Starting phenix.real_space_refine on Sat Dec 28 09:33:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gs4_34220/12_2024/8gs4_34220.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gs4_34220/12_2024/8gs4_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_34220/12_2024/8gs4_34220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gs4_34220/12_2024/8gs4_34220.map" model { file = "/net/cci-nas-00/data/ceres_data/8gs4_34220/12_2024/8gs4_34220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gs4_34220/12_2024/8gs4_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 7.10, per 1000 atoms: 0.86 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=3, 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 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: 1.94 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: 0.87 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: 2.50 Time building geometry restraints manager: 2.24 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: 4369 15.56 - 31.11: 494 31.11 - 46.67: 105 46.67 - 62.22: 11 62.22 - 77.78: 4 Dihedral angle restraints: 4983 sinusoidal: 1961 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 A 317 " pdb=" SG CYS A 317 " pdb=" SG CYS A 328 " pdb=" CB CYS A 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 4980 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: 2.03 - 2.60: 107 2.60 - 3.18: 7279 3.18 - 3.75: 11806 3.75 - 4.33: 16457 4.33 - 4.90: 27534 Nonbonded interactions: 63183 Sorted by model distance: nonbonded pdb=" SG CYS B 317 " pdb=" SG CYS B 328 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 487 " pdb=" SG CYS B 521 " model vdw 2.031 3.760 nonbonded pdb=" SG CYS B 106 " pdb=" SG CYS B 141 " model vdw 2.034 3.760 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 ... (remaining 63178 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: 0.00 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: 0.880 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.110 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- 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 8480 Z= 0.263 Angle : 0.833 10.174 11552 Z= 0.441 Chirality : 0.048 0.157 1236 Planarity : 0.007 0.097 1518 Dihedral : 13.581 77.781 3042 Min Nonbonded Distance : 2.031 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 *********************** 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 : 0.922 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: 0.1953 time to fit residues: 31.4823 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 : 0.882 ------------------------------------------------------------------------------- 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: 4.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8480 Z= 0.343 Angle : 0.800 9.311 11552 Z= 0.406 Chirality : 0.049 0.151 1236 Planarity : 0.007 0.100 1518 Dihedral : 6.757 40.230 1140 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.93 % Favored : 86.07 % Rotamer: Outliers : 1.26 % Allowed : 10.00 % Favored : 88.74 % 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: -4.42 (0.22), residues: 1034 helix: -3.09 (0.24), residues: 258 sheet: -3.72 (0.41), residues: 122 loop : -2.83 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 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 A 214 ARG 0.003 0.001 ARG A 83 *********************** 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 114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.826 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 108 average time/residue: 0.1748 time to fit residues: 27.7007 Evaluate side-chains 108 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 99 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 A residue 551 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 551 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8480 Z= 0.262 Angle : 0.724 8.298 11552 Z= 0.367 Chirality : 0.046 0.135 1236 Planarity : 0.006 0.094 1518 Dihedral : 6.385 39.949 1140 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 2.53 % Allowed : 14.25 % Favored : 83.22 % 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: -4.04 (0.23), residues: 1034 helix: -2.68 (0.27), residues: 256 sheet: -3.58 (0.42), residues: 118 loop : -2.62 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 298 HIS 0.006 0.001 HIS A 458 PHE 0.019 0.002 PHE A 262 TYR 0.014 0.001 TYR A 214 ARG 0.003 0.000 ARG A 83 *********************** 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 122 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.937 Fit side-chains REVERT: A 133 TYR cc_start: 0.7353 (OUTLIER) cc_final: 0.6640 (t80) REVERT: A 236 LEU cc_start: 0.5719 (OUTLIER) cc_final: 0.5274 (pp) REVERT: B 133 TYR cc_start: 0.7359 (OUTLIER) cc_final: 0.6648 (t80) REVERT: B 236 LEU cc_start: 0.5729 (OUTLIER) cc_final: 0.5280 (pp) outliers start: 22 outliers final: 14 residues processed: 115 average time/residue: 0.1765 time to fit residues: 29.7506 Evaluate side-chains 114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 96 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 236 LEU 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 486 HIS 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 236 LEU 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 486 HIS 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 93 optimal weight: 0.0970 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 83 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8480 Z= 0.193 Angle : 0.676 7.940 11552 Z= 0.338 Chirality : 0.045 0.147 1236 Planarity : 0.006 0.086 1518 Dihedral : 5.932 39.503 1140 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 2.18 % Allowed : 16.90 % Favored : 80.92 % 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: -3.75 (0.24), residues: 1034 helix: -2.32 (0.30), residues: 254 sheet: -3.18 (0.45), residues: 106 loop : -2.57 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 570 HIS 0.003 0.001 HIS B 458 PHE 0.012 0.001 PHE B 262 TYR 0.011 0.001 TYR A 481 ARG 0.003 0.000 ARG A 83 *********************** 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 121 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 1.028 Fit side-chains REVERT: A 133 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.6663 (t80) REVERT: A 147 TYR cc_start: 0.8441 (m-80) cc_final: 0.8164 (m-10) REVERT: A 503 GLU cc_start: 0.6911 (pm20) cc_final: 0.6021 (tm-30) REVERT: B 133 TYR cc_start: 0.7376 (OUTLIER) cc_final: 0.6665 (t80) REVERT: B 147 TYR cc_start: 0.8437 (m-80) cc_final: 0.8231 (m-10) outliers start: 19 outliers final: 11 residues processed: 118 average time/residue: 0.2001 time to fit residues: 33.4893 Evaluate side-chains 106 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.883 ------------------------------------------------------------------------------- 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 264 SER Chi-restraints excluded: chain A residue 295 ILE 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 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 568 VAL Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 33 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8480 Z= 0.264 Angle : 0.702 8.641 11552 Z= 0.356 Chirality : 0.045 0.135 1236 Planarity : 0.006 0.090 1518 Dihedral : 6.059 39.911 1140 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 3.56 % Allowed : 17.36 % Favored : 79.08 % 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: -3.70 (0.24), residues: 1034 helix: -2.26 (0.30), residues: 250 sheet: -3.29 (0.45), residues: 106 loop : -2.52 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 570 HIS 0.006 0.001 HIS A 458 PHE 0.019 0.002 PHE A 262 TYR 0.014 0.001 TYR A 481 ARG 0.003 0.000 ARG B 83 *********************** 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 128 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.879 Fit side-chains REVERT: A 133 TYR cc_start: 0.7400 (OUTLIER) cc_final: 0.6750 (t80) REVERT: B 133 TYR cc_start: 0.7406 (OUTLIER) cc_final: 0.6754 (t80) outliers start: 31 outliers final: 18 residues processed: 120 average time/residue: 0.1821 time to fit residues: 31.2034 Evaluate side-chains 116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.915 ------------------------------------------------------------------------------- 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 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 133 TYR 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 529 MET 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 90 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8480 Z= 0.326 Angle : 0.756 8.654 11552 Z= 0.384 Chirality : 0.047 0.148 1236 Planarity : 0.006 0.093 1518 Dihedral : 6.322 40.785 1140 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % Rotamer: Outliers : 4.48 % Allowed : 17.59 % 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: -3.80 (0.24), residues: 1034 helix: -2.30 (0.30), residues: 250 sheet: -3.63 (0.42), residues: 118 loop : -2.51 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP A 570 HIS 0.007 0.001 HIS A 458 PHE 0.023 0.002 PHE A 262 TYR 0.017 0.002 TYR B 214 ARG 0.004 0.000 ARG B 83 *********************** 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 137 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 98 time to evaluate : 0.949 Fit side-chains REVERT: A 102 LEU cc_start: 0.8279 (mm) cc_final: 0.7865 (mt) REVERT: A 133 TYR cc_start: 0.7548 (OUTLIER) cc_final: 0.6803 (t80) REVERT: A 311 LEU cc_start: 0.6655 (OUTLIER) cc_final: 0.6445 (pt) REVERT: A 446 MET cc_start: 0.6039 (OUTLIER) cc_final: 0.5752 (ttt) REVERT: A 535 MET cc_start: 0.8114 (mtp) cc_final: 0.7839 (mtp) REVERT: B 102 LEU cc_start: 0.8302 (mm) cc_final: 0.7878 (mt) REVERT: B 133 TYR cc_start: 0.7511 (OUTLIER) cc_final: 0.6758 (t80) REVERT: B 446 MET cc_start: 0.6026 (OUTLIER) cc_final: 0.5747 (ttt) REVERT: B 535 MET cc_start: 0.8115 (mtp) cc_final: 0.7855 (mtp) outliers start: 39 outliers final: 29 residues processed: 124 average time/residue: 0.1743 time to fit residues: 31.6208 Evaluate side-chains 131 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 97 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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 118 MET Chi-restraints excluded: chain A residue 133 TYR Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 533 VAL 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 118 MET Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 190 GLU 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 363 ASP Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 529 MET Chi-restraints excluded: chain B residue 533 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 59 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 582 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8480 Z= 0.173 Angle : 0.661 9.366 11552 Z= 0.332 Chirality : 0.043 0.142 1236 Planarity : 0.006 0.083 1518 Dihedral : 5.617 39.279 1140 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 3.22 % Allowed : 20.11 % Favored : 76.67 % 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: -3.56 (0.24), residues: 1034 helix: -2.00 (0.32), residues: 248 sheet: -3.31 (0.44), residues: 108 loop : -2.47 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 570 HIS 0.003 0.001 HIS A 609 PHE 0.017 0.001 PHE A 523 TYR 0.018 0.001 TYR A 418 ARG 0.003 0.000 ARG A 83 *********************** 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 130 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.929 Fit side-chains REVERT: A 102 LEU cc_start: 0.8138 (mm) cc_final: 0.7825 (mt) REVERT: A 133 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6653 (t80) REVERT: A 147 TYR cc_start: 0.8478 (m-80) cc_final: 0.8239 (m-10) REVERT: A 448 ARG cc_start: 0.6330 (ttt180) cc_final: 0.6049 (ttm-80) REVERT: A 503 GLU cc_start: 0.6915 (pm20) cc_final: 0.6106 (tm-30) REVERT: B 102 LEU cc_start: 0.8149 (mm) cc_final: 0.7825 (mt) REVERT: B 133 TYR cc_start: 0.7399 (OUTLIER) cc_final: 0.6703 (t80) REVERT: B 147 TYR cc_start: 0.8486 (m-80) cc_final: 0.8278 (m-10) REVERT: B 448 ARG cc_start: 0.6331 (ttt180) cc_final: 0.6047 (ttm-80) outliers start: 28 outliers final: 18 residues processed: 124 average time/residue: 0.1804 time to fit residues: 32.2105 Evaluate side-chains 112 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 A residue 602 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 118 MET 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 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 30 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 49 optimal weight: 0.0570 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 overall best weight: 1.5904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8480 Z= 0.256 Angle : 0.714 10.370 11552 Z= 0.359 Chirality : 0.045 0.180 1236 Planarity : 0.006 0.089 1518 Dihedral : 5.855 39.652 1140 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 3.45 % Allowed : 21.03 % Favored : 75.52 % 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: -3.57 (0.24), residues: 1034 helix: -1.98 (0.31), residues: 248 sheet: -3.30 (0.45), residues: 108 loop : -2.48 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 570 HIS 0.005 0.001 HIS A 458 PHE 0.018 0.002 PHE A 262 TYR 0.015 0.001 TYR B 418 ARG 0.003 0.000 ARG B 83 *********************** 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 123 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.843 Fit side-chains REVERT: A 102 LEU cc_start: 0.8174 (mm) cc_final: 0.7876 (mt) REVERT: A 133 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.6656 (t80) REVERT: A 446 MET cc_start: 0.5305 (OUTLIER) cc_final: 0.4883 (ttt) REVERT: A 503 GLU cc_start: 0.7127 (pm20) cc_final: 0.6101 (tm-30) REVERT: B 102 LEU cc_start: 0.8145 (mm) cc_final: 0.7839 (mt) REVERT: B 133 TYR cc_start: 0.7440 (OUTLIER) cc_final: 0.6673 (t80) REVERT: B 446 MET cc_start: 0.5295 (OUTLIER) cc_final: 0.4871 (ttt) outliers start: 30 outliers final: 23 residues processed: 117 average time/residue: 0.1728 time to fit residues: 29.6556 Evaluate side-chains 111 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 293 THR 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 446 MET Chi-restraints excluded: chain A residue 533 VAL 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 133 TYR 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 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 533 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.7980 chunk 56 optimal weight: 0.4980 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8480 Z= 0.192 Angle : 0.683 11.573 11552 Z= 0.338 Chirality : 0.044 0.162 1236 Planarity : 0.005 0.082 1518 Dihedral : 5.450 39.320 1140 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 3.79 % Allowed : 21.72 % Favored : 74.48 % 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 (0.24), residues: 1034 helix: -1.95 (0.31), residues: 260 sheet: -3.11 (0.45), residues: 106 loop : -2.45 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 570 HIS 0.004 0.001 HIS A 582 PHE 0.011 0.001 PHE A 541 TYR 0.021 0.001 TYR A 484 ARG 0.003 0.000 ARG B 83 *********************** 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 127 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.958 Fit side-chains REVERT: A 102 LEU cc_start: 0.8082 (mm) cc_final: 0.7774 (mt) REVERT: A 133 TYR cc_start: 0.7389 (OUTLIER) cc_final: 0.6719 (t80) REVERT: A 147 TYR cc_start: 0.8470 (m-80) cc_final: 0.8243 (m-10) REVERT: A 368 MET cc_start: 0.5940 (OUTLIER) cc_final: 0.5687 (ttt) REVERT: A 446 MET cc_start: 0.4658 (OUTLIER) cc_final: 0.4449 (ttt) REVERT: A 448 ARG cc_start: 0.6251 (ttt180) cc_final: 0.5802 (ttm-80) REVERT: A 503 GLU cc_start: 0.6942 (pm20) cc_final: 0.6081 (tm-30) REVERT: B 102 LEU cc_start: 0.8000 (mm) cc_final: 0.7684 (mt) REVERT: B 133 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6748 (t80) REVERT: B 147 TYR cc_start: 0.8475 (m-80) cc_final: 0.8244 (m-10) REVERT: B 446 MET cc_start: 0.4659 (OUTLIER) cc_final: 0.4443 (ttt) REVERT: B 448 ARG cc_start: 0.6245 (ttt180) cc_final: 0.5790 (ttm-80) outliers start: 33 outliers final: 23 residues processed: 120 average time/residue: 0.1767 time to fit residues: 30.9540 Evaluate side-chains 116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.912 ------------------------------------------------------------------------------- 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 224 THR Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 295 ILE 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 446 MET Chi-restraints excluded: chain A residue 533 VAL 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 133 TYR 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 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 446 MET Chi-restraints excluded: chain B residue 533 VAL 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 46 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 0.0010 chunk 65 optimal weight: 6.9990 chunk 87 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8480 Z= 0.179 Angle : 0.685 11.628 11552 Z= 0.334 Chirality : 0.043 0.157 1236 Planarity : 0.005 0.082 1518 Dihedral : 5.233 38.711 1140 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 3.22 % Allowed : 22.07 % Favored : 74.71 % 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: -3.30 (0.24), residues: 1034 helix: -1.80 (0.31), residues: 262 sheet: -3.04 (0.45), residues: 106 loop : -2.31 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 570 HIS 0.003 0.001 HIS A 471 PHE 0.016 0.001 PHE A 541 TYR 0.018 0.001 TYR A 484 ARG 0.002 0.000 ARG B 83 ********************** 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 124 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 96 time to evaluate : 0.826 Fit side-chains REVERT: A 102 LEU cc_start: 0.8044 (mm) cc_final: 0.7742 (mt) REVERT: A 133 TYR cc_start: 0.7286 (OUTLIER) cc_final: 0.6590 (t80) REVERT: A 147 TYR cc_start: 0.8437 (m-80) cc_final: 0.8207 (m-10) REVERT: A 448 ARG cc_start: 0.6231 (ttt180) cc_final: 0.5885 (ttm-80) REVERT: B 102 LEU cc_start: 0.7852 (mm) cc_final: 0.7542 (mt) REVERT: B 133 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.6683 (t80) REVERT: B 147 TYR cc_start: 0.8458 (m-80) cc_final: 0.8210 (m-10) REVERT: B 448 ARG cc_start: 0.6221 (ttt180) cc_final: 0.5876 (ttm-80) outliers start: 28 outliers final: 21 residues processed: 117 average time/residue: 0.1813 time to fit residues: 30.7463 Evaluate side-chains 115 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.951 ------------------------------------------------------------------------------- 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 293 THR 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 533 VAL 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 133 TYR 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 382 VAL Chi-restraints excluded: chain B residue 440 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 568 VAL Chi-restraints excluded: chain B residue 585 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 0.5980 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 59 optimal weight: 0.0970 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 HIS B 485 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.199387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.162688 restraints weight = 10869.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.162926 restraints weight = 9005.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.164166 restraints weight = 8937.316| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8480 Z= 0.295 Angle : 0.755 10.872 11552 Z= 0.374 Chirality : 0.046 0.169 1236 Planarity : 0.006 0.090 1518 Dihedral : 5.782 40.422 1140 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.67 % Favored : 87.33 % Rotamer: Outliers : 3.10 % Allowed : 22.64 % Favored : 74.25 % 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: -3.47 (0.24), residues: 1034 helix: -1.86 (0.30), residues: 274 sheet: -3.27 (0.45), residues: 108 loop : -2.43 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 570 HIS 0.006 0.001 HIS A 458 PHE 0.020 0.002 PHE B 262 TYR 0.018 0.002 TYR A 484 ARG 0.004 0.000 ARG A 335 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1653.89 seconds wall clock time: 31 minutes 10.17 seconds (1870.17 seconds total)