Starting phenix.real_space_refine on Thu Aug 6 01:48:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnk_61621/08_2026/9jnk_61621.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnk_61621/08_2026/9jnk_61621.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jnk_61621/08_2026/9jnk_61621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnk_61621/08_2026/9jnk_61621.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jnk_61621/08_2026/9jnk_61621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnk_61621/08_2026/9jnk_61621.map" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 50 5.49 5 S 42 5.16 5 C 7860 2.51 5 N 2123 2.21 5 O 2464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12539 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2194 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain: "C" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3563 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 13, 'TRANS': 428} Chain: "B" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2194 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 7, 'TRANS': 265} Chain: "D" Number of atoms: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3563 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 13, 'TRANS': 428} Chain: "E" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 513 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Time building chain proxies: 2.56, per 1000 atoms: 0.20 Number of scatterers: 12539 At special positions: 0 Unit cell: (125.84, 154.96, 113.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 50 15.00 O 2464 8.00 N 2123 7.00 C 7860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 547.6 milliseconds 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2672 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 22 sheets defined 45.0% alpha, 13.1% beta 11 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 418 through 427 removed outlier: 4.072A pdb=" N TYR A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 455 through 466 Processing helix chain 'A' and resid 509 through 515 Processing helix chain 'A' and resid 523 through 527 Processing helix chain 'A' and resid 528 through 535 Processing helix chain 'A' and resid 557 through 561 removed outlier: 3.722A pdb=" N ASP A 561 " --> pdb=" O ALA A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 577 through 583 removed outlier: 4.227A pdb=" N PHE A 581 " --> pdb=" O TRP A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 643 removed outlier: 3.531A pdb=" N ASN A 643 " --> pdb=" O GLU A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 659 removed outlier: 3.595A pdb=" N PHE A 659 " --> pdb=" O TRP A 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 22 removed outlier: 3.591A pdb=" N ASN C 14 " --> pdb=" O SER C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 51 Processing helix chain 'C' and resid 61 through 67 Processing helix chain 'C' and resid 68 through 72 removed outlier: 3.690A pdb=" N GLY C 72 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 88 removed outlier: 3.811A pdb=" N ALA C 80 " --> pdb=" O GLY C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 130 removed outlier: 3.656A pdb=" N TYR C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 155 through 160 removed outlier: 4.003A pdb=" N LEU C 159 " --> pdb=" O PRO C 155 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN C 160 " --> pdb=" O THR C 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 155 through 160' Processing helix chain 'C' and resid 177 through 191 Processing helix chain 'C' and resid 239 through 247 removed outlier: 3.636A pdb=" N SER C 245 " --> pdb=" O GLU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 254 Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 319 through 365 removed outlier: 3.703A pdb=" N LEU C 323 " --> pdb=" O ASN C 319 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 348 " --> pdb=" O LYS C 344 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER C 365 " --> pdb=" O LYS C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 385 removed outlier: 3.751A pdb=" N GLU C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE C 385 " --> pdb=" O GLU C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 396 Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'C' and resid 406 through 427 removed outlier: 3.642A pdb=" N LEU C 411 " --> pdb=" O GLU C 407 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 439 Processing helix chain 'B' and resid 418 through 427 removed outlier: 4.008A pdb=" N TYR B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 455 removed outlier: 3.932A pdb=" N ASN B 455 " --> pdb=" O ASP B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 466 Processing helix chain 'B' and resid 509 through 515 Processing helix chain 'B' and resid 523 through 527 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 566 through 575 Processing helix chain 'B' and resid 577 through 583 removed outlier: 4.263A pdb=" N PHE B 581 " --> pdb=" O TRP B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 615 Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 643 Processing helix chain 'B' and resid 654 through 660 removed outlier: 3.863A pdb=" N GLU B 660 " --> pdb=" O LYS B 656 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 23 removed outlier: 3.567A pdb=" N ALA D 18 " --> pdb=" O ASN D 14 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR D 19 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N MET D 21 " --> pdb=" O LEU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 51 Processing helix chain 'D' and resid 61 through 67 Processing helix chain 'D' and resid 68 through 72 removed outlier: 3.680A pdb=" N GLY D 72 " --> pdb=" O ALA D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 removed outlier: 3.786A pdb=" N ALA D 80 " --> pdb=" O GLY D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 130 removed outlier: 3.613A pdb=" N TYR D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 removed outlier: 4.082A pdb=" N LEU D 159 " --> pdb=" O PRO D 155 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN D 160 " --> pdb=" O THR D 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 155 through 160' Processing helix chain 'D' and resid 177 through 191 Processing helix chain 'D' and resid 239 through 247 removed outlier: 3.504A pdb=" N SER D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 254 Processing helix chain 'D' and resid 283 through 295 Processing helix chain 'D' and resid 319 through 366 removed outlier: 3.920A pdb=" N LEU D 323 " --> pdb=" O ASN D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 385 removed outlier: 4.078A pdb=" N ILE D 385 " --> pdb=" O GLU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 389 Processing helix chain 'D' and resid 391 through 396 Processing helix chain 'D' and resid 399 through 403 Processing helix chain 'D' and resid 404 through 428 removed outlier: 3.730A pdb=" N LYS D 409 " --> pdb=" O SER D 405 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 437 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 437 removed outlier: 5.770A pdb=" N PHE A 412 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU A 437 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR A 414 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LEU A 411 " --> pdb=" O ALA A 553 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N MET A 555 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N LEU A 413 " --> pdb=" O MET A 555 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL A 552 " --> pdb=" O ARG A 587 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.503A pdb=" N SER A 544 " --> pdb=" O GLU A 475 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 490 through 495 removed outlier: 4.247A pdb=" N TRP A 482 " --> pdb=" O ILE A 522 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 505 through 508 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 605 Processing sheet with id=AA6, first strand: chain 'A' and resid 645 through 647 removed outlier: 6.276A pdb=" N TYR A 646 " --> pdb=" O ASN C 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA8, first strand: chain 'C' and resid 163 through 165 Processing sheet with id=AA9, first strand: chain 'C' and resid 207 through 211 Processing sheet with id=AB1, first strand: chain 'C' and resid 221 through 223 Processing sheet with id=AB2, first strand: chain 'C' and resid 305 through 308 removed outlier: 4.449A pdb=" N ILE C 305 " --> pdb=" O TYR C 317 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 435 through 437 removed outlier: 7.655A pdb=" N TYR B 435 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N PHE B 412 " --> pdb=" O TYR B 435 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B 437 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B 414 " --> pdb=" O LEU B 437 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LEU B 411 " --> pdb=" O ALA B 553 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N MET B 555 " --> pdb=" O LEU B 411 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N LEU B 413 " --> pdb=" O MET B 555 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL B 552 " --> pdb=" O ARG B 587 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 474 through 476 removed outlier: 3.642A pdb=" N SER B 544 " --> pdb=" O GLU B 475 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 490 through 495 removed outlier: 3.990A pdb=" N TRP B 482 " --> pdb=" O ILE B 522 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 505 through 508 Processing sheet with id=AB7, first strand: chain 'B' and resid 601 through 605 Processing sheet with id=AB8, first strand: chain 'B' and resid 645 through 647 Processing sheet with id=AB9, first strand: chain 'D' and resid 59 through 60 Processing sheet with id=AC1, first strand: chain 'D' and resid 163 through 165 Processing sheet with id=AC2, first strand: chain 'D' and resid 207 through 211 Processing sheet with id=AC3, first strand: chain 'D' and resid 221 through 223 Processing sheet with id=AC4, first strand: chain 'D' and resid 305 through 308 removed outlier: 4.006A pdb=" N ILE D 305 " --> pdb=" O TYR D 317 " (cutoff:3.500A) 490 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 2.31 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2108 1.32 - 1.44: 3512 1.44 - 1.56: 7101 1.56 - 1.68: 99 1.68 - 1.80: 78 Bond restraints: 12898 Sorted by residual: bond pdb=" CA ARG D 52 " pdb=" C ARG D 52 " ideal model delta sigma weight residual 1.525 1.466 0.059 1.28e-02 6.10e+03 2.13e+01 bond pdb=" CA ARG C 52 " pdb=" C ARG C 52 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.24e-02 6.50e+03 1.93e+01 bond pdb=" C ARG D 52 " pdb=" O ARG D 52 " ideal model delta sigma weight residual 1.235 1.200 0.035 1.19e-02 7.06e+03 8.61e+00 bond pdb=" C3' DA F 23 " pdb=" C2' DA F 23 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.28e+00 bond pdb=" C3' DT E 9 " pdb=" C2' DT E 9 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.14e+00 ... (remaining 12893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 17535 3.27 - 6.54: 54 6.54 - 9.81: 3 9.81 - 13.08: 0 13.08 - 16.35: 1 Bond angle restraints: 17593 Sorted by residual: angle pdb=" O4' DA E 24 " pdb=" C4' DA E 24 " pdb=" C3' DA E 24 " ideal model delta sigma weight residual 106.00 103.17 2.83 6.00e-01 2.78e+00 2.22e+01 angle pdb=" CA LEU D 17 " pdb=" CB LEU D 17 " pdb=" CG LEU D 17 " ideal model delta sigma weight residual 116.30 132.65 -16.35 3.50e+00 8.16e-02 2.18e+01 angle pdb=" O4' DA F 11 " pdb=" C4' DA F 11 " pdb=" C3' DA F 11 " ideal model delta sigma weight residual 106.00 103.45 2.55 6.00e-01 2.78e+00 1.81e+01 angle pdb=" C ARG A 438 " pdb=" N GLY A 439 " pdb=" CA GLY A 439 " ideal model delta sigma weight residual 122.16 118.93 3.23 7.70e-01 1.69e+00 1.76e+01 angle pdb=" N3 DT E 17 " pdb=" C4 DT E 17 " pdb=" O4 DT E 17 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 ... (remaining 17588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.92: 6839 27.92 - 55.84: 745 55.84 - 83.76: 98 83.76 - 111.68: 2 111.68 - 139.60: 2 Dihedral angle restraints: 7686 sinusoidal: 3522 harmonic: 4164 Sorted by residual: dihedral pdb=" CA PHE C 36 " pdb=" C PHE C 36 " pdb=" N LYS C 37 " pdb=" CA LYS C 37 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LEU D 17 " pdb=" C LEU D 17 " pdb=" N ALA D 18 " pdb=" CA ALA D 18 " ideal model delta harmonic sigma weight residual 180.00 158.89 21.11 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA PHE D 36 " pdb=" C PHE D 36 " pdb=" N LYS D 37 " pdb=" CA LYS D 37 " ideal model delta harmonic sigma weight residual 180.00 158.93 21.07 0 5.00e+00 4.00e-02 1.78e+01 ... (remaining 7683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1164 0.033 - 0.065: 531 0.065 - 0.097: 141 0.097 - 0.130: 73 0.130 - 0.162: 3 Chirality restraints: 1912 Sorted by residual: chirality pdb=" C3' DT F 4 " pdb=" C4' DT F 4 " pdb=" O3' DT F 4 " pdb=" C2' DT F 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.60e-01 chirality pdb=" CA ILE D 231 " pdb=" N ILE D 231 " pdb=" C ILE D 231 " pdb=" CB ILE D 231 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CG LEU A 469 " pdb=" CB LEU A 469 " pdb=" CD1 LEU A 469 " pdb=" CD2 LEU A 469 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 1909 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 408 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00 pdb=" C ASP B 408 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP B 408 " -0.013 2.00e-02 2.50e+03 pdb=" N THR B 409 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 51 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.57e+00 pdb=" C ALA D 51 " 0.028 2.00e-02 2.50e+03 pdb=" O ALA D 51 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG D 52 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 51 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.15e+00 pdb=" C ALA C 51 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA C 51 " 0.009 2.00e-02 2.50e+03 pdb=" N ARG C 52 " 0.009 2.00e-02 2.50e+03 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 374 2.70 - 3.25: 12076 3.25 - 3.80: 20858 3.80 - 4.35: 27017 4.35 - 4.90: 43900 Nonbonded interactions: 104225 Sorted by model distance: nonbonded pdb=" OD1 ASP C 239 " pdb=" OG1 THR C 242 " model vdw 2.147 3.040 nonbonded pdb=" O TRP C 91 " pdb=" OH TYR C 236 " model vdw 2.155 3.040 nonbonded pdb=" O TRP D 91 " pdb=" OH TYR D 236 " model vdw 2.168 3.040 nonbonded pdb=" OD1 ASP D 239 " pdb=" OG1 THR D 242 " model vdw 2.173 3.040 nonbonded pdb=" OG SER C 177 " pdb=" OG SER C 180 " model vdw 2.198 3.040 ... (remaining 104220 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' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 1 through 24) selection = (chain 'F' and resid 2 through 25) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.730 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 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 0.073 12898 Z= 0.257 Angle : 0.603 16.352 17593 Z= 0.420 Chirality : 0.042 0.162 1912 Planarity : 0.003 0.032 2076 Dihedral : 20.772 139.597 5014 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.48 % Allowed : 25.48 % Favored : 74.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1422 helix: 0.10 (0.22), residues: 542 sheet: -1.14 (0.45), residues: 150 loop : -0.34 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 300 TYR 0.016 0.001 TYR D 334 PHE 0.010 0.001 PHE D 204 TRP 0.010 0.001 TRP A 445 HIS 0.003 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.26 (12898) covalent geometry : angle 0.60313 / 0.42 (17593) hydrogen bonds : bond 0.18779 / 12.78 ( 512) hydrogen bonds : angle 7.25191 / 5.07 ( 1391) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 152 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: C 2 GLN cc_start: 0.8139 (mt0) cc_final: 0.7923 (mt0) REVERT: C 52 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7390 (mtp85) REVERT: C 295 PHE cc_start: 0.7571 (m-80) cc_final: 0.7231 (m-80) REVERT: C 414 GLU cc_start: 0.6263 (mt-10) cc_final: 0.5835 (mm-30) REVERT: B 498 ASP cc_start: 0.5743 (m-30) cc_final: 0.5438 (m-30) REVERT: D 52 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7498 (mtp85) outliers start: 6 outliers final: 2 residues processed: 158 average time/residue: 0.1148 time to fit residues: 26.5118 Evaluate side-chains 145 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 208 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.218402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.157147 restraints weight = 13028.133| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.29 r_work: 0.3340 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 12898 Z= 0.250 Angle : 0.631 13.807 17593 Z= 0.342 Chirality : 0.045 0.247 1912 Planarity : 0.004 0.037 2076 Dihedral : 19.881 142.466 2155 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.82 % Allowed : 24.19 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.22), residues: 1422 helix: 0.02 (0.22), residues: 538 sheet: -1.51 (0.44), residues: 150 loop : -0.49 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 300 TYR 0.018 0.002 TYR C 334 PHE 0.013 0.002 PHE D 204 TRP 0.009 0.001 TRP A 445 HIS 0.005 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.25 (12898) covalent geometry : angle 0.63105 / 0.34 (17593) hydrogen bonds : bond 0.05284 / 3.59 ( 512) hydrogen bonds : angle 5.31429 / 3.69 ( 1391) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 151 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6548 (mp0) REVERT: C 273 LYS cc_start: 0.8302 (mttt) cc_final: 0.7786 (mmmt) REVERT: C 295 PHE cc_start: 0.7933 (m-80) cc_final: 0.7627 (m-80) REVERT: C 414 GLU cc_start: 0.6458 (mt-10) cc_final: 0.6020 (mm-30) REVERT: B 582 GLU cc_start: 0.7008 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: B 597 GLN cc_start: 0.7833 (tp40) cc_final: 0.7548 (tp40) REVERT: B 624 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8235 (ptm160) REVERT: D 324 ILE cc_start: 0.6052 (OUTLIER) cc_final: 0.5703 (mp) outliers start: 35 outliers final: 22 residues processed: 177 average time/residue: 0.1166 time to fit residues: 29.7129 Evaluate side-chains 167 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 16 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 101 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN B 654 ASN D 5 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.224073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.162779 restraints weight = 12946.134| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.00 r_work: 0.3433 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12898 Z= 0.126 Angle : 0.531 13.201 17593 Z= 0.291 Chirality : 0.042 0.249 1912 Planarity : 0.003 0.031 2076 Dihedral : 19.750 140.847 2145 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.06 % Allowed : 24.35 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.22), residues: 1422 helix: 0.35 (0.22), residues: 570 sheet: -1.52 (0.44), residues: 150 loop : -0.24 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 351 TYR 0.017 0.001 TYR B 611 PHE 0.018 0.001 PHE C 95 TRP 0.008 0.001 TRP A 445 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (12898) covalent geometry : angle 0.53100 / 0.29 (17593) hydrogen bonds : bond 0.04120 / 2.77 ( 512) hydrogen bonds : angle 4.87134 / 3.38 ( 1391) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7720 (m-30) REVERT: C 273 LYS cc_start: 0.8309 (mttt) cc_final: 0.7838 (mmmt) REVERT: C 295 PHE cc_start: 0.7635 (m-80) cc_final: 0.7379 (m-80) REVERT: C 342 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.6853 (mttp) REVERT: C 439 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7347 (mp0) REVERT: B 444 SER cc_start: 0.6235 (OUTLIER) cc_final: 0.5939 (t) REVERT: B 582 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: B 618 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.7147 (mt) REVERT: D 21 MET cc_start: 0.6967 (mmt) cc_final: 0.6609 (tmm) REVERT: D 216 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: D 324 ILE cc_start: 0.5997 (OUTLIER) cc_final: 0.5676 (mp) outliers start: 38 outliers final: 19 residues processed: 184 average time/residue: 0.1139 time to fit residues: 30.6362 Evaluate side-chains 170 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 291 ILE Chi-restraints excluded: chain D residue 324 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 74 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 109 optimal weight: 0.0670 chunk 59 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 143 optimal weight: 30.0000 chunk 96 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN D 5 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.221928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.161373 restraints weight = 12857.771| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 3.00 r_work: 0.3442 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12898 Z= 0.154 Angle : 0.545 15.362 17593 Z= 0.294 Chirality : 0.042 0.251 1912 Planarity : 0.003 0.030 2076 Dihedral : 19.712 141.151 2144 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.71 % Allowed : 23.63 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.22), residues: 1422 helix: 0.56 (0.22), residues: 558 sheet: -1.52 (0.43), residues: 150 loop : -0.20 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 121 TYR 0.015 0.001 TYR C 334 PHE 0.018 0.001 PHE C 95 TRP 0.008 0.001 TRP A 445 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (12898) covalent geometry : angle 0.54502 / 0.29 (17593) hydrogen bonds : bond 0.03992 / 2.68 ( 512) hydrogen bonds : angle 4.74248 / 3.29 ( 1391) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7714 (m-30) REVERT: A 582 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6765 (mm-30) REVERT: C 273 LYS cc_start: 0.8305 (mttt) cc_final: 0.7786 (mmmt) REVERT: C 295 PHE cc_start: 0.7690 (m-80) cc_final: 0.7397 (m-80) REVERT: C 342 LYS cc_start: 0.7091 (OUTLIER) cc_final: 0.6868 (mttp) REVERT: C 414 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5867 (mm-30) REVERT: C 439 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: B 444 SER cc_start: 0.6186 (OUTLIER) cc_final: 0.5830 (t) REVERT: B 582 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6351 (mp0) REVERT: B 624 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8019 (ptm160) REVERT: D 21 MET cc_start: 0.6980 (mmt) cc_final: 0.6611 (tmm) REVERT: D 216 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: D 324 ILE cc_start: 0.6063 (OUTLIER) cc_final: 0.5674 (mp) outliers start: 46 outliers final: 29 residues processed: 182 average time/residue: 0.0987 time to fit residues: 26.2357 Evaluate side-chains 181 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 143 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 78 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 56 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN B 654 ASN D 5 ASN D 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.222305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.160097 restraints weight = 12939.451| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 3.23 r_work: 0.3419 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12898 Z= 0.146 Angle : 0.537 15.755 17593 Z= 0.289 Chirality : 0.042 0.252 1912 Planarity : 0.003 0.030 2076 Dihedral : 19.698 141.001 2144 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.87 % Allowed : 23.71 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.23), residues: 1422 helix: 0.64 (0.22), residues: 558 sheet: -1.48 (0.43), residues: 150 loop : -0.16 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 300 TYR 0.015 0.001 TYR C 334 PHE 0.019 0.001 PHE C 95 TRP 0.008 0.001 TRP A 445 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (12898) covalent geometry : angle 0.53712 / 0.29 (17593) hydrogen bonds : bond 0.03841 / 2.57 ( 512) hydrogen bonds : angle 4.63520 / 3.22 ( 1391) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 145 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7728 (m-30) REVERT: A 582 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6619 (mp0) REVERT: C 273 LYS cc_start: 0.8294 (mttt) cc_final: 0.7766 (mmmt) REVERT: C 295 PHE cc_start: 0.7729 (m-80) cc_final: 0.7446 (m-80) REVERT: C 342 LYS cc_start: 0.7075 (OUTLIER) cc_final: 0.6838 (mttp) REVERT: C 414 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.5919 (mm-30) REVERT: C 439 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7256 (mp0) REVERT: B 444 SER cc_start: 0.6134 (OUTLIER) cc_final: 0.5838 (t) REVERT: B 582 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: B 624 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8012 (ptm160) REVERT: D 21 MET cc_start: 0.6899 (mmt) cc_final: 0.6508 (tmm) REVERT: D 216 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7082 (mp0) REVERT: D 324 ILE cc_start: 0.6058 (OUTLIER) cc_final: 0.5669 (mp) REVERT: D 439 GLU cc_start: 0.8093 (mp0) cc_final: 0.7709 (mp0) outliers start: 48 outliers final: 30 residues processed: 180 average time/residue: 0.0980 time to fit residues: 25.5964 Evaluate side-chains 181 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 142 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 125 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 113 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 133 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 142 optimal weight: 50.0000 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN B 654 ASN D 5 ASN D 128 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.222460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.161137 restraints weight = 13022.402| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 3.11 r_work: 0.3395 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12898 Z= 0.139 Angle : 0.541 17.947 17593 Z= 0.287 Chirality : 0.042 0.254 1912 Planarity : 0.003 0.031 2076 Dihedral : 19.686 140.905 2144 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.11 % Allowed : 23.55 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.23), residues: 1422 helix: 0.72 (0.22), residues: 558 sheet: -1.54 (0.43), residues: 152 loop : -0.13 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 6 TYR 0.015 0.001 TYR C 334 PHE 0.017 0.001 PHE C 95 TRP 0.007 0.001 TRP A 445 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (12898) covalent geometry : angle 0.54101 / 0.29 (17593) hydrogen bonds : bond 0.03760 / 2.53 ( 512) hydrogen bonds : angle 4.54796 / 3.16 ( 1391) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 149 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7642 (m-30) REVERT: A 582 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6661 (mp0) REVERT: C 21 MET cc_start: 0.6844 (tmm) cc_final: 0.6305 (mmm) REVERT: C 273 LYS cc_start: 0.8329 (mttt) cc_final: 0.7788 (mmmt) REVERT: C 295 PHE cc_start: 0.7664 (m-80) cc_final: 0.7412 (m-80) REVERT: C 300 ARG cc_start: 0.8377 (mtm-85) cc_final: 0.7190 (mmm-85) REVERT: C 342 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6824 (mttp) REVERT: C 414 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5904 (mm-30) REVERT: C 439 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: B 444 SER cc_start: 0.6126 (OUTLIER) cc_final: 0.5873 (t) REVERT: B 582 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: D 216 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: D 265 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6777 (mm-30) REVERT: D 324 ILE cc_start: 0.6037 (OUTLIER) cc_final: 0.5654 (mp) REVERT: D 439 GLU cc_start: 0.8063 (mp0) cc_final: 0.7638 (mp0) outliers start: 51 outliers final: 31 residues processed: 188 average time/residue: 0.1102 time to fit residues: 30.2388 Evaluate side-chains 185 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 453 LEU Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 112 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 145 optimal weight: 40.0000 chunk 67 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN B 654 ASN D 5 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.221921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.162405 restraints weight = 12940.179| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.11 r_work: 0.3419 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12898 Z= 0.151 Angle : 0.535 14.447 17593 Z= 0.286 Chirality : 0.042 0.255 1912 Planarity : 0.003 0.029 2076 Dihedral : 19.655 140.916 2144 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.95 % Allowed : 23.79 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.23), residues: 1422 helix: 0.73 (0.22), residues: 558 sheet: -1.50 (0.43), residues: 152 loop : -0.11 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 6 TYR 0.015 0.001 TYR C 334 PHE 0.014 0.001 PHE C 401 TRP 0.007 0.001 TRP B 445 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (12898) covalent geometry : angle 0.53527 / 0.29 (17593) hydrogen bonds : bond 0.03747 / 2.52 ( 512) hydrogen bonds : angle 4.51794 / 3.14 ( 1391) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 150 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7688 (m-30) REVERT: A 582 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6709 (mp0) REVERT: C 273 LYS cc_start: 0.8354 (mttt) cc_final: 0.7841 (mmmt) REVERT: C 295 PHE cc_start: 0.7712 (m-80) cc_final: 0.7455 (m-80) REVERT: C 300 ARG cc_start: 0.8388 (mtm-85) cc_final: 0.7259 (mmm-85) REVERT: C 414 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6005 (mm-30) REVERT: C 439 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: B 444 SER cc_start: 0.6275 (OUTLIER) cc_final: 0.5952 (t) REVERT: B 582 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6381 (mp0) REVERT: B 624 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7300 (ptm-80) REVERT: D 21 MET cc_start: 0.6911 (mmt) cc_final: 0.6506 (tmm) REVERT: D 216 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7176 (mp0) REVERT: D 265 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6824 (mm-30) REVERT: D 324 ILE cc_start: 0.6114 (OUTLIER) cc_final: 0.5704 (mp) REVERT: D 439 GLU cc_start: 0.8071 (mp0) cc_final: 0.7627 (mp0) outliers start: 49 outliers final: 34 residues processed: 187 average time/residue: 0.1155 time to fit residues: 31.3657 Evaluate side-chains 192 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 388 TYR Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 93 optimal weight: 3.9990 chunk 49 optimal weight: 0.0570 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 142 optimal weight: 50.0000 chunk 113 optimal weight: 0.4980 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN D 5 ASN D 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.219534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.159413 restraints weight = 12910.993| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.27 r_work: 0.3383 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12898 Z= 0.157 Angle : 0.551 19.278 17593 Z= 0.290 Chirality : 0.042 0.258 1912 Planarity : 0.003 0.033 2076 Dihedral : 19.637 141.008 2144 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.27 % Allowed : 23.71 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.23), residues: 1422 helix: 0.76 (0.23), residues: 540 sheet: -1.46 (0.43), residues: 152 loop : -0.12 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 6 TYR 0.015 0.001 TYR C 334 PHE 0.014 0.001 PHE C 401 TRP 0.009 0.001 TRP B 445 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (12898) covalent geometry : angle 0.55105 / 0.29 (17593) hydrogen bonds : bond 0.03750 / 2.52 ( 512) hydrogen bonds : angle 4.48407 / 3.11 ( 1391) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 151 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7678 (m-30) REVERT: A 440 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7365 (mmtm) REVERT: A 582 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6736 (mp0) REVERT: C 295 PHE cc_start: 0.7708 (m-80) cc_final: 0.7448 (m-80) REVERT: C 414 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6070 (mm-30) REVERT: C 439 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: B 582 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: B 624 ARG cc_start: 0.8741 (OUTLIER) cc_final: 0.7261 (ptm-80) REVERT: D 27 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7051 (ttp-170) REVERT: D 216 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7166 (mp0) REVERT: D 241 GLU cc_start: 0.7567 (tp30) cc_final: 0.6966 (mt-10) REVERT: D 324 ILE cc_start: 0.6067 (OUTLIER) cc_final: 0.5645 (mp) REVERT: D 439 GLU cc_start: 0.8074 (mp0) cc_final: 0.7588 (mp0) outliers start: 53 outliers final: 36 residues processed: 191 average time/residue: 0.1188 time to fit residues: 32.7579 Evaluate side-chains 194 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 429 ASP Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 593 VAL Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 25 GLU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 388 TYR Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 95 optimal weight: 0.0980 chunk 107 optimal weight: 0.7980 chunk 131 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 98 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 112 optimal weight: 0.0030 chunk 21 optimal weight: 1.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 560 HIS D 5 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.223561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.163828 restraints weight = 12886.026| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 2.93 r_work: 0.3461 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12898 Z= 0.110 Angle : 0.517 17.890 17593 Z= 0.276 Chirality : 0.041 0.260 1912 Planarity : 0.003 0.030 2076 Dihedral : 19.617 140.815 2144 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.71 % Allowed : 24.03 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.23), residues: 1422 helix: 0.94 (0.23), residues: 542 sheet: -1.41 (0.43), residues: 152 loop : -0.00 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 6 TYR 0.015 0.001 TYR B 611 PHE 0.015 0.001 PHE C 401 TRP 0.010 0.001 TRP B 445 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (12898) covalent geometry : angle 0.51672 / 0.28 (17593) hydrogen bonds : bond 0.03432 / 2.31 ( 512) hydrogen bonds : angle 4.33874 / 3.00 ( 1391) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7658 (m-30) REVERT: A 440 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7379 (mmtm) REVERT: A 582 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6692 (mp0) REVERT: C 2 GLN cc_start: 0.8066 (mt0) cc_final: 0.7749 (mt0) REVERT: C 21 MET cc_start: 0.6865 (tmm) cc_final: 0.6365 (mmp) REVERT: C 273 LYS cc_start: 0.8308 (mttt) cc_final: 0.7820 (mmmt) REVERT: C 295 PHE cc_start: 0.7532 (m-80) cc_final: 0.7262 (m-80) REVERT: C 300 ARG cc_start: 0.8258 (mtm-85) cc_final: 0.7066 (mmm160) REVERT: C 342 LYS cc_start: 0.7163 (OUTLIER) cc_final: 0.6947 (mttp) REVERT: C 414 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6050 (mm-30) REVERT: C 439 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7316 (mp0) REVERT: B 582 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6353 (mp0) REVERT: B 624 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7281 (ptm-80) REVERT: D 216 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: D 241 GLU cc_start: 0.7503 (tp30) cc_final: 0.6922 (mt-10) REVERT: D 265 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6753 (mm-30) REVERT: D 324 ILE cc_start: 0.5961 (OUTLIER) cc_final: 0.5606 (mp) REVERT: D 439 GLU cc_start: 0.8019 (mp0) cc_final: 0.7589 (mp0) outliers start: 46 outliers final: 28 residues processed: 191 average time/residue: 0.1146 time to fit residues: 31.9743 Evaluate side-chains 187 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 342 LYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 388 TYR Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 68 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 chunk 135 optimal weight: 0.0980 chunk 42 optimal weight: 0.7980 chunk 80 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.225266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.164468 restraints weight = 12937.263| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.87 r_work: 0.3462 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12898 Z= 0.117 Angle : 0.516 18.175 17593 Z= 0.275 Chirality : 0.041 0.261 1912 Planarity : 0.003 0.030 2076 Dihedral : 19.598 140.956 2144 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.06 % Allowed : 24.44 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.23), residues: 1422 helix: 1.04 (0.23), residues: 542 sheet: -1.24 (0.41), residues: 172 loop : 0.04 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 6 TYR 0.015 0.001 TYR D 334 PHE 0.014 0.001 PHE C 401 TRP 0.009 0.001 TRP B 445 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (12898) covalent geometry : angle 0.51626 / 0.27 (17593) hydrogen bonds : bond 0.03423 / 2.30 ( 512) hydrogen bonds : angle 4.26568 / 2.95 ( 1391) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2844 Ramachandran restraints generated. 1422 Oldfield, 0 Emsley, 1422 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7639 (m-30) REVERT: A 440 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7422 (mmtm) REVERT: A 456 LYS cc_start: 0.6989 (mmmm) cc_final: 0.6744 (mmmm) REVERT: A 582 GLU cc_start: 0.7211 (mm-30) cc_final: 0.6800 (mp0) REVERT: C 2 GLN cc_start: 0.8019 (mt0) cc_final: 0.7703 (mt0) REVERT: C 21 MET cc_start: 0.6866 (tmm) cc_final: 0.6351 (mmp) REVERT: C 220 THR cc_start: 0.7238 (p) cc_final: 0.6997 (p) REVERT: C 295 PHE cc_start: 0.7541 (m-80) cc_final: 0.7334 (m-80) REVERT: C 300 ARG cc_start: 0.8250 (mtm-85) cc_final: 0.7030 (mmm160) REVERT: C 414 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.6066 (mm-30) REVERT: C 439 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7254 (mp0) REVERT: B 582 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6365 (mp0) REVERT: B 624 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7283 (ptm-80) REVERT: D 216 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7203 (mp0) REVERT: D 241 GLU cc_start: 0.7501 (tp30) cc_final: 0.6926 (mt-10) REVERT: D 265 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6756 (mm-30) REVERT: D 324 ILE cc_start: 0.5967 (OUTLIER) cc_final: 0.5588 (mp) REVERT: D 439 GLU cc_start: 0.8014 (mp0) cc_final: 0.7592 (mp0) outliers start: 38 outliers final: 26 residues processed: 183 average time/residue: 0.1110 time to fit residues: 29.7431 Evaluate side-chains 182 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 147 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 417 ASP Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 631 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 171 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 374 THR Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 414 GLU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 439 GLU Chi-restraints excluded: chain C residue 441 ILE Chi-restraints excluded: chain B residue 410 THR Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 582 GLU Chi-restraints excluded: chain B residue 607 THR Chi-restraints excluded: chain B residue 624 ARG Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 324 ILE Chi-restraints excluded: chain D residue 339 ILE Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 129 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 137 optimal weight: 5.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.220450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160495 restraints weight = 13038.886| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.90 r_work: 0.3249 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 12898 Z= 0.199 Angle : 0.572 17.816 17593 Z= 0.302 Chirality : 0.043 0.262 1912 Planarity : 0.004 0.033 2076 Dihedral : 19.630 141.337 2144 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.06 % Allowed : 24.44 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.23), residues: 1422 helix: 0.86 (0.23), residues: 540 sheet: -1.34 (0.44), residues: 152 loop : -0.09 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 6 TYR 0.017 0.002 TYR D 334 PHE 0.014 0.002 PHE C 95 TRP 0.007 0.001 TRP A 445 HIS 0.006 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.20 (12898) covalent geometry : angle 0.57230 / 0.30 (17593) hydrogen bonds : bond 0.03846 / 2.59 ( 512) hydrogen bonds : angle 4.37468 / 3.03 ( 1391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3464.12 seconds wall clock time: 60 minutes 2.92 seconds (3602.92 seconds total)