.124 Angle : 0.587 9.099 15882 Z= 0.285 Chirality : 0.040 0.282 1932 Planarity : 0.004 0.044 1929 Dihedral : 4.244 47.168 1572 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 4.07 % Allowed : 25.12 % Favored : 70.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.95 (0.22), residues: 1452 helix: 2.58 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 485 TYR 0.020 0.001 TYR C 221 PHE 0.038 0.001 PHE B 67 TRP 0.017 0.001 TRP A 432 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (11610) covalent geometry : angle 0.58740 / 0.29 (15870) SS BOND : bond 0.00156 / 0.08 ( 6) SS BOND : angle 0.58633 / 0.34 ( 12) hydrogen bonds : bond 0.04539 / 3.04 ( 872) hydrogen bonds : angle 3.77859 / 2.81 ( 2583) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 302 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7125 (tt) REVERT: A 134 LYS cc_start: 0.8552 (mmtp) cc_final: 0.8299 (mmtp) REVERT: A 138 ASN cc_start: 0.7100 (OUTLIER) cc_final: 0.6866 (t0) REVERT: A 149 ASN cc_start: 0.7893 (m-40) cc_final: 0.7433 (m110) REVERT: A 153 ASP cc_start: 0.8043 (t0) cc_final: 0.7723 (m-30) REVERT: A 204 ARG cc_start: 0.8764 (ttp-170) cc_final: 0.8486 (ptt-90) REVERT: A 205 ASP cc_start: 0.8323 (m-30) cc_final: 0.8045 (m-30) REVERT: A 222 LEU cc_start: 0.8746 (mt) cc_final: 0.8540 (mm) REVERT: A 327 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7732 (tm) REVERT: A 346 ASP cc_start: 0.8030 (t0) cc_final: 0.7597 (t0) REVERT: A 356 ARG cc_start: 0.7658 (ttt-90) cc_final: 0.6302 (ttt-90) REVERT: A 453 LEU cc_start: 0.5800 (OUTLIER) cc_final: 0.5523 (tm) REVERT: A 468 SER cc_start: 0.8116 (p) cc_final: 0.7857 (m) REVERT: A 471 ASP cc_start: 0.7081 (m-30) cc_final: 0.6868 (m-30) REVERT: A 480 ARG cc_start: 0.8521 (mmm-85) cc_final: 0.7678 (mtm180) REVERT: B 85 LYS cc_start: 0.8029 (tmtt) cc_final: 0.7704 (tmtt) REVERT: B 90 TYR cc_start: 0.7395 (t80) cc_final: 0.7011 (t80) REVERT: B 147 PHE cc_start: 0.7617 (m-10) cc_final: 0.7391 (m-80) REVERT: B 310 ASN cc_start: 0.8324 (t0) cc_final: 0.8111 (t0) REVERT: B 316 LYS cc_start: 0.8599 (mptt) cc_final: 0.8265 (mptt) REVERT: B 331 LYS cc_start: 0.8358 (mtpt) cc_final: 0.8084 (mtmm) REVERT: B 339 LEU cc_start: 0.8770 (mt) cc_final: 0.8552 (mm) REVERT: B 346 ASP cc_start: 0.8046 (t0) cc_final: 0.7662 (t0) REVERT: B 351 ASP cc_start: 0.8441 (p0) cc_final: 0.8206 (p0) REVERT: B 366 SER cc_start: 0.8322 (m) cc_final: 0.7981 (p) REVERT: B 371 VAL cc_start: 0.8618 (t) cc_final: 0.8266 (m) REVERT: B 372 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8151 (mm) REVERT: B 387 LEU cc_start: 0.2996 (OUTLIER) cc_final: 0.2726 (pp) REVERT: B 480 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.8098 (mtm180) REVERT: C 54 ARG cc_start: 0.8346 (ttm110) cc_final: 0.7878 (ttm110) REVERT: C 67 PHE cc_start: 0.8478 (t80) cc_final: 0.8036 (t80) REVERT: C 85 LYS cc_start: 0.8582 (mtpm) cc_final: 0.8163 (mtpp) REVERT: C 125 ASN cc_start: 0.8434 (OUTLIER) cc_final: 0.8171 (t0) REVERT: C 239 PHE cc_start: 0.8750 (t80) cc_final: 0.8503 (t80) REVERT: C 315 ARG cc_start: 0.7983 (mpt180) cc_final: 0.7694 (mpt180) REVERT: C 327 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8435 (tm) REVERT: C 371 VAL cc_start: 0.8804 (t) cc_final: 0.8554 (m) REVERT: C 429 SER cc_start: 0.8431 (t) cc_final: 0.8195 (p) REVERT: C 452 ARG cc_start: 0.8322 (mtm110) cc_final: 0.8107 (mtm110) REVERT: C 471 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7683 (m-30) REVERT: C 489 SER cc_start: 0.8584 (t) cc_final: 0.8322 (p) outliers start: 50 outliers final: 25 residues processed: 330 average time/residue: 0.3375 time to fit residues: 124.3259 Evaluate side-chains 330 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 296 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 138 ASN Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 372 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 39 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 0.1980 chunk 64 optimal weight: 0.5980 chunk 128 optimal weight: 3.9990 chunk 50 optimal weight: 0.0770 chunk 143 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 353 ASN A 359 ASN A 442 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN B 149 ASN B 411 ASN B 434 ASN B 442 ASN B 549 GLN C 467 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.148587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.120144 restraints weight = 17661.370| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.51 r_work: 0.3487 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11616 Z= 0.126 Angle : 0.607 12.919 15882 Z= 0.292 Chirality : 0.041 0.338 1932 Planarity : 0.004 0.044 1929 Dihedral : 4.010 38.052 1570 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.01 % Allowed : 26.83 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.91 (0.22), residues: 1452 helix: 2.57 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -0.34 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 445 TYR 0.019 0.001 TYR C 221 PHE 0.018 0.001 PHE C 336 TRP 0.018 0.001 TRP A 432 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (11610) covalent geometry : angle 0.60710 / 0.29 (15870) SS BOND : bond 0.00119 / 0.06 ( 6) SS BOND : angle 0.64508 / 0.36 ( 12) hydrogen bonds : bond 0.04467 / 2.99 ( 872) hydrogen bonds : angle 3.76646 / 2.80 ( 2583) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 296 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7115 (tt) REVERT: A 134 LYS cc_start: 0.8548 (mmtp) cc_final: 0.8290 (mmtp) REVERT: A 149 ASN cc_start: 0.7904 (m-40) cc_final: 0.7411 (m110) REVERT: A 153 ASP cc_start: 0.8003 (t0) cc_final: 0.7681 (m-30) REVERT: A 204 ARG cc_start: 0.8761 (ttp-170) cc_final: 0.8474 (ptt-90) REVERT: A 205 ASP cc_start: 0.8324 (m-30) cc_final: 0.8028 (m-30) REVERT: A 222 LEU cc_start: 0.8725 (mt) cc_final: 0.8520 (mm) REVERT: A 327 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7740 (tm) REVERT: A 346 ASP cc_start: 0.8035 (t0) cc_final: 0.7596 (t0) REVERT: A 356 ARG cc_start: 0.7665 (ttt-90) cc_final: 0.6313 (ttt-90) REVERT: A 453 LEU cc_start: 0.5717 (OUTLIER) cc_final: 0.5453 (tm) REVERT: A 468 SER cc_start: 0.7968 (p) cc_final: 0.7739 (m) REVERT: A 471 ASP cc_start: 0.7084 (m-30) cc_final: 0.6866 (m-30) REVERT: A 480 ARG cc_start: 0.8508 (mmm-85) cc_final: 0.7665 (mtm180) REVERT: B 85 LYS cc_start: 0.8027 (tmtt) cc_final: 0.7679 (tmtt) REVERT: B 90 TYR cc_start: 0.7396 (t80) cc_final: 0.7015 (t80) REVERT: B 147 PHE cc_start: 0.7607 (m-10) cc_final: 0.7379 (m-80) REVERT: B 210 MET cc_start: 0.8878 (ttm) cc_final: 0.8593 (mtp) REVERT: B 310 ASN cc_start: 0.8316 (t0) cc_final: 0.8021 (t0) REVERT: B 316 LYS cc_start: 0.8608 (mptt) cc_final: 0.8298 (mptt) REVERT: B 331 LYS cc_start: 0.8387 (mtpt) cc_final: 0.8175 (mtpm) REVERT: B 339 LEU cc_start: 0.8775 (mt) cc_final: 0.8562 (mm) REVERT: B 346 ASP cc_start: 0.8055 (t0) cc_final: 0.7658 (t0) REVERT: B 351 ASP cc_start: 0.8438 (p0) cc_final: 0.8215 (p0) REVERT: B 366 SER cc_start: 0.8319 (m) cc_final: 0.7978 (p) REVERT: B 371 VAL cc_start: 0.8610 (t) cc_final: 0.8260 (m) REVERT: B 387 LEU cc_start: 0.3032 (OUTLIER) cc_final: 0.2755 (pp) REVERT: B 442 ASN cc_start: 0.8693 (m-40) cc_final: 0.8341 (m110) REVERT: B 480 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.8098 (mtm180) REVERT: C 54 ARG cc_start: 0.8357 (ttm110) cc_final: 0.7878 (ttm110) REVERT: C 85 LYS cc_start: 0.8569 (mtpm) cc_final: 0.8166 (mtpp) REVERT: C 125 ASN cc_start: 0.8441 (OUTLIER) cc_final: 0.8157 (t0) REVERT: C 154 ILE cc_start: 0.8307 (mt) cc_final: 0.8074 (mp) REVERT: C 239 PHE cc_start: 0.8727 (t80) cc_final: 0.8475 (t80) REVERT: C 244 VAL cc_start: 0.8449 (t) cc_final: 0.8163 (t) REVERT: C 315 ARG cc_start: 0.8000 (mpt180) cc_final: 0.7722 (mpt180) REVERT: C 327 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8428 (tm) REVERT: C 371 VAL cc_start: 0.8801 (t) cc_final: 0.8554 (m) REVERT: C 429 SER cc_start: 0.8419 (t) cc_final: 0.8186 (p) REVERT: C 452 ARG cc_start: 0.8328 (mtm110) cc_final: 0.8100 (mtm110) REVERT: C 471 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7687 (m-30) REVERT: C 489 SER cc_start: 0.8601 (t) cc_final: 0.8327 (p) outliers start: 37 outliers final: 23 residues processed: 312 average time/residue: 0.3784 time to fit residues: 131.0112 Evaluate side-chains 322 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 292 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 120 LYS Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 509 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN A 353 ASN A 359 ASN A 442 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 ASN B 467 ASN B 549 GLN B 581 HIS C 353 ASN C 411 ASN C 467 ASN C 549 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.146253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117822 restraints weight = 17725.719| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.48 r_work: 0.3447 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11616 Z= 0.165 Angle : 0.624 11.665 15882 Z= 0.307 Chirality : 0.042 0.353 1932 Planarity : 0.004 0.046 1929 Dihedral : 4.020 37.810 1570 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.93 % Allowed : 27.24 % Favored : 69.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.81 (0.22), residues: 1452 helix: 2.51 (0.15), residues: 1114 sheet: None (None), residues: 0 loop : -0.44 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 485 TYR 0.013 0.001 TYR C 237 PHE 0.040 0.001 PHE B 67 TRP 0.018 0.001 TRP A 432 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (11610) covalent geometry : angle 0.62439 / 0.31 (15870) SS BOND : bond 0.00150 / 0.07 ( 6) SS BOND : angle 0.69638 / 0.39 ( 12) hydrogen bonds : bond 0.05294 / 3.55 ( 872) hydrogen bonds : angle 3.88851 / 2.89 ( 2583) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 302 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7169 (tt) REVERT: A 134 LYS cc_start: 0.8563 (mmtp) cc_final: 0.8309 (mmtp) REVERT: A 149 ASN cc_start: 0.7859 (m-40) cc_final: 0.7338 (m110) REVERT: A 153 ASP cc_start: 0.8014 (t0) cc_final: 0.7720 (m-30) REVERT: A 204 ARG cc_start: 0.8814 (ttp-170) cc_final: 0.8545 (ptt-90) REVERT: A 205 ASP cc_start: 0.8395 (m-30) cc_final: 0.8145 (m-30) REVERT: A 222 LEU cc_start: 0.8805 (mt) cc_final: 0.8601 (mm) REVERT: A 327 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7778 (tm) REVERT: A 346 ASP cc_start: 0.8046 (t0) cc_final: 0.7607 (t0) REVERT: A 356 ARG cc_start: 0.7723 (ttt-90) cc_final: 0.6323 (ttt-90) REVERT: A 423 PHE cc_start: 0.7869 (m-80) cc_final: 0.7411 (m-80) REVERT: A 453 LEU cc_start: 0.5659 (OUTLIER) cc_final: 0.5397 (tm) REVERT: A 468 SER cc_start: 0.7973 (p) cc_final: 0.7754 (m) REVERT: A 471 ASP cc_start: 0.7213 (m-30) cc_final: 0.6985 (m-30) REVERT: A 480 ARG cc_start: 0.8577 (mmm-85) cc_final: 0.7740 (mtm180) REVERT: B 85 LYS cc_start: 0.8108 (tmtt) cc_final: 0.7768 (tmtt) REVERT: B 90 TYR cc_start: 0.7408 (t80) cc_final: 0.7026 (t80) REVERT: B 147 PHE cc_start: 0.7690 (m-10) cc_final: 0.7444 (m-80) REVERT: B 310 ASN cc_start: 0.8330 (t0) cc_final: 0.8043 (t0) REVERT: B 316 LYS cc_start: 0.8647 (mptt) cc_final: 0.8361 (mptt) REVERT: B 331 LYS cc_start: 0.8428 (mtpt) cc_final: 0.8215 (mtpm) REVERT: B 339 LEU cc_start: 0.8836 (mt) cc_final: 0.8608 (mm) REVERT: B 346 ASP cc_start: 0.8071 (t0) cc_final: 0.7660 (t0) REVERT: B 352 ARG cc_start: 0.8434 (mmt180) cc_final: 0.7954 (mmm-85) REVERT: B 366 SER cc_start: 0.8333 (m) cc_final: 0.7986 (p) REVERT: B 371 VAL cc_start: 0.8651 (t) cc_final: 0.8302 (m) REVERT: B 387 LEU cc_start: 0.3048 (OUTLIER) cc_final: 0.2768 (pp) REVERT: B 480 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.8089 (mtm180) REVERT: C 54 ARG cc_start: 0.8366 (ttm110) cc_final: 0.7870 (ttm110) REVERT: C 85 LYS cc_start: 0.8597 (mtpm) cc_final: 0.8157 (mtpp) REVERT: C 125 ASN cc_start: 0.8422 (t0) cc_final: 0.8153 (t0) REVERT: C 231 LEU cc_start: 0.8277 (mt) cc_final: 0.8058 (mm) REVERT: C 239 PHE cc_start: 0.8749 (t80) cc_final: 0.8511 (t80) REVERT: C 244 VAL cc_start: 0.8525 (t) cc_final: 0.8221 (t) REVERT: C 315 ARG cc_start: 0.8010 (mpt180) cc_final: 0.7748 (mpt180) REVERT: C 353 ASN cc_start: 0.8333 (m110) cc_final: 0.7858 (m110) REVERT: C 371 VAL cc_start: 0.8854 (t) cc_final: 0.8592 (m) REVERT: C 429 SER cc_start: 0.8571 (t) cc_final: 0.8278 (p) REVERT: C 452 ARG cc_start: 0.8375 (mtm110) cc_final: 0.8147 (mtm110) REVERT: C 471 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: C 489 SER cc_start: 0.8583 (t) cc_final: 0.8307 (p) outliers start: 36 outliers final: 20 residues processed: 319 average time/residue: 0.3667 time to fit residues: 130.5159 Evaluate side-chains 322 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 297 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 359 ASN Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 431 LEU Chi-restraints excluded: chain B residue 491 CYS Chi-restraints excluded: chain B residue 577 PHE Chi-restraints excluded: chain C residue 69 LYS Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 196 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 471 ASP Chi-restraints excluded: chain C residue 563 LEU Chi-restraints excluded: chain C residue 569 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 135 optimal weight: 0.3980 chunk 85 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 359 ASN A 442 ASN A 467 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 GLN B 549 GLN C 467 ASN C 549 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.147058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.118647 restraints weight = 17899.720| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.54 r_work: 0.3458 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11616 Z= 0.139 Angle : 0.629 11.784 15882 Z= 0.305 Chirality : 0.042 0.352 1932 Planarity : 0.004 0.051 1929 Dihedral : 4.034 38.210 1570 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.60 % Allowed : 28.05 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.78 (0.22), residues: 1452 helix: 2.50 (0.15), residues: 1114 sheet: None (None), residues: 0 loop : -0.46 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 485 TYR 0.017 0.001 TYR C 221 PHE 0.027 0.001 PHE C 67 TRP 0.015 0.001 TRP A 432 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (11610) covalent geometry : angle 0.62914 / 0.31 (15870) SS BOND : bond 0.00205 / 0.10 ( 6) SS BOND : angle 0.65731 / 0.36 ( 12) hydrogen bonds : bond 0.04900 / 3.27 ( 872) hydrogen bonds : angle 3.85847 / 2.87 ( 2583) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3490.73 seconds wall clock time: 60 minutes 13.83 seconds (3613.83 seconds total)