Starting phenix.real_space_refine on Thu Jul 2 06:17:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q6o_72280/07_2026/9q6o_72280_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q6o_72280/07_2026/9q6o_72280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q6o_72280/07_2026/9q6o_72280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q6o_72280/07_2026/9q6o_72280.map" model { file = "/net/cci-nas-00/data/ceres_data/9q6o_72280/07_2026/9q6o_72280_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q6o_72280/07_2026/9q6o_72280_neut.cif" } resolution = 2.65 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= 0.015 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: 7 Type Number sf(0) Gaussians Mg 2 5.21 5 S 42 5.16 5 Be 1 3.05 5 C 4411 2.51 5 N 1110 2.21 5 O 1339 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 6908 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 6853 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 32, 'TRANS': 858} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 55 Unusual residues: {' MG': 2, 'BEF': 1} Classifications: {'undetermined': 3, 'water': 49} Link IDs: {None: 51} Time building chain proxies: 1.71, per 1000 atoms: 0.25 Number of scatterers: 6908 At special positions: 0 Unit cell: (67.89, 91.14, 144.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 42 16.00 Mg 2 11.99 F 3 9.00 O 1339 8.00 N 1110 7.00 C 4411 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.60 Conformation dependent library (CDL) restraints added in 378.7 milliseconds 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1670 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 5 sheets defined 57.2% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 25 through 30 removed outlier: 3.505A pdb=" N PHE A 29 " --> pdb=" O ALA A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 42 Processing helix chain 'A' and resid 50 through 61 removed outlier: 3.530A pdb=" N VAL A 54 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 84 through 102 Processing helix chain 'A' and resid 112 through 133 removed outlier: 3.550A pdb=" N ILE A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 144 removed outlier: 4.276A pdb=" N ASN A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 247 through 250 Processing helix chain 'A' and resid 251 through 262 removed outlier: 3.657A pdb=" N GLU A 262 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 300 removed outlier: 3.526A pdb=" N LYS A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 301 through 317 removed outlier: 3.637A pdb=" N THR A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 338 removed outlier: 3.719A pdb=" N LYS A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 385 through 397 Processing helix chain 'A' and resid 405 through 416 removed outlier: 3.769A pdb=" N ILE A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 424 Processing helix chain 'A' and resid 468 through 473 removed outlier: 3.796A pdb=" N ASP A 473 " --> pdb=" O GLU A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 504 Processing helix chain 'A' and resid 525 through 529 removed outlier: 3.656A pdb=" N GLU A 529 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 569 through 581 Processing helix chain 'A' and resid 590 through 596 Processing helix chain 'A' and resid 599 through 608 removed outlier: 3.853A pdb=" N ALA A 603 " --> pdb=" O ASN A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 629 removed outlier: 3.616A pdb=" N ALA A 620 " --> pdb=" O PRO A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 648 removed outlier: 3.607A pdb=" N ALA A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA A 644 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ALA A 645 " --> pdb=" O ASN A 641 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 648 " --> pdb=" O ALA A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 665 Processing helix chain 'A' and resid 676 through 714 removed outlier: 3.602A pdb=" N LYS A 680 " --> pdb=" O MET A 676 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR A 689 " --> pdb=" O GLY A 685 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER A 709 " --> pdb=" O GLY A 705 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N VAL A 710 " --> pdb=" O ASN A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 738 Processing helix chain 'A' and resid 739 through 744 Proline residue: A 742 - end of helix No H-bonds generated for 'chain 'A' and resid 739 through 744' Processing helix chain 'A' and resid 747 through 752 removed outlier: 3.885A pdb=" N VAL A 752 " --> pdb=" O GLU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 787 Proline residue: A 771 - end of helix removed outlier: 4.059A pdb=" N PHE A 776 " --> pdb=" O THR A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 803 through 828 Processing helix chain 'A' and resid 828 through 833 Processing helix chain 'A' and resid 845 through 862 Processing helix chain 'A' and resid 865 through 871 Processing helix chain 'A' and resid 879 through 907 removed outlier: 4.445A pdb=" N TRP A 883 " --> pdb=" O ASN A 879 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 164 removed outlier: 4.436A pdb=" N ASN A 152 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 173 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE A 195 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP A 193 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 240 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA A 191 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY A 242 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE A 189 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL A 244 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG A 187 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 164 removed outlier: 4.436A pdb=" N ASN A 152 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 173 " --> pdb=" O HIS A 154 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N PHE A 195 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP A 193 " --> pdb=" O GLY A 238 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 240 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA A 191 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY A 242 " --> pdb=" O ILE A 189 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ILE A 189 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL A 244 " --> pdb=" O ARG A 187 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG A 187 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 341 through 343 removed outlier: 6.362A pdb=" N GLY A 652 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU A 670 " --> pdb=" O GLY A 652 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N SER A 654 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL A 633 " --> pdb=" O VAL A 651 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ILE A 653 " --> pdb=" O VAL A 633 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N TYR A 635 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU A 358 " --> pdb=" O LYS A 563 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU A 565 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N THR A 360 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N PHE A 611 " --> pdb=" O VAL A 562 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE A 564 " --> pdb=" O PHE A 611 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 378 removed outlier: 5.373A pdb=" N LEU A 373 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 541 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N VAL A 512 " --> pdb=" O MET A 535 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR A 537 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A 510 " --> pdb=" O TYR A 537 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA A 539 " --> pdb=" O ARG A 508 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG A 508 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N SER A 446 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 435 " --> pdb=" O SER A 446 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL A 448 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 378 removed outlier: 5.373A pdb=" N LEU A 373 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 541 " --> pdb=" O LEU A 373 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N CYS A 475 " --> pdb=" O MET A 532 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU A 534 " --> pdb=" O CYS A 475 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU A 477 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLY A 536 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N GLU A 479 " --> pdb=" O GLY A 536 " (cutoff:3.500A) removed outlier: 12.504A pdb=" N LEU A 538 " --> pdb=" O GLU A 479 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1144 1.32 - 1.44: 1673 1.44 - 1.56: 4080 1.56 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 6975 Sorted by residual: bond pdb=" CA SER A 904 " pdb=" CB SER A 904 " ideal model delta sigma weight residual 1.529 1.444 0.085 1.58e-02 4.01e+03 2.90e+01 bond pdb=" N ILE A 901 " pdb=" CA ILE A 901 " ideal model delta sigma weight residual 1.461 1.509 -0.048 1.19e-02 7.06e+03 1.66e+01 bond pdb=" CA PHE A 902 " pdb=" C PHE A 902 " ideal model delta sigma weight residual 1.523 1.473 0.050 1.35e-02 5.49e+03 1.36e+01 bond pdb=" C ARG A 508 " pdb=" O ARG A 508 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.22e-02 6.72e+03 1.13e+01 bond pdb=" C ILE A 901 " pdb=" O ILE A 901 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.17e-02 7.31e+03 8.55e+00 ... (remaining 6970 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 9241 1.77 - 3.55: 159 3.55 - 5.32: 38 5.32 - 7.10: 8 7.10 - 8.87: 5 Bond angle restraints: 9451 Sorted by residual: angle pdb=" N TYR A 906 " pdb=" CA TYR A 906 " pdb=" CB TYR A 906 " ideal model delta sigma weight residual 110.56 101.69 8.87 1.46e+00 4.69e-01 3.69e+01 angle pdb=" O LYS A 900 " pdb=" C LYS A 900 " pdb=" N ILE A 901 " ideal model delta sigma weight residual 122.07 115.91 6.16 1.03e+00 9.43e-01 3.58e+01 angle pdb=" N LEU A 909 " pdb=" CA LEU A 909 " pdb=" C LEU A 909 " ideal model delta sigma weight residual 110.50 102.28 8.22 1.41e+00 5.03e-01 3.40e+01 angle pdb=" CA LYS A 900 " pdb=" C LYS A 900 " pdb=" N ILE A 901 " ideal model delta sigma weight residual 117.07 123.67 -6.60 1.14e+00 7.69e-01 3.35e+01 angle pdb=" N GLU A 908 " pdb=" CA GLU A 908 " pdb=" CB GLU A 908 " ideal model delta sigma weight residual 110.80 102.77 8.03 1.73e+00 3.34e-01 2.15e+01 ... (remaining 9446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 3642 17.88 - 35.75: 431 35.75 - 53.63: 116 53.63 - 71.50: 33 71.50 - 89.38: 4 Dihedral angle restraints: 4226 sinusoidal: 1648 harmonic: 2578 Sorted by residual: dihedral pdb=" N GLU A 908 " pdb=" C GLU A 908 " pdb=" CA GLU A 908 " pdb=" CB GLU A 908 " ideal model delta harmonic sigma weight residual 122.80 109.72 13.08 0 2.50e+00 1.60e-01 2.74e+01 dihedral pdb=" C GLU A 908 " pdb=" N GLU A 908 " pdb=" CA GLU A 908 " pdb=" CB GLU A 908 " ideal model delta harmonic sigma weight residual -122.60 -112.23 -10.37 0 2.50e+00 1.60e-01 1.72e+01 dihedral pdb=" C ARG A 508 " pdb=" N ARG A 508 " pdb=" CA ARG A 508 " pdb=" CB ARG A 508 " ideal model delta harmonic sigma weight residual -122.60 -112.27 -10.33 0 2.50e+00 1.60e-01 1.71e+01 ... (remaining 4223 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1056 0.075 - 0.151: 76 0.151 - 0.226: 9 0.226 - 0.301: 1 0.301 - 0.377: 1 Chirality restraints: 1143 Sorted by residual: chirality pdb=" CA GLU A 908 " pdb=" N GLU A 908 " pdb=" C GLU A 908 " pdb=" CB GLU A 908 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ARG A 508 " pdb=" N ARG A 508 " pdb=" C ARG A 508 " pdb=" CB ARG A 508 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CA LEU A 909 " pdb=" N LEU A 909 " pdb=" C LEU A 909 " pdb=" CB LEU A 909 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.00e+00 ... (remaining 1140 not shown) Planarity restraints: 1180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 68 " -0.587 9.50e-02 1.11e+02 2.63e-01 4.24e+01 pdb=" NE ARG A 68 " 0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 68 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 68 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 68 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 508 " -0.578 9.50e-02 1.11e+02 2.59e-01 4.12e+01 pdb=" NE ARG A 508 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG A 508 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 508 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 508 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 508 " 0.009 2.00e-02 2.50e+03 1.93e-02 3.74e+00 pdb=" C ARG A 508 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG A 508 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 509 " 0.011 2.00e-02 2.50e+03 ... (remaining 1177 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 57 2.55 - 3.14: 5297 3.14 - 3.72: 10797 3.72 - 4.31: 15928 4.31 - 4.90: 26640 Nonbonded interactions: 58719 Sorted by model distance: nonbonded pdb=" OD2 ASP A 361 " pdb=" F3 BEF A1001 " model vdw 1.960 2.990 nonbonded pdb=" O HIS A 175 " pdb=" O HOH A1101 " model vdw 1.988 3.040 nonbonded pdb=" OH TYR A 695 " pdb=" OD1 ASP A 735 " model vdw 2.147 3.040 nonbonded pdb=" OD2 ASP A 63 " pdb=" OG1 THR A 65 " model vdw 2.197 3.040 nonbonded pdb=" O THR A 65 " pdb=" O HOH A1102 " model vdw 2.242 3.040 ... (remaining 58714 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.930 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.350 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 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 : 0.011 0.899 6976 Z= 1.098 Angle : 0.644 8.869 9451 Z= 0.409 Chirality : 0.045 0.377 1143 Planarity : 0.012 0.263 1180 Dihedral : 17.030 89.378 2556 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.70 % Favored : 97.19 % Rotamer: Outliers : 2.09 % Allowed : 23.50 % Favored : 74.41 % Cbeta Deviations : 0.24 % 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: 0.34 (0.29), residues: 889 helix: 1.07 (0.25), residues: 463 sheet: -0.09 (0.49), residues: 109 loop : -0.82 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 508 TYR 0.010 0.001 TYR A 806 PHE 0.016 0.001 PHE A 776 TRP 0.007 0.001 TRP A 278 HIS 0.002 0.001 HIS A 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.22 ( 6975) covalent geometry : angle 0.64369 / 0.41 ( 9451) hydrogen bonds : bond 0.15936 / 9.80 ( 376) hydrogen bonds : angle 7.31327 / 5.33 ( 1146) Misc. bond : bond 0.89872 / 47.30 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7605 (tp30) REVERT: A 109 GLU cc_start: 0.8640 (mt-10) cc_final: 0.7884 (tm-30) REVERT: A 111 ASN cc_start: 0.8813 (t0) cc_final: 0.8602 (t0) REVERT: A 177 SER cc_start: 0.9087 (OUTLIER) cc_final: 0.8664 (p) REVERT: A 370 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8066 (ttpp) outliers start: 16 outliers final: 5 residues processed: 88 average time/residue: 0.6294 time to fit residues: 58.2079 Evaluate side-chains 72 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 370 LYS Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 905 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 198 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.097612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.075629 restraints weight = 10882.177| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 2.47 r_work: 0.2802 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.0935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6976 Z= 0.161 Angle : 0.509 8.086 9451 Z= 0.276 Chirality : 0.042 0.130 1143 Planarity : 0.004 0.040 1180 Dihedral : 5.281 55.541 951 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.70 % Favored : 97.19 % Rotamer: Outliers : 2.87 % Allowed : 21.67 % Favored : 75.46 % 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: 0.94 (0.29), residues: 889 helix: 1.68 (0.25), residues: 473 sheet: -0.07 (0.48), residues: 115 loop : -0.77 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 492 TYR 0.009 0.001 TYR A 806 PHE 0.023 0.002 PHE A 818 TRP 0.007 0.001 TRP A 817 HIS 0.002 0.001 HIS A 726 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 6975) covalent geometry : angle 0.50946 / 0.28 ( 9451) hydrogen bonds : bond 0.05041 / 3.25 ( 376) hydrogen bonds : angle 5.09233 / 3.67 ( 1146) Misc. bond : bond 0.00134 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 67 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 GLN cc_start: 0.7922 (tp40) cc_final: 0.7549 (mt0) REVERT: A 109 GLU cc_start: 0.8735 (mt-10) cc_final: 0.7698 (tm-30) REVERT: A 432 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7793 (ttpp) REVERT: A 761 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.7922 (p) outliers start: 22 outliers final: 7 residues processed: 85 average time/residue: 0.5554 time to fit residues: 49.8101 Evaluate side-chains 70 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 895 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 19 optimal weight: 0.0040 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.097864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.075996 restraints weight = 10816.256| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.47 r_work: 0.2815 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2696 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6976 Z= 0.137 Angle : 0.482 7.809 9451 Z= 0.260 Chirality : 0.041 0.129 1143 Planarity : 0.004 0.042 1180 Dihedral : 4.285 35.860 935 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.92 % Favored : 96.96 % Rotamer: Outliers : 2.22 % Allowed : 22.06 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.29), residues: 889 helix: 1.96 (0.25), residues: 470 sheet: -0.05 (0.49), residues: 110 loop : -0.78 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 492 TYR 0.010 0.001 TYR A 806 PHE 0.021 0.001 PHE A 818 TRP 0.010 0.001 TRP A 817 HIS 0.002 0.000 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6975) covalent geometry : angle 0.48191 / 0.26 ( 9451) hydrogen bonds : bond 0.04378 / 2.84 ( 376) hydrogen bonds : angle 4.74175 / 3.42 ( 1146) Misc. bond : bond 0.00102 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 64 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7415 (pm20) REVERT: A 80 GLN cc_start: 0.7980 (tp40) cc_final: 0.7573 (mt0) REVERT: A 432 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7714 (ttpp) REVERT: A 761 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.7966 (p) outliers start: 17 outliers final: 8 residues processed: 79 average time/residue: 0.4965 time to fit residues: 41.4907 Evaluate side-chains 71 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 895 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 8.9990 chunk 23 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.095983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.073875 restraints weight = 10986.544| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 2.50 r_work: 0.2788 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6976 Z= 0.178 Angle : 0.502 7.657 9451 Z= 0.268 Chirality : 0.042 0.131 1143 Planarity : 0.004 0.042 1180 Dihedral : 4.377 36.940 935 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.15 % Favored : 96.74 % Rotamer: Outliers : 1.83 % Allowed : 22.58 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.29), residues: 889 helix: 1.89 (0.24), residues: 470 sheet: -0.08 (0.49), residues: 110 loop : -0.80 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.009 0.001 TYR A 806 PHE 0.019 0.002 PHE A 776 TRP 0.009 0.001 TRP A 817 HIS 0.005 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.18 ( 6975) covalent geometry : angle 0.50190 / 0.27 ( 9451) hydrogen bonds : bond 0.04718 / 3.07 ( 376) hydrogen bonds : angle 4.71612 / 3.40 ( 1146) Misc. bond : bond 0.00122 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7410 (pm20) REVERT: A 158 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.7981 (p) REVERT: A 432 LYS cc_start: 0.8024 (ttmt) cc_final: 0.7683 (ttpp) REVERT: A 459 LYS cc_start: 0.7794 (mmtp) cc_final: 0.7539 (mtpt) outliers start: 14 outliers final: 9 residues processed: 78 average time/residue: 0.5232 time to fit residues: 43.0549 Evaluate side-chains 73 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 895 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 87 optimal weight: 0.5980 chunk 65 optimal weight: 0.0570 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 42 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.097518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.075191 restraints weight = 10978.735| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.56 r_work: 0.2821 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6976 Z= 0.114 Angle : 0.462 7.149 9451 Z= 0.249 Chirality : 0.041 0.127 1143 Planarity : 0.004 0.043 1180 Dihedral : 4.225 36.883 935 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.92 % Favored : 96.96 % Rotamer: Outliers : 2.22 % Allowed : 22.45 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.29), residues: 889 helix: 1.99 (0.24), residues: 476 sheet: 0.01 (0.49), residues: 109 loop : -0.75 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.009 0.001 TYR A 806 PHE 0.019 0.001 PHE A 818 TRP 0.010 0.001 TRP A 817 HIS 0.004 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 ( 6975) covalent geometry : angle 0.46231 / 0.25 ( 9451) hydrogen bonds : bond 0.04077 / 2.65 ( 376) hydrogen bonds : angle 4.54499 / 3.28 ( 1146) Misc. bond : bond 0.00061 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.254 Fit side-chains revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8549 (tt0) cc_final: 0.8251 (tp40) REVERT: A 51 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7438 (pm20) REVERT: A 158 SER cc_start: 0.8411 (OUTLIER) cc_final: 0.7942 (p) REVERT: A 290 PHE cc_start: 0.7895 (t80) cc_final: 0.7480 (t80) REVERT: A 432 LYS cc_start: 0.7987 (ttmt) cc_final: 0.7635 (ttpp) REVERT: A 761 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.7941 (p) outliers start: 17 outliers final: 9 residues processed: 85 average time/residue: 0.5194 time to fit residues: 46.8548 Evaluate side-chains 78 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 404 LEU Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 895 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 78 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 61 optimal weight: 0.0270 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.076267 restraints weight = 10953.739| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.50 r_work: 0.2834 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6976 Z= 0.114 Angle : 0.466 6.772 9451 Z= 0.250 Chirality : 0.041 0.127 1143 Planarity : 0.004 0.042 1180 Dihedral : 4.162 36.364 935 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.37 % Favored : 96.51 % Rotamer: Outliers : 2.09 % Allowed : 22.58 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.29), residues: 889 helix: 2.09 (0.24), residues: 476 sheet: 0.07 (0.49), residues: 109 loop : -0.74 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 492 TYR 0.009 0.001 TYR A 806 PHE 0.018 0.001 PHE A 818 TRP 0.011 0.001 TRP A 817 HIS 0.004 0.000 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 ( 6975) covalent geometry : angle 0.46579 / 0.25 ( 9451) hydrogen bonds : bond 0.03973 / 2.58 ( 376) hydrogen bonds : angle 4.47488 / 3.23 ( 1146) Misc. bond : bond 0.00057 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.295 Fit side-chains revert: symmetry clash REVERT: A 40 GLN cc_start: 0.8534 (tt0) cc_final: 0.8238 (tp40) REVERT: A 51 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7430 (pm20) REVERT: A 158 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.7949 (p) REVERT: A 290 PHE cc_start: 0.7879 (t80) cc_final: 0.7489 (t80) REVERT: A 432 LYS cc_start: 0.7978 (ttmt) cc_final: 0.7618 (ttpp) REVERT: A 761 SER cc_start: 0.8264 (OUTLIER) cc_final: 0.7937 (p) outliers start: 16 outliers final: 10 residues processed: 80 average time/residue: 0.5716 time to fit residues: 48.3162 Evaluate side-chains 76 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 895 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.073661 restraints weight = 10929.454| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 2.50 r_work: 0.2787 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2668 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6976 Z= 0.189 Angle : 0.509 6.775 9451 Z= 0.271 Chirality : 0.043 0.131 1143 Planarity : 0.004 0.041 1180 Dihedral : 4.337 37.865 935 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.09 % Allowed : 22.58 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.29), residues: 889 helix: 1.93 (0.24), residues: 476 sheet: 0.01 (0.49), residues: 109 loop : -0.78 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 187 TYR 0.009 0.001 TYR A 806 PHE 0.020 0.002 PHE A 776 TRP 0.008 0.001 TRP A 817 HIS 0.004 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 ( 6975) covalent geometry : angle 0.50945 / 0.27 ( 9451) hydrogen bonds : bond 0.04689 / 3.06 ( 376) hydrogen bonds : angle 4.62497 / 3.33 ( 1146) Misc. bond : bond 0.00135 / 0.07 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.273 Fit side-chains REVERT: A 40 GLN cc_start: 0.8571 (tt0) cc_final: 0.8275 (tp40) REVERT: A 51 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7439 (pm20) REVERT: A 158 SER cc_start: 0.8429 (OUTLIER) cc_final: 0.7990 (p) REVERT: A 432 LYS cc_start: 0.8031 (tmmt) cc_final: 0.7658 (ttpp) REVERT: A 761 SER cc_start: 0.8333 (OUTLIER) cc_final: 0.7968 (p) outliers start: 16 outliers final: 9 residues processed: 80 average time/residue: 0.5879 time to fit residues: 49.5574 Evaluate side-chains 73 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 895 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.096628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.074583 restraints weight = 10989.204| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.52 r_work: 0.2801 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6976 Z= 0.149 Angle : 0.494 6.159 9451 Z= 0.265 Chirality : 0.042 0.129 1143 Planarity : 0.004 0.043 1180 Dihedral : 4.298 38.539 935 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.83 % Allowed : 23.24 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.29), residues: 889 helix: 1.98 (0.24), residues: 476 sheet: 0.08 (0.49), residues: 109 loop : -0.78 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 492 TYR 0.009 0.001 TYR A 806 PHE 0.018 0.001 PHE A 776 TRP 0.009 0.001 TRP A 817 HIS 0.004 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 6975) covalent geometry : angle 0.49407 / 0.26 ( 9451) hydrogen bonds : bond 0.04392 / 2.86 ( 376) hydrogen bonds : angle 4.57142 / 3.29 ( 1146) Misc. bond : bond 0.00098 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 64 time to evaluate : 0.201 Fit side-chains REVERT: A 22 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7739 (tp30) REVERT: A 40 GLN cc_start: 0.8592 (tt0) cc_final: 0.8298 (tp40) REVERT: A 51 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7441 (pm20) REVERT: A 158 SER cc_start: 0.8421 (OUTLIER) cc_final: 0.7984 (p) REVERT: A 290 PHE cc_start: 0.7940 (t80) cc_final: 0.7546 (t80) REVERT: A 432 LYS cc_start: 0.8029 (tmmt) cc_final: 0.7645 (ttpp) REVERT: A 761 SER cc_start: 0.8348 (OUTLIER) cc_final: 0.7981 (p) REVERT: A 892 MET cc_start: 0.7689 (mmm) cc_final: 0.7406 (mmt) outliers start: 14 outliers final: 9 residues processed: 77 average time/residue: 0.6035 time to fit residues: 49.0325 Evaluate side-chains 75 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 GLU Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 895 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 chunk 5 optimal weight: 0.0070 chunk 7 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 chunk 80 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 87 optimal weight: 0.4980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.098584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.076791 restraints weight = 10907.203| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.52 r_work: 0.2859 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6976 Z= 0.108 Angle : 0.469 5.855 9451 Z= 0.251 Chirality : 0.040 0.126 1143 Planarity : 0.004 0.044 1180 Dihedral : 4.143 37.494 935 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.70 % Allowed : 23.89 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.29), residues: 889 helix: 2.18 (0.24), residues: 476 sheet: 0.12 (0.49), residues: 109 loop : -0.74 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 492 TYR 0.010 0.001 TYR A 806 PHE 0.018 0.001 PHE A 818 TRP 0.012 0.001 TRP A 817 HIS 0.003 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 ( 6975) covalent geometry : angle 0.46910 / 0.25 ( 9451) hydrogen bonds : bond 0.03859 / 2.50 ( 376) hydrogen bonds : angle 4.44194 / 3.21 ( 1146) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.277 Fit side-chains REVERT: A 40 GLN cc_start: 0.8550 (tt0) cc_final: 0.8271 (tp40) REVERT: A 51 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7398 (pm20) REVERT: A 158 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8057 (p) REVERT: A 290 PHE cc_start: 0.7906 (t80) cc_final: 0.7521 (t80) REVERT: A 432 LYS cc_start: 0.8012 (tmmt) cc_final: 0.7647 (ttpp) REVERT: A 761 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.7949 (p) outliers start: 13 outliers final: 11 residues processed: 72 average time/residue: 0.5997 time to fit residues: 45.6395 Evaluate side-chains 73 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 198 GLN Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 546 GLU Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 895 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 32 optimal weight: 0.0070 chunk 28 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 1 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 0.0030 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 2 optimal weight: 0.0980 overall best weight: 0.1608 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.078797 restraints weight = 10824.356| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.52 r_work: 0.2887 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6976 Z= 0.091 Angle : 0.454 7.799 9451 Z= 0.242 Chirality : 0.040 0.123 1143 Planarity : 0.004 0.045 1180 Dihedral : 3.941 36.339 935 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.57 % Allowed : 23.89 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.30), residues: 889 helix: 2.39 (0.25), residues: 476 sheet: 0.26 (0.50), residues: 109 loop : -0.67 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 627 TYR 0.009 0.001 TYR A 806 PHE 0.019 0.001 PHE A 818 TRP 0.016 0.001 TRP A 817 HIS 0.003 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 ( 6975) covalent geometry : angle 0.45374 / 0.24 ( 9451) hydrogen bonds : bond 0.03424 / 2.21 ( 376) hydrogen bonds : angle 4.31253 / 3.13 ( 1146) Misc. bond : bond 0.00015 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1778 Ramachandran restraints generated. 889 Oldfield, 0 Emsley, 889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.301 Fit side-chains REVERT: A 40 GLN cc_start: 0.8506 (tt0) cc_final: 0.8244 (tp40) REVERT: A 51 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7330 (pm20) REVERT: A 74 LEU cc_start: 0.8362 (tp) cc_final: 0.8128 (tm) REVERT: A 290 PHE cc_start: 0.7895 (t80) cc_final: 0.7552 (t80) REVERT: A 405 MET cc_start: 0.8106 (mtm) cc_final: 0.7767 (mtt) REVERT: A 432 LYS cc_start: 0.7955 (tmmt) cc_final: 0.7647 (ttpp) REVERT: A 761 SER cc_start: 0.8246 (OUTLIER) cc_final: 0.7964 (p) outliers start: 12 outliers final: 6 residues processed: 73 average time/residue: 0.5938 time to fit residues: 45.7552 Evaluate side-chains 70 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 431 THR Chi-restraints excluded: chain A residue 486 HIS Chi-restraints excluded: chain A residue 761 SER Chi-restraints excluded: chain A residue 854 MET Chi-restraints excluded: chain A residue 895 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 85 optimal weight: 0.0770 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.098384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.076543 restraints weight = 10802.729| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.50 r_work: 0.2859 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6976 Z= 0.129 Angle : 0.487 10.896 9451 Z= 0.256 Chirality : 0.041 0.128 1143 Planarity : 0.004 0.045 1180 Dihedral : 4.037 36.883 935 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.31 % Allowed : 24.80 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.29), residues: 889 helix: 2.27 (0.24), residues: 478 sheet: 0.29 (0.49), residues: 109 loop : -0.70 (0.37), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 492 TYR 0.010 0.001 TYR A 806 PHE 0.017 0.001 PHE A 818 TRP 0.014 0.001 TRP A 817 HIS 0.004 0.001 HIS A 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 6975) covalent geometry : angle 0.48725 / 0.26 ( 9451) hydrogen bonds : bond 0.03955 / 2.57 ( 376) hydrogen bonds : angle 4.38633 / 3.17 ( 1146) Misc. bond : bond 0.00054 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2468.93 seconds wall clock time: 42 minutes 59.06 seconds (2579.06 seconds total)