Starting phenix.real_space_refine on Sun May 11 16:33:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gs4_34220/05_2025/8gs4_34220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gs4_34220/05_2025/8gs4_34220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gs4_34220/05_2025/8gs4_34220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gs4_34220/05_2025/8gs4_34220.map" model { file = "/net/cci-nas-00/data/ceres_data/8gs4_34220/05_2025/8gs4_34220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gs4_34220/05_2025/8gs4_34220.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.085 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 5288 2.51 5 N 1412 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8250 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4125 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 34, 'TRANS': 490} Chain breaks: 3 Restraints were copied for chains: B Time building chain proxies: 7.30, per 1000 atoms: 0.88 Number of scatterers: 8250 At special positions: 0 Unit cell: (65.32, 153.64, 81.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 1514 8.00 N 1412 7.00 C 5288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 317 " - pdb=" SG CYS A 328 " distance=2.03 Simple disulfide: pdb=" SG CYS A 487 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS B 106 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 317 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS B 487 " - pdb=" SG CYS B 521 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.0 seconds 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 34.1% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 120 through 126 removed outlier: 3.564A pdb=" N THR A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 126 " --> pdb=" O TRP A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 132 removed outlier: 3.716A pdb=" N THR A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 removed outlier: 3.859A pdb=" N ASP A 197 " --> pdb=" O ASN A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.981A pdb=" N GLY A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 221 removed outlier: 3.893A pdb=" N GLY A 220 " --> pdb=" O GLY A 217 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A 221 " --> pdb=" O VAL A 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 217 through 221' Processing helix chain 'A' and resid 232 through 248 removed outlier: 3.598A pdb=" N LEU A 236 " --> pdb=" O ASN A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 268 through 273 removed outlier: 3.799A pdb=" N ASN A 272 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 268 through 273' Processing helix chain 'A' and resid 303 through 309 removed outlier: 3.759A pdb=" N TYR A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 405 through 417 removed outlier: 4.100A pdb=" N VAL A 410 " --> pdb=" O PHE A 406 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N SER A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN A 412 " --> pdb=" O PHE A 408 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 4.596A pdb=" N LEU A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 441 removed outlier: 4.163A pdb=" N ARG A 441 " --> pdb=" O TRP A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 Processing helix chain 'A' and resid 454 through 460 removed outlier: 3.923A pdb=" N HIS A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN A 459 " --> pdb=" O PHE A 455 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP A 460 " --> pdb=" O THR A 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 454 through 460' Processing helix chain 'A' and resid 463 through 474 removed outlier: 3.536A pdb=" N LEU A 470 " --> pdb=" O ALA A 466 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.635A pdb=" N VAL A 513 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 545 removed outlier: 4.160A pdb=" N LEU A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 533 " --> pdb=" O MET A 529 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TRP A 538 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR A 539 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA A 542 " --> pdb=" O TRP A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 604 removed outlier: 3.628A pdb=" N LEU A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 609 removed outlier: 3.971A pdb=" N LEU A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS A 609 " --> pdb=" O VAL A 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 604 through 609' Processing helix chain 'B' and resid 120 through 126 removed outlier: 3.564A pdb=" N THR B 124 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 126 " --> pdb=" O TRP B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 removed outlier: 3.716A pdb=" N THR B 132 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 197 removed outlier: 3.859A pdb=" N ASP B 197 " --> pdb=" O ASN B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.981A pdb=" N GLY B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 221 removed outlier: 3.892A pdb=" N GLY B 220 " --> pdb=" O GLY B 217 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE B 221 " --> pdb=" O VAL B 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 217 through 221' Processing helix chain 'B' and resid 232 through 248 removed outlier: 3.599A pdb=" N LEU B 236 " --> pdb=" O ASN B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.799A pdb=" N ASN B 272 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 268 through 273' Processing helix chain 'B' and resid 303 through 309 removed outlier: 3.758A pdb=" N TYR B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 363 through 368 removed outlier: 3.504A pdb=" N MET B 368 " --> pdb=" O PRO B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 417 removed outlier: 4.091A pdb=" N VAL B 410 " --> pdb=" O PHE B 406 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N SER B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN B 412 " --> pdb=" O PHE B 408 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL B 414 " --> pdb=" O VAL B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 removed outlier: 4.596A pdb=" N LEU B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 441 removed outlier: 4.163A pdb=" N ARG B 441 " --> pdb=" O TRP B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 453 Processing helix chain 'B' and resid 454 through 460 removed outlier: 3.924A pdb=" N HIS B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 459 " --> pdb=" O PHE B 455 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP B 460 " --> pdb=" O THR B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 454 through 460' Processing helix chain 'B' and resid 463 through 474 removed outlier: 3.534A pdb=" N LEU B 470 " --> pdb=" O ALA B 466 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 509 Processing helix chain 'B' and resid 510 through 514 removed outlier: 3.636A pdb=" N VAL B 513 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 545 removed outlier: 4.160A pdb=" N LEU B 530 " --> pdb=" O ASN B 526 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL B 533 " --> pdb=" O MET B 529 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP B 538 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ALA B 542 " --> pdb=" O TRP B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 604 removed outlier: 3.626A pdb=" N LEU B 604 " --> pdb=" O PHE B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 609 removed outlier: 3.966A pdb=" N LEU B 608 " --> pdb=" O LEU B 604 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N HIS B 609 " --> pdb=" O VAL B 605 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 604 through 609' Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 57 removed outlier: 3.720A pdb=" N VAL A 66 " --> pdb=" O ARG A 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73 Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210 removed outlier: 4.213A pdb=" N ALA A 210 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS A 177 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU A 257 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL A 179 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ILE A 259 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU A 181 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 210 removed outlier: 4.213A pdb=" N ALA A 210 " --> pdb=" O MET A 180 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N PHE A 262 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU A 181 " --> pdb=" O PHE A 262 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 290 removed outlier: 8.448A pdb=" N PHE A 483 " --> pdb=" O ILE A 380 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL A 382 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 46 Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57 removed outlier: 3.720A pdb=" N VAL B 66 " --> pdb=" O ARG B 56 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 73 Processing sheet with id=AB1, first strand: chain 'B' and resid 208 through 210 removed outlier: 4.213A pdb=" N ALA B 210 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS B 177 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU B 257 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N VAL B 179 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE B 259 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU B 181 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 210 removed outlier: 4.213A pdb=" N ALA B 210 " --> pdb=" O MET B 180 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N PHE B 262 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 181 " --> pdb=" O PHE B 262 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 289 through 290 removed outlier: 8.448A pdb=" N PHE B 483 " --> pdb=" O ILE B 380 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL B 382 " --> pdb=" O PHE B 483 " (cutoff:3.500A) 157 hydrogen bonds defined for protein. 411 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: 1.94 Time building geometry restraints manager: 2.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2713 1.34 - 1.46: 2003 1.46 - 1.58: 3706 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 8480 Sorted by residual: bond pdb=" CG LEU A 581 " pdb=" CD1 LEU A 581 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.46e+00 bond pdb=" CG LEU B 581 " pdb=" CD1 LEU B 581 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.46e+00 bond pdb=" C GLN B 549 " pdb=" N PRO B 550 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.56e+00 bond pdb=" C GLN A 549 " pdb=" N PRO A 550 " ideal model delta sigma weight residual 1.334 1.363 -0.029 2.34e-02 1.83e+03 1.56e+00 bond pdb=" CA ASP A 440 " pdb=" CB ASP A 440 " ideal model delta sigma weight residual 1.524 1.540 -0.016 1.62e-02 3.81e+03 9.59e-01 ... (remaining 8475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 11175 2.03 - 4.07: 319 4.07 - 6.10: 46 6.10 - 8.14: 6 8.14 - 10.17: 6 Bond angle restraints: 11552 Sorted by residual: angle pdb=" N VAL B 359 " pdb=" CA VAL B 359 " pdb=" C VAL B 359 " ideal model delta sigma weight residual 113.53 108.90 4.63 9.80e-01 1.04e+00 2.23e+01 angle pdb=" N VAL A 359 " pdb=" CA VAL A 359 " pdb=" C VAL A 359 " ideal model delta sigma weight residual 113.53 108.90 4.63 9.80e-01 1.04e+00 2.23e+01 angle pdb=" C VAL A 461 " pdb=" N ALA A 462 " pdb=" CA ALA A 462 " ideal model delta sigma weight residual 121.80 112.76 9.04 2.44e+00 1.68e-01 1.37e+01 angle pdb=" C VAL B 461 " pdb=" N ALA B 462 " pdb=" CA ALA B 462 " ideal model delta sigma weight residual 121.80 112.76 9.04 2.44e+00 1.68e-01 1.37e+01 angle pdb=" C GLY A 545 " pdb=" N ASP A 546 " pdb=" CA ASP A 546 " ideal model delta sigma weight residual 120.69 110.52 10.17 2.95e+00 1.15e-01 1.19e+01 ... (remaining 11547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.56: 4370 15.56 - 31.11: 496 31.11 - 46.67: 108 46.67 - 62.22: 14 62.22 - 77.78: 4 Dihedral angle restraints: 4992 sinusoidal: 1970 harmonic: 3022 Sorted by residual: dihedral pdb=" CA ALA A 462 " pdb=" C ALA A 462 " pdb=" N PRO A 463 " pdb=" CA PRO A 463 " ideal model delta harmonic sigma weight residual 180.00 141.19 38.81 0 5.00e+00 4.00e-02 6.02e+01 dihedral pdb=" CA ALA B 462 " pdb=" C ALA B 462 " pdb=" N PRO B 463 " pdb=" CA PRO B 463 " ideal model delta harmonic sigma weight residual 180.00 141.19 38.81 0 5.00e+00 4.00e-02 6.02e+01 dihedral pdb=" CB CYS B 317 " pdb=" SG CYS B 317 " pdb=" SG CYS B 328 " pdb=" CB CYS B 328 " ideal model delta sinusoidal sigma weight residual 93.00 153.84 -60.84 1 1.00e+01 1.00e-02 4.92e+01 ... (remaining 4989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 637 0.031 - 0.063: 383 0.063 - 0.094: 127 0.094 - 0.126: 74 0.126 - 0.157: 15 Chirality restraints: 1236 Sorted by residual: chirality pdb=" CB THR A 101 " pdb=" CA THR A 101 " pdb=" OG1 THR A 101 " pdb=" CG2 THR A 101 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CB THR B 101 " pdb=" CA THR B 101 " pdb=" OG1 THR B 101 " pdb=" CG2 THR B 101 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA LEU A 581 " pdb=" N LEU A 581 " pdb=" C LEU A 581 " pdb=" CB LEU A 581 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.14e-01 ... (remaining 1233 not shown) Planarity restraints: 1518 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 462 " 0.064 5.00e-02 4.00e+02 9.73e-02 1.51e+01 pdb=" N PRO A 463 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 462 " 0.064 5.00e-02 4.00e+02 9.73e-02 1.51e+01 pdb=" N PRO B 463 " -0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 463 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 463 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 298 " 0.021 2.00e-02 2.50e+03 2.04e-02 1.04e+01 pdb=" CG TRP B 298 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP B 298 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 298 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 298 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 298 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 298 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 298 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 298 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 298 " 0.003 2.00e-02 2.50e+03 ... (remaining 1515 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2002 2.78 - 3.31: 7699 3.31 - 3.84: 12585 3.84 - 4.37: 14988 4.37 - 4.90: 25900 Nonbonded interactions: 63174 Sorted by model distance: nonbonded pdb=" OG SER A 269 " pdb=" OG SER A 299 " model vdw 2.251 3.040 nonbonded pdb=" OG SER B 269 " pdb=" OG SER B 299 " model vdw 2.252 3.040 nonbonded pdb=" O GLU A 327 " pdb=" NH2 ARG A 331 " model vdw 2.255 3.120 nonbonded pdb=" O GLU B 327 " pdb=" NH2 ARG B 331 " model vdw 2.255 3.120 nonbonded pdb=" O SER B 575 " pdb=" NZ LYS B 578 " model vdw 2.271 3.120 ... (remaining 63169 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.370 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 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 0.052 8486 Z= 0.184 Angle : 0.838 10.174 11564 Z= 0.443 Chirality : 0.048 0.157 1236 Planarity : 0.007 0.097 1518 Dihedral : 13.581 77.781 3042 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.35 % Favored : 86.65 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.70 (0.22), residues: 1034 helix: -3.64 (0.23), residues: 266 sheet: -3.45 (0.45), residues: 110 loop : -2.97 (0.21), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP B 298 HIS 0.006 0.001 HIS B 582 PHE 0.026 0.002 PHE B 262 TYR 0.017 0.002 TYR B 580 ARG 0.003 0.000 ARG A 447 Details of bonding type rmsd hydrogen bonds : bond 0.22035 ( 151) hydrogen bonds : angle 8.76489 ( 411) SS BOND : bond 0.00182 ( 6) SS BOND : angle 2.88898 ( 12) covalent geometry : bond 0.00411 ( 8480) covalent geometry : angle 0.83280 (11552) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.908 Fit side-chains REVERT: A 260 THR cc_start: 0.8752 (m) cc_final: 0.8511 (p) REVERT: B 260 THR cc_start: 0.8739 (m) cc_final: 0.8499 (p) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1976 time to fit residues: 31.7370 Evaluate side-chains 94 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 0.2980 chunk 78 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.195841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.158945 restraints weight = 10807.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.158402 restraints weight = 9037.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.159944 restraints weight = 9116.330| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8486 Z= 0.224 Angle : 0.802 9.355 11564 Z= 0.408 Chirality : 0.049 0.151 1236 Planarity : 0.007 0.100 1518 Dihedral : 6.787 40.136 1140 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.73 % Favored : 86.27 % Rotamer: Outliers : 1.15 % Allowed : 9.89 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.41 (0.22), residues: 1034 helix: -3.09 (0.24), residues: 258 sheet: -3.71 (0.42), residues: 122 loop : -2.82 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 298 HIS 0.007 0.001 HIS A 458 PHE 0.024 0.002 PHE A 262 TYR 0.018 0.002 TYR B 214 ARG 0.003 0.001 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.04893 ( 151) hydrogen bonds : angle 6.45036 ( 411) SS BOND : bond 0.00138 ( 6) SS BOND : angle 1.62893 ( 12) covalent geometry : bond 0.00530 ( 8480) covalent geometry : angle 0.80054 (11552) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.845 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 107 average time/residue: 0.1678 time to fit residues: 26.0956 Evaluate side-chains 105 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 529 MET Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 529 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 8 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 43 optimal weight: 0.0970 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.199240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.163235 restraints weight = 10900.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.164067 restraints weight = 8965.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.165537 restraints weight = 8425.406| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8486 Z= 0.148 Angle : 0.699 7.845 11564 Z= 0.354 Chirality : 0.045 0.137 1236 Planarity : 0.006 0.091 1518 Dihedral : 6.250 39.688 1140 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 2.30 % Allowed : 14.60 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.24), residues: 1034 helix: -2.62 (0.28), residues: 256 sheet: -3.20 (0.46), residues: 106 loop : -2.63 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 298 HIS 0.004 0.001 HIS B 458 PHE 0.016 0.002 PHE A 262 TYR 0.012 0.001 TYR A 481 ARG 0.003 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 151) hydrogen bonds : angle 5.85836 ( 411) SS BOND : bond 0.00213 ( 6) SS BOND : angle 1.12346 ( 12) covalent geometry : bond 0.00349 ( 8480) covalent geometry : angle 0.69814 (11552) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 133 TYR cc_start: 0.7163 (OUTLIER) cc_final: 0.6414 (t80) REVERT: A 503 GLU cc_start: 0.7079 (pm20) cc_final: 0.5882 (tm-30) REVERT: B 133 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.6417 (t80) REVERT: B 503 GLU cc_start: 0.7089 (pm20) cc_final: 0.5891 (tm-30) outliers start: 20 outliers final: 12 residues processed: 117 average time/residue: 0.1951 time to fit residues: 32.2981 Evaluate side-chains 111 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 65 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 99 optimal weight: 0.0060 chunk 26 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 56 optimal weight: 0.0370 chunk 80 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 chunk 83 optimal weight: 0.0070 overall best weight: 0.1470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.206531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.170865 restraints weight = 10722.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.172242 restraints weight = 10000.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.173755 restraints weight = 9212.196| |-----------------------------------------------------------------------------| r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8486 Z= 0.107 Angle : 0.638 7.430 11564 Z= 0.316 Chirality : 0.044 0.163 1236 Planarity : 0.005 0.076 1518 Dihedral : 5.398 38.221 1140 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.25 % Favored : 89.75 % Rotamer: Outliers : 1.15 % Allowed : 16.32 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.25), residues: 1034 helix: -2.00 (0.32), residues: 246 sheet: -3.04 (0.44), residues: 110 loop : -2.40 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 570 HIS 0.003 0.000 HIS B 609 PHE 0.011 0.001 PHE A 483 TYR 0.009 0.001 TYR A 435 ARG 0.002 0.000 ARG B 448 Details of bonding type rmsd hydrogen bonds : bond 0.03030 ( 151) hydrogen bonds : angle 5.14395 ( 411) SS BOND : bond 0.00389 ( 6) SS BOND : angle 0.64324 ( 12) covalent geometry : bond 0.00247 ( 8480) covalent geometry : angle 0.63764 (11552) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 103 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 LEU cc_start: 0.8037 (mm) cc_final: 0.7756 (mt) REVERT: A 133 TYR cc_start: 0.6951 (OUTLIER) cc_final: 0.6340 (t80) REVERT: A 147 TYR cc_start: 0.8455 (m-80) cc_final: 0.8100 (m-10) REVERT: A 448 ARG cc_start: 0.6114 (ttt180) cc_final: 0.5828 (ttm-80) REVERT: B 102 LEU cc_start: 0.8045 (mm) cc_final: 0.7764 (mt) REVERT: B 133 TYR cc_start: 0.6974 (OUTLIER) cc_final: 0.6369 (t80) REVERT: B 147 TYR cc_start: 0.8451 (m-80) cc_final: 0.8100 (m-10) REVERT: B 448 ARG cc_start: 0.6105 (ttt180) cc_final: 0.5821 (ttm-80) outliers start: 10 outliers final: 4 residues processed: 113 average time/residue: 0.2019 time to fit residues: 31.7232 Evaluate side-chains 100 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 94 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 440 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 9 optimal weight: 8.9990 chunk 55 optimal weight: 0.0270 chunk 60 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 44 optimal weight: 0.0970 overall best weight: 1.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.201392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.165077 restraints weight = 10823.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.166191 restraints weight = 9065.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.167311 restraints weight = 8541.798| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8486 Z= 0.137 Angle : 0.652 8.174 11564 Z= 0.327 Chirality : 0.044 0.131 1236 Planarity : 0.006 0.090 1518 Dihedral : 5.581 38.789 1140 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 2.53 % Allowed : 17.01 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.25), residues: 1034 helix: -2.01 (0.31), residues: 250 sheet: -3.12 (0.43), residues: 110 loop : -2.37 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 570 HIS 0.005 0.001 HIS B 471 PHE 0.012 0.001 PHE B 262 TYR 0.013 0.001 TYR A 481 ARG 0.002 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.03508 ( 151) hydrogen bonds : angle 5.30371 ( 411) SS BOND : bond 0.00256 ( 6) SS BOND : angle 0.93255 ( 12) covalent geometry : bond 0.00330 ( 8480) covalent geometry : angle 0.65144 (11552) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.822 Fit side-chains REVERT: A 133 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.6475 (t80) REVERT: B 133 TYR cc_start: 0.7110 (OUTLIER) cc_final: 0.6476 (t80) outliers start: 22 outliers final: 16 residues processed: 115 average time/residue: 0.1893 time to fit residues: 30.4039 Evaluate side-chains 104 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.198941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.162673 restraints weight = 10829.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.163176 restraints weight = 9051.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.164387 restraints weight = 8714.811| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8486 Z= 0.175 Angle : 0.700 8.829 11564 Z= 0.353 Chirality : 0.045 0.141 1236 Planarity : 0.006 0.089 1518 Dihedral : 5.866 40.403 1140 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 2.53 % Allowed : 19.54 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.25), residues: 1034 helix: -2.02 (0.31), residues: 250 sheet: -3.25 (0.43), residues: 110 loop : -2.38 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B 570 HIS 0.007 0.001 HIS B 458 PHE 0.017 0.002 PHE A 262 TYR 0.015 0.002 TYR A 481 ARG 0.003 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 151) hydrogen bonds : angle 5.46620 ( 411) SS BOND : bond 0.00205 ( 6) SS BOND : angle 1.08138 ( 12) covalent geometry : bond 0.00414 ( 8480) covalent geometry : angle 0.69941 (11552) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.928 Fit side-chains REVERT: A 102 LEU cc_start: 0.8198 (mm) cc_final: 0.7931 (mt) REVERT: A 133 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6528 (t80) REVERT: A 222 LEU cc_start: 0.2222 (OUTLIER) cc_final: 0.1831 (mm) REVERT: B 102 LEU cc_start: 0.8191 (mm) cc_final: 0.7920 (mt) REVERT: B 133 TYR cc_start: 0.7253 (OUTLIER) cc_final: 0.6519 (t80) REVERT: B 222 LEU cc_start: 0.2220 (OUTLIER) cc_final: 0.1823 (mm) outliers start: 22 outliers final: 18 residues processed: 112 average time/residue: 0.1718 time to fit residues: 27.8744 Evaluate side-chains 110 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.198661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.162204 restraints weight = 10885.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.163082 restraints weight = 9178.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.164237 restraints weight = 8768.072| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8486 Z= 0.173 Angle : 0.697 9.301 11564 Z= 0.353 Chirality : 0.045 0.139 1236 Planarity : 0.006 0.089 1518 Dihedral : 5.890 40.299 1140 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.90 % Favored : 88.10 % Rotamer: Outliers : 3.22 % Allowed : 19.20 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.25), residues: 1034 helix: -2.00 (0.31), residues: 250 sheet: -3.28 (0.43), residues: 110 loop : -2.38 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 570 HIS 0.006 0.001 HIS A 458 PHE 0.022 0.002 PHE B 541 TYR 0.016 0.001 TYR A 481 ARG 0.003 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 151) hydrogen bonds : angle 5.44549 ( 411) SS BOND : bond 0.00223 ( 6) SS BOND : angle 1.06149 ( 12) covalent geometry : bond 0.00412 ( 8480) covalent geometry : angle 0.69690 (11552) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 94 time to evaluate : 0.955 Fit side-chains REVERT: A 102 LEU cc_start: 0.8236 (mm) cc_final: 0.7967 (mt) REVERT: A 133 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.6500 (t80) REVERT: A 222 LEU cc_start: 0.2360 (OUTLIER) cc_final: 0.1967 (mm) REVERT: B 102 LEU cc_start: 0.8223 (mm) cc_final: 0.7958 (mt) REVERT: B 133 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6490 (t80) REVERT: B 222 LEU cc_start: 0.2355 (OUTLIER) cc_final: 0.1971 (mm) outliers start: 28 outliers final: 22 residues processed: 118 average time/residue: 0.1637 time to fit residues: 28.3259 Evaluate side-chains 116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 4 optimal weight: 0.0050 chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 80 optimal weight: 0.4980 chunk 94 optimal weight: 4.9990 chunk 7 optimal weight: 0.0970 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.202493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.166565 restraints weight = 10999.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.166812 restraints weight = 9145.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.168304 restraints weight = 8696.660| |-----------------------------------------------------------------------------| r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8486 Z= 0.124 Angle : 0.658 10.464 11564 Z= 0.327 Chirality : 0.043 0.134 1236 Planarity : 0.005 0.083 1518 Dihedral : 5.505 39.661 1140 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 2.76 % Allowed : 19.77 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.25), residues: 1034 helix: -1.94 (0.31), residues: 260 sheet: -3.18 (0.43), residues: 110 loop : -2.35 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 570 HIS 0.003 0.001 HIS A 458 PHE 0.019 0.001 PHE A 541 TYR 0.016 0.001 TYR A 418 ARG 0.002 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.03313 ( 151) hydrogen bonds : angle 5.24527 ( 411) SS BOND : bond 0.00283 ( 6) SS BOND : angle 0.84822 ( 12) covalent geometry : bond 0.00297 ( 8480) covalent geometry : angle 0.65778 (11552) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 0.841 Fit side-chains REVERT: A 102 LEU cc_start: 0.8176 (mm) cc_final: 0.7919 (mt) REVERT: A 133 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6477 (t80) REVERT: A 222 LEU cc_start: 0.1985 (OUTLIER) cc_final: 0.1574 (mm) REVERT: A 448 ARG cc_start: 0.6451 (ttt180) cc_final: 0.6069 (ttm-80) REVERT: B 102 LEU cc_start: 0.8184 (mm) cc_final: 0.7925 (mt) REVERT: B 133 TYR cc_start: 0.7228 (OUTLIER) cc_final: 0.6458 (t80) REVERT: B 222 LEU cc_start: 0.2077 (OUTLIER) cc_final: 0.1683 (mm) REVERT: B 448 ARG cc_start: 0.6452 (ttt180) cc_final: 0.6067 (ttm-80) outliers start: 24 outliers final: 20 residues processed: 108 average time/residue: 0.1821 time to fit residues: 28.5426 Evaluate side-chains 110 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 195 MET Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 43 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.199538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.163394 restraints weight = 11044.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.165054 restraints weight = 9060.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.166177 restraints weight = 8314.645| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8486 Z= 0.160 Angle : 0.708 11.342 11564 Z= 0.352 Chirality : 0.045 0.135 1236 Planarity : 0.006 0.088 1518 Dihedral : 5.694 39.884 1140 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.32 % Favored : 88.68 % Rotamer: Outliers : 3.79 % Allowed : 19.43 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.25), residues: 1034 helix: -1.96 (0.30), residues: 260 sheet: -3.22 (0.43), residues: 110 loop : -2.31 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 570 HIS 0.005 0.001 HIS B 458 PHE 0.016 0.002 PHE B 262 TYR 0.015 0.001 TYR B 418 ARG 0.003 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.03718 ( 151) hydrogen bonds : angle 5.36145 ( 411) SS BOND : bond 0.00242 ( 6) SS BOND : angle 1.05810 ( 12) covalent geometry : bond 0.00382 ( 8480) covalent geometry : angle 0.70757 (11552) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.895 Fit side-chains REVERT: A 102 LEU cc_start: 0.8271 (mm) cc_final: 0.8003 (mt) REVERT: A 133 TYR cc_start: 0.7289 (OUTLIER) cc_final: 0.6521 (t80) REVERT: A 222 LEU cc_start: 0.2086 (OUTLIER) cc_final: 0.1659 (mm) REVERT: B 102 LEU cc_start: 0.8255 (mm) cc_final: 0.7985 (mt) REVERT: B 133 TYR cc_start: 0.7282 (OUTLIER) cc_final: 0.6518 (t80) REVERT: B 222 LEU cc_start: 0.2072 (OUTLIER) cc_final: 0.1638 (mm) outliers start: 33 outliers final: 23 residues processed: 117 average time/residue: 0.1723 time to fit residues: 29.4113 Evaluate side-chains 109 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 88 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.201466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.164175 restraints weight = 10970.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.164125 restraints weight = 9308.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.166117 restraints weight = 9470.916| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8486 Z= 0.141 Angle : 0.700 11.479 11564 Z= 0.343 Chirality : 0.044 0.176 1236 Planarity : 0.005 0.085 1518 Dihedral : 5.563 40.094 1140 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.03 % Favored : 88.97 % Rotamer: Outliers : 3.68 % Allowed : 19.43 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.25), residues: 1034 helix: -1.84 (0.31), residues: 260 sheet: -3.13 (0.44), residues: 110 loop : -2.31 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 570 HIS 0.004 0.001 HIS B 458 PHE 0.016 0.002 PHE A 69 TYR 0.022 0.001 TYR B 418 ARG 0.003 0.000 ARG B 83 Details of bonding type rmsd hydrogen bonds : bond 0.03471 ( 151) hydrogen bonds : angle 5.34378 ( 411) SS BOND : bond 0.00268 ( 6) SS BOND : angle 0.97884 ( 12) covalent geometry : bond 0.00337 ( 8480) covalent geometry : angle 0.69975 (11552) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2068 Ramachandran restraints generated. 1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 91 time to evaluate : 0.891 Fit side-chains REVERT: A 102 LEU cc_start: 0.8158 (mm) cc_final: 0.7895 (mt) REVERT: A 133 TYR cc_start: 0.7243 (OUTLIER) cc_final: 0.6478 (t80) REVERT: A 222 LEU cc_start: 0.2103 (OUTLIER) cc_final: 0.1694 (mm) REVERT: A 368 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5564 (ttt) REVERT: B 102 LEU cc_start: 0.8255 (mm) cc_final: 0.7989 (mt) REVERT: B 133 TYR cc_start: 0.7234 (OUTLIER) cc_final: 0.6463 (t80) REVERT: B 222 LEU cc_start: 0.2099 (OUTLIER) cc_final: 0.1686 (mm) outliers start: 32 outliers final: 24 residues processed: 117 average time/residue: 0.1700 time to fit residues: 28.8839 Evaluate side-chains 120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 106 CYS Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 355 VAL Chi-restraints excluded: chain A residue 368 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 106 CYS Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 222 LEU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 295 ILE Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 95 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.203407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.165930 restraints weight = 11143.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.166383 restraints weight = 9145.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.167898 restraints weight = 9186.038| |-----------------------------------------------------------------------------| r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8486 Z= 0.124 Angle : 0.678 11.424 11564 Z= 0.332 Chirality : 0.044 0.165 1236 Planarity : 0.005 0.083 1518 Dihedral : 5.335 39.533 1140 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 3.45 % Allowed : 19.66 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.25), residues: 1034 helix: -1.72 (0.31), residues: 260 sheet: -3.00 (0.45), residues: 110 loop : -2.24 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 570 HIS 0.003 0.001 HIS B 609 PHE 0.011 0.001 PHE B 262 TYR 0.020 0.001 TYR A 418 ARG 0.002 0.000 ARG A 83 Details of bonding type rmsd hydrogen bonds : bond 0.03241 ( 151) hydrogen bonds : angle 5.25494 ( 411) SS BOND : bond 0.00304 ( 6) SS BOND : angle 0.84766 ( 12) covalent geometry : bond 0.00296 ( 8480) covalent geometry : angle 0.67756 (11552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2382.45 seconds wall clock time: 42 minutes 31.09 seconds (2551.09 seconds total)