Starting phenix.real_space_refine on Wed Feb 4 15:57:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ps8_71826/02_2026/9ps8_71826.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ps8_71826/02_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_71826/02_2026/9ps8_71826.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ps8_71826/02_2026/9ps8_71826.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ps8_71826/02_2026/9ps8_71826.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ps8_71826/02_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-2.0-5952/lib/python3.9/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, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.63, per 1000 atoms: 0.23 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: 0.83 Conformation dependent library (CDL) restraints added in 476.6 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: 0.24 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: 1.55 Time building geometry restraints manager: 1.09 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 2.510 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: 0.01 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: 2.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.020 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 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:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 covalent geometry : bond 0.00385 (11610) covalent geometry : angle 0.71325 (15870) SS BOND : bond 0.00263 ( 6) SS BOND : angle 0.43503 ( 12) hydrogen bonds : bond 0.14749 ( 872) hydrogen bonds : angle 6.46627 ( 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 : 0.378 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: 0.7465 (ttm110) REVERT: B 67 PHE cc_start: 0.8707 (t80) cc_final: 0.8397 (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: 0.7176 (t0) REVERT: B 352 ARG cc_start: 0.8194 (mmt180) cc_final: 0.7593 (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: 0.3435 time to fit residues: 131.7570 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 : 0.292 ------------------------------------------------------------------------------- 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: 0.7980 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... Flipped N/Q/H residues before XYZ refinement: A 353 ASN A 359 ASN B 125 ASN B 149 ASN B 481 GLN C 60 ASN C 411 ASN ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.149879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.121099 restraints weight = 18029.367| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.53 r_work: 0.3500 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11616 Z= 0.151 Angle : 0.625 8.820 15882 Z= 0.305 Chirality : 0.041 0.216 1932 Planarity : 0.004 0.050 1929 Dihedral : 5.461 60.463 1585 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 4.63 % Allowed : 20.49 % 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: 2.23 (0.15), residues: 1128 sheet: None (None), residues: 0 loop : 0.10 (0.37), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 485 TYR 0.016 0.001 TYR A 83 PHE 0.027 0.001 PHE B 147 TRP 0.013 0.001 TRP C 354 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00319 (11610) covalent geometry : angle 0.62505 (15870) SS BOND : bond 0.00048 ( 6) SS BOND : angle 0.30202 ( 12) hydrogen bonds : bond 0.05482 ( 872) hydrogen bonds : angle 4.22239 ( 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: 57 poor density : 300 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7198 (tt) REVERT: A 134 LYS cc_start: 0.8604 (mmtp) cc_final: 0.8317 (mmtp) REVERT: A 139 VAL cc_start: 0.8292 (p) cc_final: 0.8075 (t) REVERT: A 205 ASP cc_start: 0.8303 (m-30) cc_final: 0.8099 (m-30) REVERT: A 305 LEU cc_start: 0.8591 (tp) cc_final: 0.8316 (tm) REVERT: A 327 LEU cc_start: 0.7763 (tt) cc_final: 0.7524 (tm) REVERT: A 346 ASP cc_start: 0.7867 (t0) cc_final: 0.7579 (t0) REVERT: A 356 ARG cc_start: 0.7301 (ttt-90) cc_final: 0.5965 (ttt-90) REVERT: A 480 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.7458 (mtm180) REVERT: A 498 ASN cc_start: 0.8323 (m-40) cc_final: 0.8079 (m-40) REVERT: A 501 VAL cc_start: 0.8688 (OUTLIER) cc_final: 0.8426 (t) REVERT: B 57 CYS cc_start: 0.7400 (p) cc_final: 0.6958 (p) REVERT: B 67 PHE cc_start: 0.8790 (t80) cc_final: 0.8558 (t80) REVERT: B 83 TYR cc_start: 0.8510 (m-80) cc_final: 0.8174 (m-80) REVERT: B 90 TYR cc_start: 0.7412 (t80) cc_final: 0.6964 (t80) REVERT: B 147 PHE cc_start: 0.7809 (m-80) cc_final: 0.7483 (m-80) REVERT: B 227 LEU cc_start: 0.8536 (tt) cc_final: 0.8327 (tm) REVERT: B 310 ASN cc_start: 0.8225 (t0) cc_final: 0.7915 (t0) REVERT: B 346 ASP cc_start: 0.7941 (t0) cc_final: 0.7450 (t0) REVERT: B 352 ARG cc_start: 0.8377 (mmt180) cc_final: 0.7902 (mmm-85) REVERT: B 359 ASN cc_start: 0.8242 (m-40) cc_final: 0.8035 (m-40) REVERT: B 366 SER cc_start: 0.8163 (m) cc_final: 0.7952 (p) REVERT: B 371 VAL cc_start: 0.8592 (t) cc_final: 0.8256 (m) REVERT: B 387 LEU cc_start: 0.3123 (OUTLIER) cc_final: 0.2869 (pp) REVERT: B 432 TRP cc_start: 0.8504 (t-100) cc_final: 0.8301 (m100) REVERT: B 442 ASN cc_start: 0.8658 (m-40) cc_final: 0.8347 (m110) REVERT: B 455 ASN cc_start: 0.5305 (OUTLIER) cc_final: 0.5059 (p0) REVERT: B 480 ARG cc_start: 0.8308 (mmm-85) cc_final: 0.8016 (mtm180) REVERT: C 54 ARG cc_start: 0.8116 (ttm110) cc_final: 0.7715 (ttm110) REVERT: C 64 ARG cc_start: 0.8310 (mmt90) cc_final: 0.7991 (mpt-90) REVERT: C 85 LYS cc_start: 0.8652 (mtpm) cc_final: 0.8421 (mtpp) REVERT: C 125 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8201 (t0) REVERT: C 239 PHE cc_start: 0.8608 (t80) cc_final: 0.8291 (t80) REVERT: C 315 ARG cc_start: 0.7960 (mpt180) cc_final: 0.7711 (mpt180) REVERT: C 332 LEU cc_start: 0.8529 (mt) cc_final: 0.8266 (mt) REVERT: C 335 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: C 371 VAL cc_start: 0.8660 (t) cc_final: 0.8459 (m) REVERT: C 452 ARG cc_start: 0.8492 (mtm110) cc_final: 0.8183 (mtm110) REVERT: C 486 MET cc_start: 0.8452 (mmp) cc_final: 0.8230 (mmp) REVERT: C 489 SER cc_start: 0.8526 (t) cc_final: 0.8292 (p) REVERT: C 505 LEU cc_start: 0.8340 (tp) cc_final: 0.8071 (tp) REVERT: C 563 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8453 (tt) outliers start: 57 outliers final: 24 residues processed: 333 average time/residue: 0.3250 time to fit residues: 120.8147 Evaluate side-chains 316 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 444 LEU Chi-restraints excluded: chain B residue 455 ASN 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: 0.8980 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3995 r_free = 0.3995 target = 0.148159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.119498 restraints weight = 18014.920| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.53 r_work: 0.3474 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11616 Z= 0.153 Angle : 0.585 7.791 15882 Z= 0.289 Chirality : 0.041 0.241 1932 Planarity : 0.004 0.041 1929 Dihedral : 5.037 59.642 1579 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 4.15 % Allowed : 21.95 % Favored : 73.90 % 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: 2.48 (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 0.007 0.001 ARG C 445 TYR 0.018 0.001 TYR C 221 PHE 0.017 0.001 PHE B 147 TRP 0.010 0.001 TRP C 354 HIS 0.005 0.001 HIS A 581 Details of bonding type rmsd covalent geometry : bond 0.00337 (11610) covalent geometry : angle 0.58511 (15870) SS BOND : bond 0.00070 ( 6) SS BOND : angle 0.26353 ( 12) hydrogen bonds : bond 0.05299 ( 872) hydrogen bonds : angle 3.99377 ( 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 339 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 288 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7153 (tt) REVERT: A 134 LYS cc_start: 0.8632 (mmtp) cc_final: 0.8340 (mmtp) REVERT: A 149 ASN cc_start: 0.7964 (m-40) cc_final: 0.7589 (m110) REVERT: A 205 ASP cc_start: 0.8353 (m-30) cc_final: 0.8073 (m-30) REVERT: A 222 LEU cc_start: 0.8776 (mt) cc_final: 0.8557 (mm) REVERT: A 305 LEU cc_start: 0.8624 (tp) cc_final: 0.8367 (tm) REVERT: A 327 LEU cc_start: 0.7854 (tt) cc_final: 0.7615 (tm) REVERT: A 346 ASP cc_start: 0.7914 (t0) cc_final: 0.7539 (t0) REVERT: A 356 ARG cc_start: 0.7491 (ttt-90) cc_final: 0.6181 (ttt-90) REVERT: A 442 ASN cc_start: 0.6697 (m-40) cc_final: 0.6474 (m110) REVERT: A 453 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.5683 (tm) REVERT: A 480 ARG cc_start: 0.8538 (mmm-85) cc_final: 0.7587 (mtm180) REVERT: A 501 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8453 (t) REVERT: B 67 PHE cc_start: 0.8791 (t80) cc_final: 0.8574 (t80) REVERT: B 90 TYR cc_start: 0.7404 (t80) cc_final: 0.6958 (t80) REVERT: B 147 PHE cc_start: 0.7775 (m-80) cc_final: 0.7425 (m-80) REVERT: B 227 LEU cc_start: 0.8551 (tt) cc_final: 0.8316 (tm) REVERT: B 310 ASN cc_start: 0.8253 (t0) cc_final: 0.7972 (t0) REVERT: B 346 ASP cc_start: 0.7973 (t0) cc_final: 0.7521 (t0) REVERT: B 351 ASP cc_start: 0.8362 (p0) cc_final: 0.8138 (p0) REVERT: B 366 SER cc_start: 0.8208 (m) cc_final: 0.7960 (p) REVERT: B 371 VAL cc_start: 0.8584 (t) cc_final: 0.8261 (m) REVERT: B 387 LEU cc_start: 0.2992 (OUTLIER) cc_final: 0.2747 (pp) REVERT: B 442 ASN cc_start: 0.8730 (m-40) cc_final: 0.8470 (m110) REVERT: B 480 ARG cc_start: 0.8335 (mmm-85) cc_final: 0.8059 (mtm180) REVERT: C 54 ARG cc_start: 0.8144 (ttm110) cc_final: 0.7711 (ttm110) REVERT: C 64 ARG cc_start: 0.8301 (mmt90) cc_final: 0.7928 (mpt-90) REVERT: C 82 ASP cc_start: 0.7227 (t0) cc_final: 0.6765 (t0) REVERT: C 85 LYS cc_start: 0.8681 (mtpm) cc_final: 0.8075 (mtpp) REVERT: C 101 THR cc_start: 0.8001 (OUTLIER) cc_final: 0.7736 (m) REVERT: C 125 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8177 (t0) REVERT: C 239 PHE cc_start: 0.8727 (t80) cc_final: 0.8444 (t80) REVERT: C 315 ARG cc_start: 0.7997 (mpt180) cc_final: 0.7751 (mpt180) REVERT: C 371 VAL cc_start: 0.8733 (t) cc_final: 0.8519 (m) REVERT: C 452 ARG cc_start: 0.8460 (mtm110) cc_final: 0.8144 (mtm110) REVERT: C 486 MET cc_start: 0.8412 (mmp) cc_final: 0.8166 (mmp) REVERT: C 489 SER cc_start: 0.8571 (t) cc_final: 0.8331 (p) REVERT: C 563 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8482 (tt) outliers start: 51 outliers final: 26 residues processed: 319 average time/residue: 0.3644 time to fit residues: 129.3839 Evaluate side-chains 314 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 0.260 ------------------------------------------------------------------------------- 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 196 MET 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 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 142 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 329 VAL 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 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 218 THR Chi-restraints excluded: chain C residue 431 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 143 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.147744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.119178 restraints weight = 17877.308| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.50 r_work: 0.3469 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2334 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= 0.149 Angle : 0.581 8.863 15882 Z= 0.286 Chirality : 0.041 0.262 1932 Planarity : 0.004 0.055 1929 Dihedral : 4.768 58.306 1574 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.72 % Allowed : 22.28 % Favored : 73.01 % 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: 2.53 (0.15), residues: 1117 sheet: None (None), residues: 0 loop : -0.08 (0.36), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 485 TYR 0.020 0.001 TYR A 382 PHE 0.014 0.001 PHE B 147 TRP 0.009 0.001 TRP C 354 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00328 (11610) covalent geometry : angle 0.58072 (15870) SS BOND : bond 0.00377 ( 6) SS BOND : angle 0.36981 ( 12) hydrogen bonds : bond 0.05146 ( 872) hydrogen bonds : angle 3.90286 ( 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 342 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 284 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.7104 (tt) REVERT: A 134 LYS cc_start: 0.8592 (mmtp) cc_final: 0.8320 (mmtp) REVERT: A 204 ARG cc_start: 0.8798 (ttp-170) cc_final: 0.8574 (ttp80) REVERT: A 205 ASP cc_start: 0.8369 (m-30) cc_final: 0.8137 (m-30) REVERT: A 222 LEU cc_start: 0.8798 (mt) cc_final: 0.8581 (mm) REVERT: A 305 LEU cc_start: 0.8628 (tp) cc_final: 0.8387 (tm) REVERT: A 327 LEU cc_start: 0.7858 (tt) cc_final: 0.7619 (tm) REVERT: A 346 ASP cc_start: 0.7966 (t0) cc_final: 0.7638 (t0) REVERT: A 356 ARG cc_start: 0.7567 (ttt-90) cc_final: 0.6238 (ttt-90) REVERT: A 453 LEU cc_start: 0.5878 (OUTLIER) cc_final: 0.5647 (tm) REVERT: A 480 ARG cc_start: 0.8565 (mmm-85) cc_final: 0.7588 (mtm180) REVERT: B 67 PHE cc_start: 0.8731 (t80) cc_final: 0.8505 (t80) REVERT: B 90 TYR cc_start: 0.7450 (t80) cc_final: 0.7036 (t80) REVERT: B 147 PHE cc_start: 0.7746 (m-80) cc_final: 0.7404 (m-80) REVERT: B 227 LEU cc_start: 0.8541 (tt) cc_final: 0.8291 (tm) REVERT: B 310 ASN cc_start: 0.8276 (t0) cc_final: 0.8067 (t0) REVERT: B 339 LEU cc_start: 0.8748 (mt) cc_final: 0.8527 (mm) REVERT: B 346 ASP cc_start: 0.7974 (t0) cc_final: 0.7560 (t0) REVERT: B 352 ARG cc_start: 0.8343 (mmt180) cc_final: 0.7921 (mmm-85) REVERT: B 366 SER cc_start: 0.8234 (m) cc_final: 0.7965 (p) REVERT: B 371 VAL cc_start: 0.8590 (t) cc_final: 0.8269 (m) REVERT: B 387 LEU cc_start: 0.2946 (OUTLIER) cc_final: 0.2699 (pp) REVERT: B 480 ARG cc_start: 0.8357 (mmm-85) cc_final: 0.8058 (mtm180) REVERT: C 54 ARG cc_start: 0.8253 (ttm110) cc_final: 0.7810 (ttm110) REVERT: C 64 ARG cc_start: 0.8291 (mmt90) cc_final: 0.8081 (mmt90) REVERT: C 85 LYS cc_start: 0.8641 (mtpm) cc_final: 0.8255 (mtpp) REVERT: C 101 THR cc_start: 0.8006 (OUTLIER) cc_final: 0.7769 (m) REVERT: C 125 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.8190 (t0) REVERT: C 239 PHE cc_start: 0.8740 (t80) cc_final: 0.8461 (t80) REVERT: C 244 VAL cc_start: 0.8308 (t) cc_final: 0.7967 (t) REVERT: C 315 ARG cc_start: 0.8024 (mpt180) cc_final: 0.7751 (mpt180) REVERT: C 335 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7428 (mp0) REVERT: C 353 ASN cc_start: 0.8159 (m-40) cc_final: 0.7886 (m110) REVERT: C 355 LYS cc_start: 0.6956 (mmtp) cc_final: 0.6730 (mmtm) REVERT: C 371 VAL cc_start: 0.8758 (t) cc_final: 0.8530 (m) REVERT: C 429 SER cc_start: 0.8527 (t) cc_final: 0.8261 (p) REVERT: C 452 ARG cc_start: 0.8388 (mtm110) cc_final: 0.8052 (mtm110) REVERT: C 486 MET cc_start: 0.8415 (mmp) cc_final: 0.8154 (mmp) REVERT: C 489 SER cc_start: 0.8575 (t) cc_final: 0.8330 (p) outliers start: 58 outliers final: 31 residues processed: 315 average time/residue: 0.3625 time to fit residues: 126.0498 Evaluate side-chains 316 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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: 2.9990 chunk 0 optimal weight: 20.0000 chunk 79 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 128 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3980 r_free = 0.3980 target = 0.146858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.118107 restraints weight = 17686.168| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.50 r_work: 0.3447 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11616 Z= 0.158 Angle : 0.578 9.098 15882 Z= 0.289 Chirality : 0.041 0.282 1932 Planarity : 0.004 0.060 1929 Dihedral : 4.705 55.980 1574 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.47 % Allowed : 23.01 % Favored : 72.52 % 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: 2.52 (0.15), residues: 1116 sheet: None (None), residues: 0 loop : -0.16 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 485 TYR 0.016 0.001 TYR A 83 PHE 0.014 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 covalent geometry : bond 0.00352 (11610) covalent geometry : angle 0.57787 (15870) SS BOND : bond 0.00180 ( 6) SS BOND : angle 0.51818 ( 12) hydrogen bonds : bond 0.05295 ( 872) hydrogen bonds : angle 3.90343 ( 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: 55 poor density : 306 time to evaluate : 0.352 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: 0.8596 (mmtp) cc_final: 0.8319 (mmtp) REVERT: A 204 ARG cc_start: 0.8806 (ttp-170) cc_final: 0.8586 (ttp80) REVERT: A 205 ASP cc_start: 0.8409 (m-30) cc_final: 0.8177 (m-30) REVERT: A 222 LEU cc_start: 0.8813 (mt) cc_final: 0.8600 (mm) REVERT: A 305 LEU cc_start: 0.8628 (tp) cc_final: 0.8401 (tm) REVERT: A 327 LEU cc_start: 0.7909 (tt) cc_final: 0.7665 (tm) REVERT: A 346 ASP cc_start: 0.7998 (t0) cc_final: 0.7619 (t0) REVERT: A 356 ARG cc_start: 0.7651 (ttt-90) cc_final: 0.6208 (ttt-90) REVERT: A 442 ASN cc_start: 0.7056 (m-40) cc_final: 0.6816 (m110) REVERT: A 453 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.5645 (tm) REVERT: A 480 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.7756 (mtm180) REVERT: B 67 PHE cc_start: 0.8765 (t80) cc_final: 0.8545 (t80) REVERT: B 85 LYS cc_start: 0.8141 (tmtt) cc_final: 0.7848 (tmtt) REVERT: B 90 TYR cc_start: 0.7496 (t80) cc_final: 0.7073 (t80) REVERT: B 147 PHE cc_start: 0.7739 (m-80) cc_final: 0.7433 (m-80) REVERT: B 227 LEU cc_start: 0.8545 (tt) cc_final: 0.8290 (tm) REVERT: B 310 ASN cc_start: 0.8326 (t0) cc_final: 0.8111 (t0) REVERT: B 316 LYS cc_start: 0.8533 (mptt) cc_final: 0.8100 (mptt) REVERT: B 331 LYS cc_start: 0.8362 (mtpt) cc_final: 0.8096 (mtmm) REVERT: B 339 LEU cc_start: 0.8789 (mt) cc_final: 0.8546 (mm) REVERT: B 346 ASP cc_start: 0.7969 (t0) cc_final: 0.7552 (t0) REVERT: B 366 SER cc_start: 0.8279 (m) cc_final: 0.7976 (p) REVERT: B 371 VAL cc_start: 0.8600 (t) cc_final: 0.8268 (m) REVERT: B 387 LEU cc_start: 0.2985 (OUTLIER) cc_final: 0.2732 (pp) REVERT: B 480 ARG cc_start: 0.8395 (mmm-85) cc_final: 0.8079 (ttm170) REVERT: C 54 ARG cc_start: 0.8312 (ttm110) cc_final: 0.7860 (ttm110) REVERT: C 85 LYS cc_start: 0.8700 (mtpm) cc_final: 0.8317 (mtpp) REVERT: C 101 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7783 (m) REVERT: C 125 ASN cc_start: 0.8465 (OUTLIER) cc_final: 0.8180 (t0) REVERT: C 239 PHE cc_start: 0.8763 (t80) cc_final: 0.8495 (t80) REVERT: C 244 VAL cc_start: 0.8357 (t) cc_final: 0.8056 (t) REVERT: C 315 ARG cc_start: 0.8013 (mpt180) cc_final: 0.7730 (mpt180) REVERT: C 332 LEU cc_start: 0.8685 (mt) cc_final: 0.8406 (mt) REVERT: C 335 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7420 (mp0) REVERT: C 336 PHE cc_start: 0.8358 (t80) cc_final: 0.8151 (t80) REVERT: C 353 ASN cc_start: 0.8182 (m-40) cc_final: 0.7872 (m110) REVERT: C 371 VAL cc_start: 0.8822 (t) cc_final: 0.8586 (m) REVERT: C 429 SER cc_start: 0.8549 (t) cc_final: 0.8208 (p) REVERT: C 452 ARG cc_start: 0.8389 (mtm110) cc_final: 0.8060 (mtm110) REVERT: C 486 MET cc_start: 0.8404 (mmp) cc_final: 0.8146 (mmp) REVERT: C 489 SER cc_start: 0.8591 (t) cc_final: 0.8308 (p) outliers start: 55 outliers final: 29 residues processed: 334 average time/residue: 0.3540 time to fit residues: 131.0477 Evaluate side-chains 324 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 291 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 142 VAL Chi-restraints excluded: chain B residue 215 LEU 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 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 162 SER 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 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: 8.9990 chunk 75 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN A 359 ASN A 467 ASN B 149 ASN 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 = 0.146591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.118092 restraints weight = 17816.245| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.49 r_work: 0.3452 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11616 Z= 0.158 Angle : 0.594 10.765 15882 Z= 0.293 Chirality : 0.041 0.296 1932 Planarity : 0.004 0.049 1929 Dihedral : 4.385 49.811 1572 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 4.23 % Allowed : 24.63 % Favored : 71.14 % 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: 2.87 (0.22), residues: 1452 helix: 2.50 (0.15), residues: 1116 sheet: None (None), residues: 0 loop : -0.17 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 445 TYR 0.016 0.001 TYR B 83 PHE 0.014 0.001 PHE A 122 TRP 0.015 0.001 TRP C 354 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00354 (11610) covalent geometry : angle 0.59339 (15870) SS BOND : bond 0.00835 ( 6) SS BOND : angle 0.83307 ( 12) hydrogen bonds : bond 0.05283 ( 872) hydrogen bonds : angle 3.88428 ( 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 353 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 301 time to evaluate : 0.384 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: 0.7363 (OUTLIER) cc_final: 0.7124 (tt) REVERT: A 134 LYS cc_start: 0.8589 (mmtp) cc_final: 0.8323 (mmtp) REVERT: A 204 ARG cc_start: 0.8789 (ttp-170) cc_final: 0.8558 (ttp80) REVERT: A 205 ASP cc_start: 0.8394 (m-30) cc_final: 0.8163 (m-30) REVERT: A 222 LEU cc_start: 0.8820 (mt) cc_final: 0.8603 (mm) REVERT: A 305 LEU cc_start: 0.8609 (tp) cc_final: 0.8393 (tm) REVERT: A 327 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7754 (tm) REVERT: A 337 LEU cc_start: 0.7537 (tp) cc_final: 0.7322 (tm) REVERT: A 346 ASP cc_start: 0.8046 (t0) cc_final: 0.7670 (t0) REVERT: A 356 ARG cc_start: 0.7692 (ttt-90) cc_final: 0.6252 (ttt-90) REVERT: A 423 PHE cc_start: 0.7853 (m-80) cc_final: 0.7394 (m-80) REVERT: A 453 LEU cc_start: 0.5892 (OUTLIER) cc_final: 0.5638 (tm) REVERT: A 468 SER cc_start: 0.8254 (p) cc_final: 0.7995 (m) REVERT: A 480 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.7774 (mtm180) REVERT: B 67 PHE cc_start: 0.8727 (t80) cc_final: 0.8526 (t80) REVERT: B 85 LYS cc_start: 0.8083 (tmtt) cc_final: 0.7777 (tmtt) REVERT: B 90 TYR cc_start: 0.7415 (t80) cc_final: 0.7069 (t80) REVERT: B 147 PHE cc_start: 0.7729 (m-80) cc_final: 0.7458 (m-80) REVERT: B 227 LEU cc_start: 0.8532 (tt) cc_final: 0.8267 (tm) REVERT: B 310 ASN cc_start: 0.8328 (t0) cc_final: 0.8119 (t0) REVERT: B 316 LYS cc_start: 0.8557 (mptt) cc_final: 0.8145 (mptt) REVERT: B 331 LYS cc_start: 0.8375 (mtpt) cc_final: 0.8107 (mtmm) REVERT: B 339 LEU cc_start: 0.8802 (mt) cc_final: 0.8570 (mm) REVERT: B 346 ASP cc_start: 0.8073 (t0) cc_final: 0.7679 (t0) REVERT: B 366 SER cc_start: 0.8277 (m) cc_final: 0.7978 (p) REVERT: B 371 VAL cc_start: 0.8620 (t) cc_final: 0.8278 (m) REVERT: B 387 LEU cc_start: 0.2983 (OUTLIER) cc_final: 0.2723 (pp) REVERT: B 480 ARG cc_start: 0.8424 (mmm-85) cc_final: 0.8078 (ttm170) REVERT: C 54 ARG cc_start: 0.8347 (ttm110) cc_final: 0.7877 (ttm110) REVERT: C 67 PHE cc_start: 0.8531 (t80) cc_final: 0.8246 (t80) REVERT: C 85 LYS cc_start: 0.8721 (mtpm) cc_final: 0.8388 (mtpp) REVERT: C 101 THR cc_start: 0.7983 (OUTLIER) cc_final: 0.7768 (m) REVERT: C 125 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.8171 (t0) REVERT: C 239 PHE cc_start: 0.8784 (t80) cc_final: 0.8527 (t80) REVERT: C 244 VAL cc_start: 0.8444 (t) cc_final: 0.8141 (t) REVERT: C 315 ARG cc_start: 0.7999 (mpt180) cc_final: 0.7712 (mpt180) REVERT: C 332 LEU cc_start: 0.8704 (mt) cc_final: 0.8431 (mt) REVERT: C 335 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7454 (mp0) REVERT: C 371 VAL cc_start: 0.8840 (t) cc_final: 0.8597 (m) REVERT: C 429 SER cc_start: 0.8544 (t) cc_final: 0.8205 (p) REVERT: C 452 ARG cc_start: 0.8403 (mtm110) cc_final: 0.8065 (mtm110) REVERT: C 489 SER cc_start: 0.8576 (t) cc_final: 0.8318 (p) outliers start: 52 outliers final: 26 residues processed: 327 average time/residue: 0.3527 time to fit residues: 127.9137 Evaluate side-chains 327 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 295 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 420 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 196 MET Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 443 ILE 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=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: 0.5980 chunk 10 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN A 359 ASN A 442 ASN A 467 ASN A 552 GLN B 434 ASN B 442 ASN 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 = 0.3982 r_free = 0.3982 target = 0.146929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118309 restraints weight = 17911.568| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.51 r_work: 0.3460 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11616 Z= 0.142 Angle : 0.583 8.586 15882 Z= 0.288 Chirality : 0.041 0.304 1932 Planarity : 0.004 0.051 1929 Dihedral : 4.311 48.685 1572 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.90 % Allowed : 25.61 % Favored : 70.49 % 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 : -0.16 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 485 TYR 0.018 0.001 TYR C 221 PHE 0.013 0.001 PHE C 497 TRP 0.011 0.001 TRP C 354 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00312 (11610) covalent geometry : angle 0.58294 (15870) SS BOND : bond 0.00205 ( 6) SS BOND : angle 0.71430 ( 12) hydrogen bonds : bond 0.05023 ( 872) hydrogen bonds : angle 3.84659 ( 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 343 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 295 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8556 (mmtp) cc_final: 0.8300 (mmtp) REVERT: A 204 ARG cc_start: 0.8769 (ttp-170) cc_final: 0.8530 (ttp80) REVERT: A 205 ASP cc_start: 0.8379 (m-30) cc_final: 0.8149 (m-30) REVERT: A 222 LEU cc_start: 0.8802 (mt) cc_final: 0.8596 (mm) REVERT: A 305 LEU cc_start: 0.8611 (tp) cc_final: 0.8398 (tm) REVERT: A 327 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7761 (tm) REVERT: A 346 ASP cc_start: 0.8023 (t0) cc_final: 0.7588 (t0) REVERT: A 356 ARG cc_start: 0.7678 (ttt-90) cc_final: 0.6225 (ttt-90) REVERT: A 423 PHE cc_start: 0.7861 (m-80) cc_final: 0.7406 (m-80) REVERT: A 442 ASN cc_start: 0.7080 (m-40) cc_final: 0.6873 (m110) REVERT: A 453 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.5595 (tm) REVERT: A 468 SER cc_start: 0.8165 (p) cc_final: 0.7927 (m) REVERT: A 480 ARG cc_start: 0.8573 (mmm-85) cc_final: 0.7755 (mtm180) REVERT: B 67 PHE cc_start: 0.8806 (t80) cc_final: 0.8582 (t80) REVERT: B 85 LYS cc_start: 0.8059 (tmtt) cc_final: 0.7746 (tmtt) REVERT: B 90 TYR cc_start: 0.7316 (t80) cc_final: 0.6936 (t80) REVERT: B 147 PHE cc_start: 0.7714 (m-80) cc_final: 0.7452 (m-80) REVERT: B 227 LEU cc_start: 0.8494 (tt) cc_final: 0.8218 (tm) REVERT: B 316 LYS cc_start: 0.8560 (mptt) cc_final: 0.8158 (mptt) REVERT: B 331 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8084 (mtmm) REVERT: B 339 LEU cc_start: 0.8797 (mt) cc_final: 0.8566 (mm) REVERT: B 346 ASP cc_start: 0.8047 (t0) cc_final: 0.7613 (t0) REVERT: B 352 ARG cc_start: 0.8403 (mmt180) cc_final: 0.7826 (mmm-85) REVERT: B 366 SER cc_start: 0.8335 (m) cc_final: 0.8022 (p) REVERT: B 371 VAL cc_start: 0.8609 (t) cc_final: 0.8259 (m) REVERT: B 387 LEU cc_start: 0.3046 (OUTLIER) cc_final: 0.2774 (pp) REVERT: B 480 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.8092 (ttm170) REVERT: C 54 ARG cc_start: 0.8320 (ttm110) cc_final: 0.7859 (ttm110) REVERT: C 67 PHE cc_start: 0.8553 (t80) cc_final: 0.7991 (t80) REVERT: C 85 LYS cc_start: 0.8627 (mtpm) cc_final: 0.8234 (mtpp) REVERT: C 101 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7779 (m) REVERT: C 125 ASN cc_start: 0.8424 (OUTLIER) cc_final: 0.8151 (t0) REVERT: C 239 PHE cc_start: 0.8775 (t80) cc_final: 0.8518 (t80) REVERT: C 244 VAL cc_start: 0.8445 (t) cc_final: 0.8152 (t) REVERT: C 315 ARG cc_start: 0.8001 (mpt180) cc_final: 0.7728 (mpt180) REVERT: C 327 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8445 (tm) REVERT: C 332 LEU cc_start: 0.8723 (mt) cc_final: 0.8467 (mt) REVERT: C 335 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7400 (mp0) REVERT: C 371 VAL cc_start: 0.8849 (t) cc_final: 0.8600 (m) REVERT: C 429 SER cc_start: 0.8568 (t) cc_final: 0.8281 (p) REVERT: C 452 ARG cc_start: 0.8359 (mtm110) cc_final: 0.8135 (mtm180) REVERT: C 489 SER cc_start: 0.8591 (t) cc_final: 0.8328 (p) outliers start: 48 outliers final: 25 residues processed: 325 average time/residue: 0.3657 time to fit residues: 131.7115 Evaluate side-chains 320 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 289 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 TYR Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 142 VAL 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 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 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 526 LEU 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 84 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 125 ASN 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 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: 0.4980 chunk 27 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 88 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN A 359 ASN A 467 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN B 411 ASN B 434 ASN B 442 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 = 0.3991 r_free = 0.3991 target = 0.147497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118756 restraints weight = 17609.889| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.52 r_work: 0.3472 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11616 Z= 0.129 Angle : 0.587 12.340 15882 Z= 0.287 Chirality : 0.040 0.313 1932 Planarity : 0.004 0.039 1929 Dihedral : 4.242 47.295 1572 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.82 % Allowed : 25.93 % Favored : 70.24 % 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: 2.54 (0.15), residues: 1114 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 485 TYR 0.017 0.001 TYR C 221 PHE 0.013 0.001 PHE C 497 TRP 0.027 0.001 TRP A 432 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00275 (11610) covalent geometry : angle 0.58675 (15870) SS BOND : bond 0.00135 ( 6) SS BOND : angle 0.63161 ( 12) hydrogen bonds : bond 0.04705 ( 872) hydrogen bonds : angle 3.81564 ( 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 346 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 299 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7106 (tt) REVERT: A 134 LYS cc_start: 0.8572 (mmtp) cc_final: 0.8317 (mmtp) REVERT: A 204 ARG cc_start: 0.8720 (ttp-170) cc_final: 0.8500 (ttp80) REVERT: A 205 ASP cc_start: 0.8364 (m-30) cc_final: 0.8095 (m-30) REVERT: A 222 LEU cc_start: 0.8759 (mt) cc_final: 0.8550 (mm) REVERT: A 305 LEU cc_start: 0.8592 (tp) cc_final: 0.8378 (tm) REVERT: A 327 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7748 (tm) REVERT: A 346 ASP cc_start: 0.8037 (t0) cc_final: 0.7608 (t0) REVERT: A 356 ARG cc_start: 0.7657 (ttt-90) cc_final: 0.6239 (ttt-90) REVERT: A 453 LEU cc_start: 0.5797 (OUTLIER) cc_final: 0.5533 (tm) REVERT: A 468 SER cc_start: 0.8084 (p) cc_final: 0.7854 (m) REVERT: A 480 ARG cc_start: 0.8518 (mmm-85) cc_final: 0.7662 (mtm180) REVERT: B 67 PHE cc_start: 0.8756 (t80) cc_final: 0.8540 (t80) REVERT: B 85 LYS cc_start: 0.8044 (tmtt) cc_final: 0.7721 (tmtt) REVERT: B 90 TYR cc_start: 0.7397 (t80) cc_final: 0.7013 (t80) REVERT: B 147 PHE cc_start: 0.7700 (m-80) cc_final: 0.7427 (m-80) REVERT: B 316 LYS cc_start: 0.8576 (mptt) cc_final: 0.8172 (mptt) REVERT: B 331 LYS cc_start: 0.8356 (mtpt) cc_final: 0.8079 (mtmm) REVERT: B 339 LEU cc_start: 0.8773 (mt) cc_final: 0.8552 (mm) REVERT: B 346 ASP cc_start: 0.8057 (t0) cc_final: 0.7656 (t0) REVERT: B 352 ARG cc_start: 0.8380 (mmt180) cc_final: 0.7830 (mmm-85) REVERT: B 366 SER cc_start: 0.8330 (m) cc_final: 0.8000 (p) REVERT: B 371 VAL cc_start: 0.8606 (t) cc_final: 0.8257 (m) REVERT: B 387 LEU cc_start: 0.3062 (OUTLIER) cc_final: 0.2783 (pp) REVERT: B 480 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.8093 (mtm180) REVERT: C 67 PHE cc_start: 0.8577 (t80) cc_final: 0.8020 (t80) REVERT: C 85 LYS cc_start: 0.8603 (mtpm) cc_final: 0.8201 (mtpp) REVERT: C 101 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7750 (m) REVERT: C 125 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8167 (t0) REVERT: C 239 PHE cc_start: 0.8763 (t80) cc_final: 0.8514 (t80) REVERT: C 315 ARG cc_start: 0.7992 (mpt180) cc_final: 0.7701 (mpt180) REVERT: C 327 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8413 (tm) REVERT: C 331 LYS cc_start: 0.8610 (ttmt) cc_final: 0.8015 (ttpt) REVERT: C 332 LEU cc_start: 0.8706 (mt) cc_final: 0.8448 (mt) REVERT: C 335 GLU cc_start: 0.7844 (mt-10) cc_final: 0.7412 (mp0) REVERT: C 371 VAL cc_start: 0.8803 (t) cc_final: 0.8539 (m) REVERT: C 429 SER cc_start: 0.8500 (t) cc_final: 0.8220 (p) REVERT: C 452 ARG cc_start: 0.8357 (mtm110) cc_final: 0.8128 (mtm180) REVERT: C 489 SER cc_start: 0.8589 (t) cc_final: 0.8323 (p) outliers start: 47 outliers final: 27 residues processed: 325 average time/residue: 0.3665 time to fit residues: 132.2770 Evaluate side-chains 331 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 297 time to evaluate : 0.267 ------------------------------------------------------------------------------- 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 142 VAL 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 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 361 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 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 526 LEU 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 76 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 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 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: 0.1980 chunk 4 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 2 optimal weight: 0.0060 chunk 121 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN A 359 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN B 411 ASN B 434 ASN B 442 ASN B 549 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.148343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.119678 restraints weight = 17528.215| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.51 r_work: 0.3484 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3149 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= 0.125 Angle : 0.582 10.891 15882 Z= 0.283 Chirality : 0.040 0.340 1932 Planarity : 0.004 0.047 1929 Dihedral : 4.158 46.505 1572 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.33 % Allowed : 26.83 % 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: 2.91 (0.22), residues: 1452 helix: 2.56 (0.15), residues: 1114 sheet: None (None), residues: 0 loop : -0.28 (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 0.014 0.001 PHE C 336 TRP 0.016 0.001 TRP A 432 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00266 (11610) covalent geometry : angle 0.58151 (15870) SS BOND : bond 0.00105 ( 6) SS BOND : angle 0.65139 ( 12) hydrogen bonds : bond 0.04501 ( 872) hydrogen bonds : angle 3.77617 ( 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 330 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 289 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7085 (tt) REVERT: A 134 LYS cc_start: 0.8542 (mmtp) cc_final: 0.8294 (mmtp) REVERT: A 204 ARG cc_start: 0.8704 (ttp-170) cc_final: 0.8492 (ttp80) REVERT: A 205 ASP cc_start: 0.8343 (m-30) cc_final: 0.8073 (m-30) REVERT: A 222 LEU cc_start: 0.8723 (mt) cc_final: 0.8518 (mm) REVERT: A 305 LEU cc_start: 0.8618 (tp) cc_final: 0.8410 (tm) REVERT: A 327 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7737 (tm) REVERT: A 346 ASP cc_start: 0.8006 (t0) cc_final: 0.7535 (t0) REVERT: A 356 ARG cc_start: 0.7646 (ttt-90) cc_final: 0.6249 (ttt-90) REVERT: A 453 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.5483 (tm) REVERT: A 468 SER cc_start: 0.7941 (p) cc_final: 0.7715 (m) REVERT: A 480 ARG cc_start: 0.8514 (mmm-85) cc_final: 0.7631 (mtm180) REVERT: A 498 ASN cc_start: 0.8374 (m-40) cc_final: 0.8040 (m110) REVERT: B 67 PHE cc_start: 0.8825 (t80) cc_final: 0.8591 (t80) REVERT: B 85 LYS cc_start: 0.8003 (tmtt) cc_final: 0.7651 (tmtt) REVERT: B 90 TYR cc_start: 0.7357 (t80) cc_final: 0.6971 (t80) REVERT: B 147 PHE cc_start: 0.7679 (m-80) cc_final: 0.7400 (m-80) REVERT: B 210 MET cc_start: 0.8795 (mtp) cc_final: 0.8472 (mtm) REVERT: B 316 LYS cc_start: 0.8582 (mptt) cc_final: 0.8227 (mptt) REVERT: B 331 LYS cc_start: 0.8380 (mtpt) cc_final: 0.8162 (mtpm) REVERT: B 339 LEU cc_start: 0.8770 (mt) cc_final: 0.8549 (mm) REVERT: B 346 ASP cc_start: 0.8063 (t0) cc_final: 0.7610 (t0) REVERT: B 352 ARG cc_start: 0.8452 (mmt180) cc_final: 0.7850 (mmm-85) REVERT: B 366 SER cc_start: 0.8337 (m) cc_final: 0.8000 (p) REVERT: B 371 VAL cc_start: 0.8584 (t) cc_final: 0.8225 (m) REVERT: B 372 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8131 (mm) REVERT: B 387 LEU cc_start: 0.3059 (OUTLIER) cc_final: 0.2780 (pp) REVERT: B 480 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.8075 (ttm170) REVERT: C 67 PHE cc_start: 0.8594 (t80) cc_final: 0.8199 (t80) REVERT: C 85 LYS cc_start: 0.8621 (mtpm) cc_final: 0.8207 (mtpp) REVERT: C 125 ASN cc_start: 0.8419 (OUTLIER) cc_final: 0.8130 (t0) REVERT: C 239 PHE cc_start: 0.8737 (t80) cc_final: 0.8494 (t80) REVERT: C 315 ARG cc_start: 0.7968 (mpt180) cc_final: 0.7703 (mpt180) REVERT: C 429 SER cc_start: 0.8481 (t) cc_final: 0.8213 (p) REVERT: C 452 ARG cc_start: 0.8332 (mtm110) cc_final: 0.8106 (mtm110) REVERT: C 489 SER cc_start: 0.8594 (t) cc_final: 0.8326 (p) outliers start: 41 outliers final: 26 residues processed: 314 average time/residue: 0.3720 time to fit residues: 129.2456 Evaluate side-chains 317 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 285 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 142 VAL 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 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 313 ASP Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 372 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 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 84 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 443 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 120 optimal weight: 0.0060 chunk 25 optimal weight: 0.1980 chunk 27 optimal weight: 0.9990 chunk 95 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 135 optimal weight: 0.2980 chunk 64 optimal weight: 0.8980 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN A 359 ASN A 442 ASN A 467 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN B 411 ASN B 434 ASN B 442 ASN B 549 GLN C 411 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.149335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.120903 restraints weight = 17821.829| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.51 r_work: 0.3498 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11616 Z= 0.120 Angle : 0.594 10.864 15882 Z= 0.288 Chirality : 0.041 0.335 1932 Planarity : 0.004 0.047 1929 Dihedral : 3.972 38.425 1570 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.01 % Allowed : 27.56 % Favored : 69.43 % 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: 2.92 (0.22), residues: 1452 helix: 2.59 (0.15), residues: 1113 sheet: None (None), residues: 0 loop : -0.35 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 485 TYR 0.014 0.001 TYR A 83 PHE 0.017 0.001 PHE A 121 TRP 0.016 0.001 TRP A 432 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00248 (11610) covalent geometry : angle 0.59445 (15870) SS BOND : bond 0.00109 ( 6) SS BOND : angle 0.64932 ( 12) hydrogen bonds : bond 0.04278 ( 872) hydrogen bonds : angle 3.76020 ( 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 327 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 290 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7090 (tt) REVERT: A 134 LYS cc_start: 0.8554 (mmtp) cc_final: 0.8302 (mmtp) REVERT: A 204 ARG cc_start: 0.8687 (ttp-170) cc_final: 0.8459 (ptt-90) REVERT: A 205 ASP cc_start: 0.8337 (m-30) cc_final: 0.7999 (m-30) REVERT: A 305 LEU cc_start: 0.8606 (tp) cc_final: 0.8398 (tm) REVERT: A 327 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7730 (tm) REVERT: A 346 ASP cc_start: 0.8016 (t0) cc_final: 0.7590 (t0) REVERT: A 356 ARG cc_start: 0.7553 (ttt-90) cc_final: 0.6197 (ttt-90) REVERT: A 453 LEU cc_start: 0.5591 (OUTLIER) cc_final: 0.5330 (tm) REVERT: A 468 SER cc_start: 0.7875 (p) cc_final: 0.7664 (m) REVERT: A 480 ARG cc_start: 0.8460 (mmm-85) cc_final: 0.7590 (mtm180) REVERT: A 498 ASN cc_start: 0.8382 (m-40) cc_final: 0.8056 (m110) REVERT: B 67 PHE cc_start: 0.8743 (t80) cc_final: 0.8513 (t80) REVERT: B 85 LYS cc_start: 0.7995 (tmtt) cc_final: 0.7644 (tmtt) REVERT: B 90 TYR cc_start: 0.7419 (t80) cc_final: 0.7016 (t80) REVERT: B 147 PHE cc_start: 0.7654 (m-80) cc_final: 0.7396 (m-80) REVERT: B 210 MET cc_start: 0.8795 (mtp) cc_final: 0.8480 (mtm) REVERT: B 316 LYS cc_start: 0.8595 (mptt) cc_final: 0.8252 (mptt) REVERT: B 331 LYS cc_start: 0.8365 (mtpt) cc_final: 0.8138 (mtpm) REVERT: B 339 LEU cc_start: 0.8764 (mt) cc_final: 0.8554 (mm) REVERT: B 346 ASP cc_start: 0.8056 (t0) cc_final: 0.7639 (t0) REVERT: B 352 ARG cc_start: 0.8400 (mmt180) cc_final: 0.7834 (mmm-85) REVERT: B 366 SER cc_start: 0.8322 (m) cc_final: 0.7973 (p) REVERT: B 371 VAL cc_start: 0.8573 (t) cc_final: 0.8217 (m) REVERT: B 372 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8115 (mm) REVERT: B 387 LEU cc_start: 0.3002 (OUTLIER) cc_final: 0.2722 (pp) REVERT: B 442 ASN cc_start: 0.8683 (m-40) cc_final: 0.8301 (m110) REVERT: B 480 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.8081 (mtm180) REVERT: C 67 PHE cc_start: 0.8591 (t80) cc_final: 0.8256 (t80) REVERT: C 85 LYS cc_start: 0.8587 (mtpm) cc_final: 0.8181 (mtpp) REVERT: C 125 ASN cc_start: 0.8432 (OUTLIER) cc_final: 0.8158 (t0) REVERT: C 126 LEU cc_start: 0.7406 (tp) cc_final: 0.7123 (tm) REVERT: C 239 PHE cc_start: 0.8718 (t80) cc_final: 0.8474 (t80) REVERT: C 315 ARG cc_start: 0.7965 (mpt180) cc_final: 0.7684 (mpt180) REVERT: C 429 SER cc_start: 0.8437 (t) cc_final: 0.8175 (p) REVERT: C 452 ARG cc_start: 0.8293 (mtm110) cc_final: 0.8066 (mtm110) REVERT: C 483 TYR cc_start: 0.8296 (m-80) cc_final: 0.7898 (m-80) REVERT: C 489 SER cc_start: 0.8608 (t) cc_final: 0.8337 (p) outliers start: 37 outliers final: 25 residues processed: 310 average time/residue: 0.4024 time to fit residues: 137.5864 Evaluate side-chains 319 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 288 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LYS 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 142 VAL 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 142 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 224 ARG Chi-restraints excluded: chain B residue 313 ASP Chi-restraints excluded: chain B residue 329 VAL 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 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 69 LYS Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain C residue 443 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 57 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 42 optimal weight: 0.0030 chunk 135 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 120 optimal weight: 0.0980 overall best weight: 0.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 ASN A 359 ASN A 442 ASN ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN B 549 GLN 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 = 0.148787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.119935 restraints weight = 17810.999| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.56 r_work: 0.3491 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11616 Z= 0.121 Angle : 0.589 10.213 15882 Z= 0.286 Chirality : 0.040 0.326 1932 Planarity : 0.004 0.047 1929 Dihedral : 3.887 38.326 1570 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.68 % Allowed : 28.21 % Favored : 69.11 % 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: 2.61 (0.15), residues: 1113 sheet: None (None), residues: 0 loop : -0.36 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 485 TYR 0.017 0.001 TYR A 209 PHE 0.016 0.001 PHE C 336 TRP 0.015 0.001 TRP A 432 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00255 (11610) covalent geometry : angle 0.58932 (15870) SS BOND : bond 0.00137 ( 6) SS BOND : angle 0.69173 ( 12) hydrogen bonds : bond 0.04261 ( 872) hydrogen bonds : angle 3.74788 ( 2583) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3487.67 seconds wall clock time: 60 minutes 3.51 seconds (3603.51 seconds total)