Starting phenix.real_space_refine on Fri Jul 3 07:28:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnk_61621/07_2026/9jnk_61621.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnk_61621/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9jnk_61621/07_2026/9jnk_61621.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnk_61621/07_2026/9jnk_61621.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnk_61621/07_2026/9jnk_61621.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnk_61621/07_2026/9jnk_61621.cif" } 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-dev-6108/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: 2.42, per 1000 atoms: 0.19 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: 0.67 Conformation dependent library (CDL) restraints added in 390.3 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: 1.39 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: 1.89 Time building geometry restraints manager: 0.94 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: 1.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.380 Find NCS groups from input model: 0.150 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.000 ------------------------------------------------------------------------------- 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 : 0.601 16.352 17593 Z= 0.418 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 0.60139 / 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 : 0.342 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: 0.0911 time to fit residues: 20.7707 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 : 0.265 ------------------------------------------------------------------------------- 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 = 0.218360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.155977 restraints weight = 13030.141| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.44 r_work: 0.3361 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.0789 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= 0.256 Angle : 0.634 13.634 17593 Z= 0.344 Chirality : 0.045 0.230 1912 Planarity : 0.005 0.037 2076 Dihedral : 19.912 142.903 2155 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.82 % Allowed : 24.11 % Favored : 73.06 % 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: 0.04 (0.22), residues: 536 sheet: -1.50 (0.44), residues: 150 loop : -0.50 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 121 TYR 0.018 0.002 TYR C 334 PHE 0.013 0.002 PHE D 204 TRP 0.011 0.001 TRP A 445 HIS 0.005 0.001 HIS C 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.26 (12898) covalent geometry : angle 0.63378 / 0.34 (17593) hydrogen bonds : bond 0.05013 / 3.41 ( 512) hydrogen bonds : angle 5.27240 / 3.66 ( 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 : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 582 GLU cc_start: 0.7052 (mm-30) cc_final: 0.6717 (mm-30) REVERT: C 273 LYS cc_start: 0.8310 (mttt) cc_final: 0.7794 (mmmt) REVERT: C 295 PHE cc_start: 0.7935 (m-80) cc_final: 0.7630 (m-80) REVERT: C 414 GLU cc_start: 0.6465 (mt-10) cc_final: 0.6032 (mm-30) REVERT: B 582 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6544 (mp0) REVERT: B 597 GLN cc_start: 0.7824 (tp40) cc_final: 0.7532 (tp40) REVERT: B 624 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8287 (ptm160) REVERT: D 324 ILE cc_start: 0.6060 (OUTLIER) cc_final: 0.5710 (mp) outliers start: 35 outliers final: 22 residues processed: 177 average time/residue: 0.0976 time to fit residues: 24.7919 Evaluate side-chains 168 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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: 0.6980 chunk 78 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 88 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4420 r_free = 0.4420 target = 0.222566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.161705 restraints weight = 13073.827| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 3.16 r_work: 0.3415 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.0879 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= 0.127 Angle : 0.530 13.054 17593 Z= 0.291 Chirality : 0.042 0.226 1912 Planarity : 0.003 0.031 2076 Dihedral : 19.788 141.402 2145 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.15 % Allowed : 24.44 % 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: -0.33 (0.22), residues: 1422 helix: 0.36 (0.22), residues: 568 sheet: -1.51 (0.44), residues: 150 loop : -0.27 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 351 TYR 0.018 0.001 TYR B 611 PHE 0.017 0.001 PHE C 95 TRP 0.009 0.001 TRP A 445 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (12898) covalent geometry : angle 0.52962 / 0.29 (17593) hydrogen bonds : bond 0.04157 / 2.79 ( 512) hydrogen bonds : angle 4.88411 / 3.39 ( 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 199 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: C 273 LYS cc_start: 0.8310 (mttt) cc_final: 0.7840 (mmmt) REVERT: C 295 PHE cc_start: 0.7652 (m-80) cc_final: 0.7446 (m-80) REVERT: C 342 LYS cc_start: 0.7102 (OUTLIER) cc_final: 0.6865 (mttp) REVERT: C 439 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: B 444 SER cc_start: 0.6250 (OUTLIER) cc_final: 0.5958 (t) REVERT: B 582 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6486 (mp0) REVERT: B 618 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7148 (mt) REVERT: D 21 MET cc_start: 0.7005 (mmt) cc_final: 0.6637 (tmm) REVERT: D 216 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: D 324 ILE cc_start: 0.6034 (OUTLIER) cc_final: 0.5706 (mp) outliers start: 39 outliers final: 21 residues processed: 186 average time/residue: 0.1171 time to fit residues: 31.6522 Evaluate side-chains 173 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 439 GLU 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 618 LEU Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain D residue 25 GLU 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 Chi-restraints excluded: chain D residue 400 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 74 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 71 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 143 optimal weight: 40.0000 chunk 96 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.4428 r_free = 0.4428 target = 0.222880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.161887 restraints weight = 12854.108| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.11 r_work: 0.3416 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12898 Z= 0.159 Angle : 0.546 15.324 17593 Z= 0.295 Chirality : 0.042 0.231 1912 Planarity : 0.003 0.030 2076 Dihedral : 19.748 141.646 2144 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.55 % Allowed : 23.71 % Favored : 72.74 % 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: -0.19 (0.22), residues: 1422 helix: 0.53 (0.22), residues: 558 sheet: -1.54 (0.43), residues: 150 loop : -0.20 (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 0.015 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 0.00372 / 0.16 (12898) covalent geometry : angle 0.54638 / 0.29 (17593) hydrogen bonds : bond 0.04012 / 2.69 ( 512) hydrogen bonds : angle 4.75505 / 3.30 ( 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 193 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7973 (OUTLIER) cc_final: 0.7715 (m-30) REVERT: A 582 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6771 (mm-30) REVERT: C 273 LYS cc_start: 0.8294 (mttt) cc_final: 0.7774 (mmmt) REVERT: C 295 PHE cc_start: 0.7695 (m-80) cc_final: 0.7381 (m-80) REVERT: C 342 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6833 (mttp) REVERT: C 414 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5835 (mm-30) REVERT: C 439 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: B 444 SER cc_start: 0.6192 (OUTLIER) cc_final: 0.5842 (t) REVERT: B 582 GLU cc_start: 0.6903 (OUTLIER) cc_final: 0.6346 (mp0) REVERT: B 624 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7279 (ptm-80) REVERT: D 21 MET cc_start: 0.6988 (mmt) cc_final: 0.6608 (tmm) REVERT: D 216 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: D 324 ILE cc_start: 0.6057 (OUTLIER) cc_final: 0.5668 (mp) outliers start: 44 outliers final: 29 residues processed: 183 average time/residue: 0.1182 time to fit residues: 31.3442 Evaluate side-chains 183 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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 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 25 GLU 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: 4.9990 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 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: 1.4586 ------------------------------------------------------------------------------- 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 = 0.4413 r_free = 0.4413 target = 0.221360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.160495 restraints weight = 12945.978| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 3.11 r_work: 0.3413 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12898 Z= 0.173 Angle : 0.553 16.000 17593 Z= 0.297 Chirality : 0.042 0.233 1912 Planarity : 0.003 0.031 2076 Dihedral : 19.743 141.670 2144 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.35 % Allowed : 23.47 % Favored : 72.18 % 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: -1.49 (0.43), residues: 150 loop : -0.21 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 300 TYR 0.016 0.001 TYR C 334 PHE 0.018 0.001 PHE C 95 TRP 0.008 0.001 TRP A 445 HIS 0.005 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.17 (12898) covalent geometry : angle 0.55313 / 0.30 (17593) hydrogen bonds : bond 0.03983 / 2.67 ( 512) hydrogen bonds : angle 4.69765 / 3.27 ( 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 202 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 148 time to evaluate : 0.458 Fit side-chains revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: A 582 GLU cc_start: 0.7093 (mm-30) cc_final: 0.6623 (mp0) REVERT: C 273 LYS cc_start: 0.8303 (mttt) cc_final: 0.7795 (mmmt) REVERT: C 295 PHE cc_start: 0.7770 (m-80) cc_final: 0.7477 (m-80) REVERT: C 342 LYS cc_start: 0.7101 (OUTLIER) cc_final: 0.6866 (mttp) REVERT: C 414 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.5994 (mm-30) REVERT: C 439 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: B 444 SER cc_start: 0.6158 (OUTLIER) cc_final: 0.5873 (t) REVERT: B 582 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: B 624 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7348 (ptm-80) REVERT: D 21 MET cc_start: 0.6998 (mmt) cc_final: 0.6606 (tmm) REVERT: D 205 ARG cc_start: 0.8176 (mtm110) cc_final: 0.7866 (mtm110) REVERT: D 216 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7020 (mp0) REVERT: D 324 ILE cc_start: 0.6115 (OUTLIER) cc_final: 0.5706 (mp) REVERT: D 439 GLU cc_start: 0.8130 (mp0) cc_final: 0.7731 (mp0) outliers start: 54 outliers final: 35 residues processed: 187 average time/residue: 0.1112 time to fit residues: 29.9395 Evaluate side-chains 190 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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 624 ARG Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain D residue 25 GLU 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 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 291 ILE 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: 0.9990 chunk 29 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 44 optimal weight: 0.3980 chunk 113 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 142 optimal weight: 50.0000 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.221960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.161727 restraints weight = 12932.737| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.90 r_work: 0.3437 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12898 Z= 0.127 Angle : 0.528 14.019 17593 Z= 0.284 Chirality : 0.041 0.235 1912 Planarity : 0.003 0.029 2076 Dihedral : 19.730 141.271 2144 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % 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: -0.02 (0.23), residues: 1422 helix: 0.71 (0.22), residues: 558 sheet: -1.49 (0.43), residues: 150 loop : -0.13 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 6 TYR 0.016 0.001 TYR B 611 PHE 0.015 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 0.00285 / 0.13 (12898) covalent geometry : angle 0.52792 / 0.28 (17593) hydrogen bonds : bond 0.03735 / 2.51 ( 512) hydrogen bonds : angle 4.55013 / 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: 48 poor density : 152 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7957 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: A 582 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6603 (mp0) REVERT: C 21 MET cc_start: 0.6870 (tmm) cc_final: 0.6331 (mmm) REVERT: C 273 LYS cc_start: 0.8331 (mttt) cc_final: 0.7803 (mmmt) REVERT: C 295 PHE cc_start: 0.7675 (m-80) cc_final: 0.7357 (m-80) REVERT: C 342 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.6828 (mttp) REVERT: C 414 GLU cc_start: 0.6503 (OUTLIER) cc_final: 0.5908 (mm-30) REVERT: C 439 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7296 (mp0) REVERT: B 444 SER cc_start: 0.6119 (OUTLIER) cc_final: 0.5872 (t) REVERT: B 582 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: B 624 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.7265 (ptm-80) REVERT: D 21 MET cc_start: 0.6967 (mmt) cc_final: 0.6588 (tmm) REVERT: D 216 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: D 241 GLU cc_start: 0.7585 (tp30) cc_final: 0.7026 (mt-10) REVERT: D 324 ILE cc_start: 0.6014 (OUTLIER) cc_final: 0.5651 (mp) REVERT: D 439 GLU cc_start: 0.8067 (mp0) cc_final: 0.7630 (mp0) outliers start: 48 outliers final: 32 residues processed: 187 average time/residue: 0.1124 time to fit residues: 30.3955 Evaluate side-chains 188 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 94 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 LYS 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 25 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 112 optimal weight: 0.0670 chunk 38 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 145 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- 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 = 0.4413 r_free = 0.4413 target = 0.221275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.160855 restraints weight = 12865.312| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.85 r_work: 0.3426 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12898 Z= 0.153 Angle : 0.544 16.564 17593 Z= 0.289 Chirality : 0.042 0.236 1912 Planarity : 0.003 0.029 2076 Dihedral : 19.710 141.352 2144 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.11 % Allowed : 23.71 % Favored : 72.18 % 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 (0.22), residues: 1422 helix: 0.72 (0.22), residues: 558 sheet: -1.52 (0.43), residues: 152 loop : -0.11 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 6 TYR 0.015 0.001 TYR C 334 PHE 0.023 0.001 PHE C 95 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 0.00359 / 0.15 (12898) covalent geometry : angle 0.54355 / 0.29 (17593) hydrogen bonds : bond 0.03757 / 2.53 ( 512) hydrogen bonds : angle 4.52476 / 3.15 ( 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 204 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 153 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7669 (m-30) REVERT: A 582 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6660 (mp0) REVERT: C 273 LYS cc_start: 0.8338 (mttt) cc_final: 0.7807 (mmmt) REVERT: C 295 PHE cc_start: 0.7741 (m-80) cc_final: 0.7463 (m-80) REVERT: C 342 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6839 (mttp) REVERT: C 414 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.5970 (mm-30) REVERT: C 439 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: B 444 SER cc_start: 0.6286 (OUTLIER) cc_final: 0.5971 (t) REVERT: B 582 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: B 624 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.7288 (ptm-80) REVERT: D 21 MET cc_start: 0.6903 (mmt) cc_final: 0.6533 (tmm) REVERT: D 27 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7093 (ttp-170) REVERT: D 216 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7143 (mp0) REVERT: D 241 GLU cc_start: 0.7553 (tp30) cc_final: 0.7041 (mt-10) REVERT: D 324 ILE cc_start: 0.6051 (OUTLIER) cc_final: 0.5661 (mp) REVERT: D 439 GLU cc_start: 0.8053 (mp0) cc_final: 0.7593 (mp0) outliers start: 51 outliers final: 35 residues processed: 193 average time/residue: 0.1176 time to fit residues: 32.8264 Evaluate side-chains 193 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 90 THR Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 LYS 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 93 optimal weight: 0.4980 chunk 49 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 128 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 142 optimal weight: 50.0000 chunk 113 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4438 r_free = 0.4438 target = 0.224550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.165468 restraints weight = 12846.290| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 3.02 r_work: 0.3406 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12898 Z= 0.127 Angle : 0.529 18.575 17593 Z= 0.282 Chirality : 0.041 0.238 1912 Planarity : 0.003 0.030 2076 Dihedral : 19.676 141.199 2144 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.27 % Allowed : 23.55 % Favored : 72.18 % 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: 0.84 (0.22), residues: 558 sheet: -1.50 (0.43), residues: 152 loop : -0.05 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 6 TYR 0.015 0.001 TYR B 611 PHE 0.021 0.001 PHE C 95 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 0.00287 / 0.13 (12898) covalent geometry : angle 0.52944 / 0.28 (17593) hydrogen bonds : bond 0.03593 / 2.41 ( 512) hydrogen bonds : angle 4.45156 / 3.09 ( 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 207 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 154 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7935 (OUTLIER) cc_final: 0.7670 (m-30) REVERT: A 440 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7314 (mmtm) REVERT: A 582 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6670 (mp0) REVERT: C 273 LYS cc_start: 0.8335 (mttt) cc_final: 0.7829 (mmmt) REVERT: C 295 PHE cc_start: 0.7674 (m-80) cc_final: 0.7346 (m-80) REVERT: C 300 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.7254 (mmm-85) REVERT: C 342 LYS cc_start: 0.7074 (OUTLIER) cc_final: 0.6840 (mttp) REVERT: C 414 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6063 (mm-30) REVERT: C 439 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: B 582 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6389 (mp0) REVERT: B 624 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7245 (ptm-80) REVERT: D 27 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7043 (ttp-170) REVERT: D 216 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: D 251 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6867 (mt) REVERT: D 265 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6770 (mm-30) REVERT: D 324 ILE cc_start: 0.6060 (OUTLIER) cc_final: 0.5673 (mp) REVERT: D 439 GLU cc_start: 0.8053 (mp0) cc_final: 0.7597 (mp0) outliers start: 53 outliers final: 35 residues processed: 195 average time/residue: 0.1234 time to fit residues: 34.5628 Evaluate side-chains 196 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 149 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 94 ASN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 LYS 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 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 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 251 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.0980 chunk 11 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN B 560 HIS D 5 ASN D 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.224762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.163208 restraints weight = 12865.247| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.18 r_work: 0.3424 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12898 Z= 0.123 Angle : 0.527 18.015 17593 Z= 0.280 Chirality : 0.041 0.239 1912 Planarity : 0.003 0.030 2076 Dihedral : 19.656 141.186 2144 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.03 % Allowed : 23.71 % 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: 0.18 (0.23), residues: 1422 helix: 0.90 (0.23), residues: 542 sheet: -1.43 (0.43), residues: 152 loop : -0.01 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 6 TYR 0.015 0.001 TYR D 334 PHE 0.024 0.001 PHE C 95 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 0.00277 / 0.12 (12898) covalent geometry : angle 0.52667 / 0.28 (17593) hydrogen bonds : bond 0.03522 / 2.37 ( 512) hydrogen bonds : angle 4.38036 / 3.03 ( 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 205 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 155 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7655 (m-30) REVERT: A 440 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7347 (mmtm) REVERT: A 582 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6684 (mp0) REVERT: C 273 LYS cc_start: 0.8318 (mttt) cc_final: 0.7809 (mmmt) REVERT: C 295 PHE cc_start: 0.7695 (m-80) cc_final: 0.7419 (m-80) REVERT: C 300 ARG cc_start: 0.8364 (mtm-85) cc_final: 0.7093 (mmm160) REVERT: C 414 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.5985 (mm-30) REVERT: C 439 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: B 582 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6353 (mp0) REVERT: B 624 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7289 (ptm-80) REVERT: D 27 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7037 (ttp-170) REVERT: D 216 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: D 251 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6991 (mt) REVERT: D 265 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6754 (mm-30) REVERT: D 324 ILE cc_start: 0.6005 (OUTLIER) cc_final: 0.5626 (mp) REVERT: D 439 GLU cc_start: 0.8022 (mp0) cc_final: 0.7574 (mp0) outliers start: 50 outliers final: 37 residues processed: 193 average time/residue: 0.1175 time to fit residues: 32.8198 Evaluate side-chains 200 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 152 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 94 ASN 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 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 251 LEU 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: 5.9990 chunk 36 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 42 optimal weight: 0.0670 chunk 80 optimal weight: 20.0000 chunk 88 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 105 optimal weight: 0.0000 chunk 70 optimal weight: 3.9990 overall best weight: 0.7726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN ** B 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4443 r_free = 0.4443 target = 0.225150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.163719 restraints weight = 12957.651| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 3.00 r_work: 0.3446 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12898 Z= 0.124 Angle : 0.525 18.367 17593 Z= 0.279 Chirality : 0.041 0.240 1912 Planarity : 0.003 0.030 2076 Dihedral : 19.646 141.270 2144 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % 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: 0.22 (0.23), residues: 1422 helix: 0.95 (0.23), residues: 542 sheet: -1.40 (0.43), residues: 152 loop : -0.00 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 6 TYR 0.014 0.001 TYR B 611 PHE 0.021 0.001 PHE C 95 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 0.00280 / 0.12 (12898) covalent geometry : angle 0.52529 / 0.28 (17593) hydrogen bonds : bond 0.03492 / 2.35 ( 512) hydrogen bonds : angle 4.34014 / 3.01 ( 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 206 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 157 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 417 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7646 (m-30) REVERT: A 440 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7376 (mmtm) REVERT: A 569 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7676 (t) REVERT: A 582 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6788 (mp0) REVERT: C 21 MET cc_start: 0.6844 (tmm) cc_final: 0.6383 (mmp) REVERT: C 295 PHE cc_start: 0.7595 (m-80) cc_final: 0.7263 (m-80) REVERT: C 300 ARG cc_start: 0.8346 (mtm-85) cc_final: 0.7116 (mmm160) REVERT: C 414 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6080 (mm-30) REVERT: C 439 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7263 (mp0) REVERT: B 582 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6367 (mp0) REVERT: B 624 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7282 (ptm-80) REVERT: D 27 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7024 (ttp-170) REVERT: D 216 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: D 251 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6978 (mt) REVERT: D 265 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6777 (mm-30) REVERT: D 324 ILE cc_start: 0.6019 (OUTLIER) cc_final: 0.5631 (mp) REVERT: D 439 GLU cc_start: 0.8034 (mp0) cc_final: 0.7598 (mp0) outliers start: 49 outliers final: 35 residues processed: 193 average time/residue: 0.1152 time to fit residues: 32.3411 Evaluate side-chains 202 residues out of total 1240 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 569 SER 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 94 ASN 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 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 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 251 LEU 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: 0.5980 chunk 67 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 114 optimal weight: 0.0870 chunk 117 optimal weight: 3.9990 chunk 130 optimal weight: 0.6980 chunk 90 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN ** B 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.224452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.165243 restraints weight = 12889.328| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 3.04 r_work: 0.3461 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12898 Z= 0.117 Angle : 0.524 19.365 17593 Z= 0.278 Chirality : 0.041 0.242 1912 Planarity : 0.003 0.030 2076 Dihedral : 19.634 141.261 2144 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.63 % Allowed : 24.19 % Favored : 72.18 % 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: 0.29 (0.23), residues: 1422 helix: 1.05 (0.23), residues: 542 sheet: -1.33 (0.43), residues: 152 loop : -0.00 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 6 TYR 0.014 0.001 TYR B 611 PHE 0.022 0.001 PHE C 95 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 0.00260 / 0.12 (12898) covalent geometry : angle 0.52365 / 0.28 (17593) hydrogen bonds : bond 0.03425 / 2.30 ( 512) hydrogen bonds : angle 4.28272 / 2.97 ( 1391) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3573.17 seconds wall clock time: 62 minutes 0.57 seconds (3720.57 seconds total)